From dbdba9efbafd2623d76bda2c53eac971b7ac05f2 Mon Sep 17 00:00:00 2001
From: Romain Boman <romain.boman@gmail.com>
Date: Wed, 23 Mar 2022 13:30:01 +0100
Subject: [PATCH] add amfe dependency (spirou:OK except lift3)
---
.gitignore | 1 +
.gitlab-ci.yml | 11 +
.gitmodules | 3 +
CMake/FindEIGEN.cmake | 78 ---
CMake/FindMUMPS.cmake | 81 ---
CMake/FindNUMPY.cmake | 21 -
CMake/FindPYTEUCHOS.cmake | 21 -
CMake/FindTBB.cmake | 281 --------
CMake/codeblocks.cmake | 20 -
CMake/fwkMacros.cmake | 63 --
CMake/spring.cmake | 24 -
CMake/ubuntu.cmake | 23 -
CMakeLists.txt | 65 +-
README.md | 7 +-
ext/CMakeLists.txt | 1 +
ext/amfe | 1 +
flow/_src/CMakeLists.txt | 15 +-
flow/default.py | 3 +-
flow/src/CMakeLists.txt | 2 +
fwk/CMakeLists.txt | 20 -
fwk/__init__.py | 8 -
fwk/_src/CMakeLists.txt | 43 --
fwk/_src/fwkw.h | 24 -
fwk/_src/fwkw.i | 124 ----
fwk/_src/fwkw.swg | 105 ---
fwk/_src/wCppBuf2Py.cpp | 102 ---
fwk/_src/wCppBuf2Py.h | 69 --
fwk/coloring.py | 24 -
fwk/src/CMakeLists.txt | 26 -
fwk/src/fwk.cpp | 73 --
fwk/src/fwk.h | 67 --
fwk/src/wExtract.cpp | 35 -
fwk/src/wExtract.h | 44 --
fwk/src/wHMSTime.cpp | 73 --
fwk/src/wHMSTime.h | 46 --
fwk/src/wObject.cpp | 44 --
fwk/src/wObject.h | 74 --
fwk/src/wObserver.cpp | 25 -
fwk/src/wObserver.h | 39 --
fwk/src/wTime.cpp | 73 --
fwk/src/wTime.h | 115 ----
fwk/src/wTimer.cpp | 78 ---
fwk/src/wTimer.h | 56 --
fwk/src/wTimers.cpp | 56 --
fwk/src/wTimers.h | 47 --
fwk/src/wTimes.cpp | 56 --
fwk/src/wTimes.h | 75 --
fwk/src/wTimes.inl | 53 --
fwk/testing.py | 80 ---
fwk/tests/timers.py | 71 --
fwk/wutils.py | 270 --------
heat/_src/CMakeLists.txt | 15 +-
heat/src/CMakeLists.txt | 2 +
katoptron/_src/CMakeLists.txt | 32 +-
katoptron/exe/CMakeLists.txt | 4 +-
katoptron/src/CMakeLists.txt | 7 +-
.../src/wVtkExport_KIM2CLEAN.cpp | 0
.../src/wVtkExport_KIM2CLEAN.h | 4 +-
mirrors/_src/CMakeLists.txt | 15 +-
mirrors/src/CMakeLists.txt | 2 +
run.py | 92 +--
tbox/CMakeLists.txt | 20 -
tbox/__init__.py | 21 -
tbox/_src/CMakeLists.txt | 47 --
tbox/_src/tboxw.h | 67 --
tbox/_src/tboxw.i | 268 --------
tbox/gmsh.py | 136 ----
tbox/solvers.py | 38 --
tbox/src/CMakeLists.txt | 98 ---
tbox/src/eigen_extra.cpp | 38 --
tbox/src/eigen_extra.h | 31 -
tbox/src/std_extra.h | 43 --
tbox/src/tbox.h | 111 ---
tbox/src/wCache.cpp | 28 -
tbox/src/wCache.h | 52 --
tbox/src/wCache.inl | 35 -
tbox/src/wCacheHex8.cpp | 40 --
tbox/src/wCacheHex8.h | 46 --
tbox/src/wCacheLine2.cpp | 40 --
tbox/src/wCacheLine2.h | 46 --
tbox/src/wCachePoint1.cpp | 23 -
tbox/src/wCachePoint1.h | 41 --
tbox/src/wCacheQuad4.cpp | 40 --
tbox/src/wCacheQuad4.h | 46 --
tbox/src/wCacheTetra4.cpp | 40 --
tbox/src/wCacheTetra4.h | 46 --
tbox/src/wCacheTri3.cpp | 40 --
tbox/src/wCacheTri3.h | 46 --
tbox/src/wElement.cpp | 196 ------
tbox/src/wElement.h | 137 ----
tbox/src/wElement.inl | 166 -----
tbox/src/wFct0.cpp | 114 ----
tbox/src/wFct0.h | 125 ----
tbox/src/wFct1.cpp | 24 -
tbox/src/wFct1.h | 82 ---
tbox/src/wFct2.cpp | 132 ----
tbox/src/wFct2.h | 141 ----
tbox/src/wGauss.cpp | 23 -
tbox/src/wGauss.h | 51 --
tbox/src/wGauss.inl | 39 --
tbox/src/wGaussHex8.cpp | 36 -
tbox/src/wGaussHex8.h | 38 --
tbox/src/wGaussLine2.cpp | 51 --
tbox/src/wGaussLine2.h | 38 --
tbox/src/wGaussQuad4.cpp | 35 -
tbox/src/wGaussQuad4.h | 38 --
tbox/src/wGaussTetra4.cpp | 56 --
tbox/src/wGaussTetra4.h | 38 --
tbox/src/wGaussTri3.cpp | 61 --
tbox/src/wGaussTri3.h | 38 --
tbox/src/wGmres.cpp | 51 --
tbox/src/wGmres.h | 63 --
tbox/src/wGmshExport.cpp | 304 ---------
tbox/src/wGmshExport.h | 48 --
tbox/src/wGmshImport.cpp | 620 -----------------
tbox/src/wGmshImport.h | 62 --
tbox/src/wGroup.cpp | 55 --
tbox/src/wGroup.h | 46 --
tbox/src/wGroups.cpp | 63 --
tbox/src/wGroups.h | 48 --
tbox/src/wHex8.cpp | 132 ----
tbox/src/wHex8.h | 60 --
tbox/src/wHex8.inl | 24 -
tbox/src/wLazy.h | 61 --
tbox/src/wLine2.cpp | 223 ------
tbox/src/wLine2.h | 66 --
tbox/src/wLine2.inl | 24 -
tbox/src/wLinearSolver.cpp | 61 --
tbox/src/wLinearSolver.h | 50 --
tbox/src/wLinesearch.cpp | 397 -----------
tbox/src/wLinesearch.h | 127 ----
tbox/src/wMshConvert.cpp | 346 ----------
tbox/src/wMshConvert.h | 48 --
tbox/src/wMshCrack.cpp | 295 --------
tbox/src/wMshCrack.h | 71 --
tbox/src/wMshData.cpp | 68 --
tbox/src/wMshData.h | 57 --
tbox/src/wMshDeform.cpp | 511 --------------
tbox/src/wMshDeform.h | 87 ---
tbox/src/wMshExport.cpp | 34 -
tbox/src/wMshExport.h | 50 --
tbox/src/wMshImport.cpp | 34 -
tbox/src/wMshImport.h | 47 --
tbox/src/wMumps.cpp | 171 -----
tbox/src/wMumps.h | 75 --
tbox/src/wNode.cpp | 35 -
tbox/src/wNode.h | 49 --
tbox/src/wPardiso.cpp | 56 --
tbox/src/wPardiso.h | 60 --
tbox/src/wPoint1.cpp | 37 -
tbox/src/wPoint1.h | 43 --
tbox/src/wQuad4.cpp | 195 ------
tbox/src/wQuad4.h | 64 --
tbox/src/wQuad4.inl | 24 -
tbox/src/wResults.cpp | 79 ---
tbox/src/wResults.h | 58 --
tbox/src/wSfHex8.cpp | 69 --
tbox/src/wSfHex8.h | 40 --
tbox/src/wSfLine2.cpp | 36 -
tbox/src/wSfLine2.h | 40 --
tbox/src/wSfQuad4.cpp | 47 --
tbox/src/wSfQuad4.h | 40 --
tbox/src/wSfTetra4.cpp | 50 --
tbox/src/wSfTetra4.h | 40 --
tbox/src/wSfTri3.cpp | 42 --
tbox/src/wSfTri3.h | 40 --
tbox/src/wSparseLu.cpp | 41 --
tbox/src/wSparseLu.h | 57 --
tbox/src/wTag.cpp | 36 -
tbox/src/wTag.h | 60 --
tbox/src/wTetra4.cpp | 195 ------
tbox/src/wTetra4.h | 63 --
tbox/src/wTetra4.inl | 24 -
tbox/src/wTri3.cpp | 311 ---------
tbox/src/wTri3.h | 69 --
tbox/src/wTri3.inl | 24 -
tbox/src/wUnitTest.cpp | 98 ---
tbox/src/wUnitTest.h | 44 --
tbox/tests/basicops.py | 35 -
tbox/tests/fem/elem1s.py | 34 -
tbox/tests/fem/hex1.geo | 49 --
tbox/tests/fem/quad1.geo | 36 -
tbox/tests/fem/tri1.geo | 21 -
tbox/tests/gmshio.py | 51 --
tbox/tests/helloworld.slurm.sh | 18 -
tbox/tests/meshDeformation.py | 73 --
tbox/tests/meshDeformation3.py | 72 --
tbox/tests/models/beam.geo | 21 -
tbox/tests/models/beam3.geo | 47 --
tbox/tests/models/model.geo | 14 -
tbox/tests/mpi/helloworld.py | 32 -
tbox/utils.py | 96 ---
tbox/viewer.py | 44 --
tboxVtk/CMakeLists.txt | 20 -
tboxVtk/__init__.py | 21 -
tboxVtk/_src/CMakeLists.txt | 49 --
tboxVtk/_src/tboxVtkw.h | 17 -
tboxVtk/_src/tboxVtkw.i | 55 --
tboxVtk/cutter.py | 89 ---
tboxVtk/lineExtractor.py | 153 -----
tboxVtk/qt5vtk6/QVTKRenderWindowInteractor.py | 644 ------------------
tboxVtk/qt5vtk6/README.txt | 4 -
tboxVtk/qt5vtk6/__init__.py | 0
tboxVtk/reader.py | 45 --
tboxVtk/src/CMakeLists.txt | 66 --
tboxVtk/src/tboxVtk.h | 46 --
tboxVtk/src/wVtkExport.cpp | 260 -------
tboxVtk/src/wVtkExport.h | 58 --
tboxVtk/tests/models/model.geo | 14 -
tboxVtk/tests/vtkio.py | 44 --
tlnos/_src/CMakeLists.txt | 18 +-
tlnos/src/CMakeLists.txt | 3 +-
waves-config.cmake.in | 39 --
waves/CMakeLists.txt | 11 +
waves/_src/CMakeLists.txt | 15 +-
waves/exe/CMakeLists.txt | 2 +-
waves/src/CMakeLists.txt | 2 +
waves_config.h.in | 2 -
218 files changed, 154 insertions(+), 14986 deletions(-)
create mode 100644 .gitmodules
delete mode 100644 CMake/FindEIGEN.cmake
delete mode 100644 CMake/FindMUMPS.cmake
delete mode 100644 CMake/FindNUMPY.cmake
delete mode 100644 CMake/FindPYTEUCHOS.cmake
delete mode 100644 CMake/FindTBB.cmake
delete mode 100644 CMake/codeblocks.cmake
delete mode 100644 CMake/fwkMacros.cmake
delete mode 100644 CMake/spring.cmake
delete mode 100644 CMake/ubuntu.cmake
create mode 100644 ext/CMakeLists.txt
create mode 160000 ext/amfe
delete mode 100644 fwk/CMakeLists.txt
delete mode 100644 fwk/__init__.py
delete mode 100644 fwk/_src/CMakeLists.txt
delete mode 100644 fwk/_src/fwkw.h
delete mode 100644 fwk/_src/fwkw.i
delete mode 100644 fwk/_src/fwkw.swg
delete mode 100644 fwk/_src/wCppBuf2Py.cpp
delete mode 100644 fwk/_src/wCppBuf2Py.h
delete mode 100644 fwk/coloring.py
delete mode 100644 fwk/src/CMakeLists.txt
delete mode 100644 fwk/src/fwk.cpp
delete mode 100644 fwk/src/fwk.h
delete mode 100644 fwk/src/wExtract.cpp
delete mode 100644 fwk/src/wExtract.h
delete mode 100644 fwk/src/wHMSTime.cpp
delete mode 100644 fwk/src/wHMSTime.h
delete mode 100644 fwk/src/wObject.cpp
delete mode 100644 fwk/src/wObject.h
delete mode 100644 fwk/src/wObserver.cpp
delete mode 100644 fwk/src/wObserver.h
delete mode 100644 fwk/src/wTime.cpp
delete mode 100644 fwk/src/wTime.h
delete mode 100644 fwk/src/wTimer.cpp
delete mode 100644 fwk/src/wTimer.h
delete mode 100644 fwk/src/wTimers.cpp
delete mode 100644 fwk/src/wTimers.h
delete mode 100644 fwk/src/wTimes.cpp
delete mode 100644 fwk/src/wTimes.h
delete mode 100644 fwk/src/wTimes.inl
delete mode 100644 fwk/testing.py
delete mode 100644 fwk/tests/timers.py
delete mode 100644 fwk/wutils.py
rename {tboxVtk => katoptron}/src/wVtkExport_KIM2CLEAN.cpp (100%)
rename {tboxVtk => katoptron}/src/wVtkExport_KIM2CLEAN.h (97%)
delete mode 100644 tbox/CMakeLists.txt
delete mode 100644 tbox/__init__.py
delete mode 100644 tbox/_src/CMakeLists.txt
delete mode 100644 tbox/_src/tboxw.h
delete mode 100644 tbox/_src/tboxw.i
delete mode 100644 tbox/gmsh.py
delete mode 100644 tbox/solvers.py
delete mode 100644 tbox/src/CMakeLists.txt
delete mode 100644 tbox/src/eigen_extra.cpp
delete mode 100644 tbox/src/eigen_extra.h
delete mode 100644 tbox/src/std_extra.h
delete mode 100644 tbox/src/tbox.h
delete mode 100644 tbox/src/wCache.cpp
delete mode 100644 tbox/src/wCache.h
delete mode 100644 tbox/src/wCache.inl
delete mode 100644 tbox/src/wCacheHex8.cpp
delete mode 100644 tbox/src/wCacheHex8.h
delete mode 100644 tbox/src/wCacheLine2.cpp
delete mode 100644 tbox/src/wCacheLine2.h
delete mode 100644 tbox/src/wCachePoint1.cpp
delete mode 100644 tbox/src/wCachePoint1.h
delete mode 100644 tbox/src/wCacheQuad4.cpp
delete mode 100644 tbox/src/wCacheQuad4.h
delete mode 100644 tbox/src/wCacheTetra4.cpp
delete mode 100644 tbox/src/wCacheTetra4.h
delete mode 100644 tbox/src/wCacheTri3.cpp
delete mode 100644 tbox/src/wCacheTri3.h
delete mode 100644 tbox/src/wElement.cpp
delete mode 100644 tbox/src/wElement.h
delete mode 100644 tbox/src/wElement.inl
delete mode 100644 tbox/src/wFct0.cpp
delete mode 100644 tbox/src/wFct0.h
delete mode 100644 tbox/src/wFct1.cpp
delete mode 100644 tbox/src/wFct1.h
delete mode 100644 tbox/src/wFct2.cpp
delete mode 100644 tbox/src/wFct2.h
delete mode 100644 tbox/src/wGauss.cpp
delete mode 100644 tbox/src/wGauss.h
delete mode 100644 tbox/src/wGauss.inl
delete mode 100644 tbox/src/wGaussHex8.cpp
delete mode 100644 tbox/src/wGaussHex8.h
delete mode 100644 tbox/src/wGaussLine2.cpp
delete mode 100644 tbox/src/wGaussLine2.h
delete mode 100644 tbox/src/wGaussQuad4.cpp
delete mode 100644 tbox/src/wGaussQuad4.h
delete mode 100644 tbox/src/wGaussTetra4.cpp
delete mode 100644 tbox/src/wGaussTetra4.h
delete mode 100644 tbox/src/wGaussTri3.cpp
delete mode 100644 tbox/src/wGaussTri3.h
delete mode 100644 tbox/src/wGmres.cpp
delete mode 100644 tbox/src/wGmres.h
delete mode 100644 tbox/src/wGmshExport.cpp
delete mode 100644 tbox/src/wGmshExport.h
delete mode 100644 tbox/src/wGmshImport.cpp
delete mode 100644 tbox/src/wGmshImport.h
delete mode 100644 tbox/src/wGroup.cpp
delete mode 100644 tbox/src/wGroup.h
delete mode 100644 tbox/src/wGroups.cpp
delete mode 100644 tbox/src/wGroups.h
delete mode 100644 tbox/src/wHex8.cpp
delete mode 100644 tbox/src/wHex8.h
delete mode 100644 tbox/src/wHex8.inl
delete mode 100644 tbox/src/wLazy.h
delete mode 100644 tbox/src/wLine2.cpp
delete mode 100644 tbox/src/wLine2.h
delete mode 100644 tbox/src/wLine2.inl
delete mode 100644 tbox/src/wLinearSolver.cpp
delete mode 100644 tbox/src/wLinearSolver.h
delete mode 100644 tbox/src/wLinesearch.cpp
delete mode 100644 tbox/src/wLinesearch.h
delete mode 100644 tbox/src/wMshConvert.cpp
delete mode 100644 tbox/src/wMshConvert.h
delete mode 100644 tbox/src/wMshCrack.cpp
delete mode 100644 tbox/src/wMshCrack.h
delete mode 100644 tbox/src/wMshData.cpp
delete mode 100644 tbox/src/wMshData.h
delete mode 100644 tbox/src/wMshDeform.cpp
delete mode 100644 tbox/src/wMshDeform.h
delete mode 100644 tbox/src/wMshExport.cpp
delete mode 100644 tbox/src/wMshExport.h
delete mode 100644 tbox/src/wMshImport.cpp
delete mode 100644 tbox/src/wMshImport.h
delete mode 100644 tbox/src/wMumps.cpp
delete mode 100644 tbox/src/wMumps.h
delete mode 100644 tbox/src/wNode.cpp
delete mode 100644 tbox/src/wNode.h
delete mode 100644 tbox/src/wPardiso.cpp
delete mode 100644 tbox/src/wPardiso.h
delete mode 100644 tbox/src/wPoint1.cpp
delete mode 100644 tbox/src/wPoint1.h
delete mode 100644 tbox/src/wQuad4.cpp
delete mode 100644 tbox/src/wQuad4.h
delete mode 100644 tbox/src/wQuad4.inl
delete mode 100644 tbox/src/wResults.cpp
delete mode 100644 tbox/src/wResults.h
delete mode 100644 tbox/src/wSfHex8.cpp
delete mode 100644 tbox/src/wSfHex8.h
delete mode 100644 tbox/src/wSfLine2.cpp
delete mode 100644 tbox/src/wSfLine2.h
delete mode 100644 tbox/src/wSfQuad4.cpp
delete mode 100644 tbox/src/wSfQuad4.h
delete mode 100644 tbox/src/wSfTetra4.cpp
delete mode 100644 tbox/src/wSfTetra4.h
delete mode 100644 tbox/src/wSfTri3.cpp
delete mode 100644 tbox/src/wSfTri3.h
delete mode 100644 tbox/src/wSparseLu.cpp
delete mode 100644 tbox/src/wSparseLu.h
delete mode 100644 tbox/src/wTag.cpp
delete mode 100644 tbox/src/wTag.h
delete mode 100644 tbox/src/wTetra4.cpp
delete mode 100644 tbox/src/wTetra4.h
delete mode 100644 tbox/src/wTetra4.inl
delete mode 100644 tbox/src/wTri3.cpp
delete mode 100644 tbox/src/wTri3.h
delete mode 100644 tbox/src/wTri3.inl
delete mode 100644 tbox/src/wUnitTest.cpp
delete mode 100644 tbox/src/wUnitTest.h
delete mode 100644 tbox/tests/basicops.py
delete mode 100644 tbox/tests/fem/elem1s.py
delete mode 100644 tbox/tests/fem/hex1.geo
delete mode 100644 tbox/tests/fem/quad1.geo
delete mode 100644 tbox/tests/fem/tri1.geo
delete mode 100755 tbox/tests/gmshio.py
delete mode 100755 tbox/tests/helloworld.slurm.sh
delete mode 100644 tbox/tests/meshDeformation.py
delete mode 100644 tbox/tests/meshDeformation3.py
delete mode 100644 tbox/tests/models/beam.geo
delete mode 100644 tbox/tests/models/beam3.geo
delete mode 100644 tbox/tests/models/model.geo
delete mode 100644 tbox/tests/mpi/helloworld.py
delete mode 100644 tbox/utils.py
delete mode 100644 tbox/viewer.py
delete mode 100644 tboxVtk/CMakeLists.txt
delete mode 100644 tboxVtk/__init__.py
delete mode 100644 tboxVtk/_src/CMakeLists.txt
delete mode 100644 tboxVtk/_src/tboxVtkw.h
delete mode 100644 tboxVtk/_src/tboxVtkw.i
delete mode 100644 tboxVtk/cutter.py
delete mode 100644 tboxVtk/lineExtractor.py
delete mode 100644 tboxVtk/qt5vtk6/QVTKRenderWindowInteractor.py
delete mode 100644 tboxVtk/qt5vtk6/README.txt
delete mode 100644 tboxVtk/qt5vtk6/__init__.py
delete mode 100644 tboxVtk/reader.py
delete mode 100644 tboxVtk/src/CMakeLists.txt
delete mode 100644 tboxVtk/src/tboxVtk.h
delete mode 100644 tboxVtk/src/wVtkExport.cpp
delete mode 100644 tboxVtk/src/wVtkExport.h
delete mode 100644 tboxVtk/tests/models/model.geo
delete mode 100755 tboxVtk/tests/vtkio.py
delete mode 100644 waves-config.cmake.in
delete mode 100644 waves_config.h.in
diff --git a/.gitignore b/.gitignore
index f177c5cc..c75d6969 100644
--- a/.gitignore
+++ b/.gitignore
@@ -15,6 +15,7 @@
# Misc
core
*.pyc
+__pycache__/
*.*~
# OS
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 451ca6ee..6b823055 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -13,6 +13,11 @@ default:
- mn2l
# - warson # you can choose a set of runners here
+variables:
+ GIT_SUBMODULE_STRATEGY: recursive
+ GIT_STRATEGY: clone # workaround full clone for each pipeline (https://gitlab.com/gitlab-org/gitlab-runner/-/issues/26993)
+ GIT_LFS_SKIP_SMUDGE: 1 # do not pull LFS
+
stages:
- build
- test
@@ -36,6 +41,8 @@ build-no-tlnos:
<<: *global_tag_def
stage: build
script:
+ - git submodule init
+ - git submodule update
- rm -rf build workspace
- mkdir build
- cd build
@@ -46,6 +53,8 @@ build:
<<: *global_tag_def
stage: build
script:
+ - git submodule init
+ - git submodule update
- rm -rf build workspace
- mkdir build
- cd build
@@ -61,6 +70,8 @@ build-red:
image: rboman/waves-py3-red:2020.3
stage: build
script:
+ - git submodule init
+ - git submodule update
- rm -rf build workspace
- mkdir build
- cd build
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 00000000..e84a099a
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "ext/amfe"]
+ path = ext/amfe
+ url = ../amfe.git
diff --git a/CMake/FindEIGEN.cmake b/CMake/FindEIGEN.cmake
deleted file mode 100644
index 6ac879ee..00000000
--- a/CMake/FindEIGEN.cmake
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# FindEIGEN.cmake - try to find Eigen 3 headers
-# The logic that checks the version comes from FindEigen3.cmake (source dir)
-# ----------------------------------------------------------------------------
-# output:
-# EIGEN_FOUND : TRUE/FALSE
-# EIGEN_INCLUDE_DIRS : where the Eigen/*.h are [cached]
-# EIGEN_VERSION : version number of Eigen
-# ----------------------------------------------------------------------------
-# autodetection:
-# utiliser "CMAKE_PREFIX_PATH=c:\local"
-# ou "CMAKE_INCLUDE_PATH=c:\local\include"
-# ou "INCLUDE=c:\local\include"
-# ----------------------------------------------------------------------------
-
-# Check version (only for Eigen 3)
-macro(_eigen3_check_version)
- file(READ "${EIGEN_INCLUDE_DIRS}/Eigen/src/Core/util/Macros.h" _eigen3_version_header)
-
- string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}")
- set(EIGEN_WORLD_VERSION "${CMAKE_MATCH_1}")
- string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}")
- set(EIGEN_MAJOR_VERSION "${CMAKE_MATCH_1}")
- string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}")
- set(EIGEN_MINOR_VERSION "${CMAKE_MATCH_1}")
-
- set(EIGEN_VERSION ${EIGEN_WORLD_VERSION}.${EIGEN_MAJOR_VERSION}.${EIGEN_MINOR_VERSION})
-
- if(${EIGEN_VERSION} VERSION_LESS ${EIGEN_FIND_VERSION})
- message(FATAL_ERROR "Eigen version ${EIGEN_VERSION} found in ${EIGEN_INCLUDE_DIRS}, but at least version ${EIGEN_FIND_VERSION} is required!")
- endif()
-endmacro()
-
-# Set a dummy version if not provided
-if(NOT EIGEN_FIND_VERSION)
- if(NOT EIGEN_FIND_VERSION_MAJOR)
- set(EIGEN_FIND_VERSION_MAJOR 3)
- endif()
- if(NOT EIGEN_FIND_VERSION_MINOR)
- set(EIGEN_FIND_VERSION_MINOR 3)
- endif()
- if(NOT EIGEN_FIND_VERSION_PATCH)
- set(EIGEN_FIND_VERSION_PATCH 4)
- endif()
-
- set(EIGEN_FIND_VERSION "${EIGEN_FIND_VERSION_MAJOR}.${EIGEN_FIND_VERSION_MINOR}.${EIGEN_FIND_VERSION_PATCH}")
-endif()
-
-# Find the header and check the version
-find_path(EIGEN_INCLUDE_DIRS "Eigen/Dense" PATHS "/usr/include/eigen3")
-if (EIGEN_INCLUDE_DIRS)
- _eigen3_check_version()
-else()
- message(FATAL_ERROR "Eigen3 headers not found! Define the path in the INCLUDE environment variable.")
-endif()
-
-# handle the QUIETLY and REQUIRED arguments and set EIGEN_FOUND to TRUE
-# if all listed variables are TRUE
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(EIGEN
- FOUND_VAR EIGEN_FOUND
- REQUIRED_VARS EIGEN_INCLUDE_DIRS
- VERSION_VAR EIGEN_VERSION)
-
-#MESSAGE(STATUS "EIGEN_FOUND = ${EIGEN_FOUND}")
diff --git a/CMake/FindMUMPS.cmake b/CMake/FindMUMPS.cmake
deleted file mode 100644
index 78a24c74..00000000
--- a/CMake/FindMUMPS.cmake
+++ /dev/null
@@ -1,81 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# FindMUMPS.cmake - try to find MUMPS and associated libraries
-# (RoBo)
-# ----------------------------------------------------------------------------
-# output:
-# MUMPS_FOUND : TRUE/FALSE
-# MUMPS_LIBRARIES : list of MUMPS libraries to link with
-# MUMPS_INCLUDE_DIRS : where the *.h are [cached]
-# ----------------------------------------------------------------------------
-
-
-find_path(MUMPS_INCLUDE_DIRS NAMES "dmumps_c.h")
-
-set(MUMPS_LIBRARIES "")
-if(MSVC)
- SET(_MUMPS_LIBSET_SO dmumps_pord_seq_mkl) # mumps/seq (dynamic)
- SET(_MUMPS_LIBSET_A dmumps_c dmumps_fortran
- mumps_common_c pord_c libseq_c
- libseq_fortran ifconsol libifcoremd
- libifportmd libmmd libirc svml_dispmd) # mumps/seq (static)
-else()
- SET(_MUMPS_LIBSET_SO dmumps_seq
- dmumps_pord_seq
- dmumps_pord_seq_mkl
- dmumps_pord_seq_openblas) # mumps/seq (dynamic)
- SET(_MUMPS_LIBSET_A dmumps mumps_common pord mpiseq) # mumps/seq (static)
-endif()
-
-# try the dyn libs first
-find_library(FOUND_LIB_SO NAMES ${_MUMPS_LIBSET_SO})
-#MESSAGE(STATUS "${_MUMPS_LIBSET_SO} = ${FOUND_LIB_SO}")
-if(FOUND_LIB_SO)
- list(APPEND MUMPS_LIBRARIES ${FOUND_LIB_SO})
-else()
- # ".so" not found => try ".a"
- foreach(LIB ${_MUMPS_LIBSET_A})
- find_library(FOUND_LIB_A ${LIB})
- MESSAGE(STATUS "${LIB}=${FOUND_LIB_A}")
- if(FOUND_LIB_A)
- list(APPEND MUMPS_LIBRARIES ${FOUND_LIB_A})
- endif()
- unset(FOUND_LIB_A CACHE)
- endforeach()
-
- # add fortran libs
- IF(MUMPS_LIBRARIES)
- IF(CMAKE_CXX_COMPILER_ID MATCHES "GNU")
- list(APPEND MUMPS_LIBRARIES -lgfortran)
- ENDIF()
- IF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
- list(APPEND MUMPS_LIBRARIES -lifcoremt)
- ENDIF()
- ENDIF()
-endif()
-unset(FOUND_LIB_SO CACHE)
-
-
-#MESSAGE(STATUS "MUMPS_LIBRARIES = ${MUMPS_LIBRARIES}")
-
-# ----------------------------------------------------------------------------
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(MUMPS DEFAULT_MSG
- MUMPS_INCLUDE_DIRS
- MUMPS_LIBRARIES)
-
-#MESSAGE(STATUS "MUMPS_FOUND = ${MUMPS_FOUND}")
-# ----------------------------------------------------------------------------
diff --git a/CMake/FindNUMPY.cmake b/CMake/FindNUMPY.cmake
deleted file mode 100644
index 1196c8e6..00000000
--- a/CMake/FindNUMPY.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-find_path(NUMPY_INCLUDE_DIR "numpy/arrayobject.h")
-
-# ----------------------------------------------------------------------------
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(NUMPY DEFAULT_MSG
- NUMPY_INCLUDE_DIR)
diff --git a/CMake/FindPYTEUCHOS.cmake b/CMake/FindPYTEUCHOS.cmake
deleted file mode 100644
index 87f87ef1..00000000
--- a/CMake/FindPYTEUCHOS.cmake
+++ /dev/null
@@ -1,21 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-find_path(PYTEUCHOS_INCLUDE_DIR "Teuchos.i")
-
-# ----------------------------------------------------------------------------
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(PYTEUCHOS DEFAULT_MSG
- PYTEUCHOS_INCLUDE_DIR)
diff --git a/CMake/FindTBB.cmake b/CMake/FindTBB.cmake
deleted file mode 100644
index 71565cc7..00000000
--- a/CMake/FindTBB.cmake
+++ /dev/null
@@ -1,281 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# FindTBB.cmake - try to find Intel Threading Building Blocks libraries
-# (RoBo)
-# ----------------------------------------------------------------------------
-# input:
-# ENABLE_TBBMALLOC : ON/OFF
-# output:
-# TBB_FOUND : TRUE/FALSE
-# TBB_LIBRARIES : list of tbb libraries to link with
-# TBB_LIB_PATH : where the optimized .so/.lib are [cached]
-# TBB_LIB_PATH_DEBUG : where the debug .so/.lib are [cached]
-# TBB_INCLUDE_DIRS : where the tbb/*.h are [cached]
-# TBB_VERSION_INTERFACE :
-# TBB_VERSION_MAJOR :
-# TBB_VERSION_MINOR :
-# TBB_VERSION_STRING : version such as "4.2"
-# TBB_CXX_FLAGS_DEBUG : to be added to
-# ----------------------------------------------------------------------------
-# todo:
-# TBB_DEFINITIONS ? (args suppl en debug)
-#
-# autodetection:
-# succeeds if tbb.dll/tbb_debug.dll are in the PATH/LD_LIBRARY_PATH
-# otherwise, you may set TBB_LIB_PATH, TBB_LIB_PATH_DEBUG manually
-#
-# main advantage:
-# the link will be always performed with the library corresponding
-# to dynamic lib the PATH
-# => avoids problem when 2 sets of libs are installed in the system
-#
-# remarks:
-# $ENV{TBBROOT} is *not* used here because it is rather difficult
-# to guess the wanted target architecture
-#
-# tested on:
-# win7-msvc + official tbb binaries
-# winxp-mingw32 + tbb compiled from src
-# linux + installed parallel studio
-#
-# memo:
-# http://www.cmake.org/Wiki/CMake:How_To_Find_Libraries#Writing_find_modules
-# ----------------------------------------------------------------------------
-
-set (_VERB 0) # set to 1 for debugging
-
-OPTION(ENABLE_TBBMALLOC "Use TBBMALLOC" OFF)
-
-IF(_VERB) # Debug
- MESSAGE(STATUS "-------------------------------------")
- MESSAGE(STATUS " FindTBB")
- MESSAGE(STATUS "-------------------------------------")
-
- MESSAGE(STATUS "CMAKE_SHARED_LIBRARY_SUFFIX=${CMAKE_SHARED_LIBRARY_SUFFIX}")
- MESSAGE(STATUS "CMAKE_SHARED_MODULE_SUFFIX=${CMAKE_SHARED_MODULE_SUFFIX}")
- MESSAGE(STATUS "CMAKE_FIND_LIBRARY_SUFFIX=${CMAKE_FIND_LIBRARY_SUFFIX}")
- MESSAGE(STATUS "TBB_FIND_REQUIRED=${TBB_FIND_REQUIRED}") # automatiquement à 1 si REQUIRED
- MESSAGE(STATUS "TBB_USE_TBBMALLOC=${TBB_USE_TBBMALLOC}")
- MESSAGE(STATUS "WIN32=${WIN32}")
- MESSAGE(STATUS "MSVC=${MSVC}")
- MESSAGE(STATUS "MINGW=${MINGW}")
- MESSAGE(STATUS "TBBROOT=$ENV{TBBROOT}")
-ENDIF()
-
-SET(TBB_CXX_FLAGS_DEBUG "-DTBB_USE_THREADING_TOOLS=1 -DTBB_USE_DEBUG=1")
-
-# --- List of libraries to be found ---
-
-IF(DEFINED ENV{ONEAPI_ROOT})
- set(_TBB_TBBLIB_NAME "tbb12")
-ELSE()
- set(_TBB_TBBLIB_NAME "tbb")
-ENDIF()
-set(_TBB_PROXYLIB_NAME "tbbmalloc_proxy")
-set(_TBB_MALLOCLIB_NAME "tbbmalloc")
-
-set(_TBB_LIBSET1 ${_TBB_TBBLIB_NAME})
-set(_TBB_LIBSET2 ${_TBB_PROXYLIB_NAME} ${_TBB_MALLOCLIB_NAME})
-
-# ----------------------------------------------------------------------------
-# --- TBB_LIB_PATH ---
-# ----------------------------------------------------------------------------
-# method:
-# - look for the dynamic lib in the PATH/LD_LIBRARY_PATH
-# on linux or win/mingw; this path is correct
-# - on win/msvc, replace "bin" => "lib" in the path previously found
-
-SET(_TBB_LIB_PATH ${TBB_LIB_PATH}) # copy cached value
-IF(NOT _TBB_LIB_PATH) # work on copy
- # try to find "(lib)tbb.dll/so" from the env variables
- IF(MSVC)
- find_file(_TBB_TBBDLL "${_TBB_TBBLIB_NAME}.dll" PATHS "$ENV{TBBROOT}/lib/$ENV{TBB_ARCH_PLATFORM}" )
- ELSEIF(APPLE)
- find_library(_TBB_TBBDLL ${_TBB_TBBLIB_NAME} PATHS "" ENV DYLD_LIBRARY_PATH)
- ELSE()
- find_library(_TBB_TBBDLL ${_TBB_TBBLIB_NAME} PATHS "" ENV LD_LIBRARY_PATH)
- ENDIF()
- #MESSAGE(STATUS "_TBB_TBBDLL=${_TBB_TBBDLL}")
- IF(_TBB_TBBDLL)
- get_filename_component(_TBB_DLL_PATH ${_TBB_TBBDLL} PATH CACHE)
- unset(_TBB_TBBDLL CACHE)
-
- IF(MSVC)
- STRING(REPLACE "/bin/" "/lib/" _TBB_LIB_PATH ${_TBB_DLL_PATH})
- ELSE()
- SET(_TBB_LIB_PATH ${_TBB_DLL_PATH})
- ENDIF()
- unset(_TBB_DLL_PATH CACHE)
- #MESSAGE(STATUS "_TBB_LIB_PATH=${_TBB_LIB_PATH}")
- ELSE()
- MESSAGE(WARNING "!!!!!!!! ${CMAKE_SHARED_LIBRARY_PREFIX}${_TBB_TBBLIB_NAME}${CMAKE_SHARED_LIBRARY_SUFFIX} should be in PATH/LD_LIBRARY_PATH !!!!!!!!!")
- ENDIF()
- unset(_TBB_TBBDLL CACHE)
-ENDIF()
-IF(NOT TBB_LIB_PATH) # set cache if needed
- SET(TBB_LIB_PATH "${_TBB_LIB_PATH}" CACHE PATH "where the optimized .so/.lib are" FORCE)
-ENDIF()
-
-# ----------------------------------------------------------------------------
-# --- TBB_LIB_PATH_DEBUG ---
-# ----------------------------------------------------------------------------
-# same method for debug libs
-
-SET(_TBB_LIB_PATH_DEBUG ${TBB_LIB_PATH_DEBUG}) # copy cached value
-IF(NOT _TBB_LIB_PATH_DEBUG) # work on copy
- # try to find "(lib)tbb_debug.dll/so" from the env variables
- IF(MSVC)
- find_file(_TBB_TBBDLL_DEBUG "${_TBB_TBBLIB_NAME}_debug.dll" "${_TBB_TBBLIB_NAME}.dll" PATHS "$ENV{TBBROOT}/lib/$ENV{TBB_ARCH_PLATFORM}" )
- ELSEIF(APPLE)
- find_library(_TBB_TBBDLL_DEBUG "${_TBB_TBBLIB_NAME}_debug" ${_TBB_TBBLIB_NAME} PATHS "" ENV DYLD_LIBRARY_PATH)
- ELSE()
- find_library(_TBB_TBBDLL_DEBUG "${_TBB_TBBLIB_NAME}_debug" ${_TBB_TBBLIB_NAME} PATHS "" ENV LD_LIBRARY_PATH)
- ENDIF()
- #MESSAGE(STATUS "_TBB_TBBDLL_DEBUG=${_TBB_TBBDLL_DEBUG}")
- IF(_TBB_TBBDLL_DEBUG)
- get_filename_component(_TBB_DLL_PATH_DEBUG ${_TBB_TBBDLL_DEBUG} PATH CACHE)
- unset(_TBB_TBBDLL_DEBUG CACHE)
-
- IF(MSVC)
- STRING(REPLACE "/bin/" "/lib/" _TBB_LIB_PATH_DEBUG ${_TBB_DLL_PATH_DEBUG})
- ELSE()
- SET(_TBB_LIB_PATH_DEBUG ${_TBB_DLL_PATH_DEBUG})
- ENDIF()
- unset(_TBB_DLL_PATH_DEBUG CACHE)
- #MESSAGE(STATUS "_TBB_LIB_PATH_DEBUG=${_TBB_LIB_PATH_DEBUG}")
- ELSE()
- MESSAGE(WARNING "!!!!!!!! ${CMAKE_SHARED_LIBRARY_PREFIX}${_TBB_TBBLIB_NAME}_debug${CMAKE_SHARED_LIBRARY_SUFFIX} should be in PATH/LD_LIBRARY_PATH !!!!!!!!!")
- ENDIF()
- unset(_TBB_TBBDLL_DEBUG CACHE)
-ENDIF()
-IF(NOT TBB_LIB_PATH_DEBUG) # set cache if needed
- SET(TBB_LIB_PATH_DEBUG ${_TBB_LIB_PATH_DEBUG} CACHE PATH "where the debug .so/.lib are" FORCE)
-ENDIF()
-
-# ----------------------------------------------------------------------------
-# TBB_LIBRARIES: search full path of all libraries
-# ----------------------------------------------------------------------------
-
-macro(resolveLibs VARNAME LISTNAME)
- foreach(LIB ${${LISTNAME}})
- # look for optimized version
- find_library(FOUND_LIB ${LIB} PATHS ${TBB_LIB_PATH} "$ENV{TBBROOT}/lib/$ENV{TBB_ARCH_PLATFORM}")
- #MESSAGE(STATUS "FOUND_LIB=${FOUND_LIB}")
- if(FOUND_LIB)
- list(APPEND ${VARNAME} "optimized" ${FOUND_LIB})
- endif()
- unset(FOUND_LIB CACHE)
- # look for debug version
- find_library(FOUND_LIB ${LIB}_debug PATHS ${TBB_LIB_PATH_DEBUG} "$ENV{TBBROOT}/lib/$ENV{TBB_ARCH_PLATFORM}")
- #MESSAGE(STATUS "FOUND_LIB=${FOUND_LIB}")
- if(FOUND_LIB)
- list(APPEND ${VARNAME} "debug" ${FOUND_LIB})
- endif()
- unset(FOUND_LIB CACHE)
- endforeach()
-endmacro()
-
-# search for all libs
-IF( TBB_LIB_PATH AND TBB_LIB_PATH_DEBUG)
- resolveLibs(_TBB_LIBSET1_DIRS _TBB_LIBSET1)
- resolveLibs(_TBB_LIBSET2_DIRS _TBB_LIBSET2)
-ENDIF()
-
-# build full list of libs
-set(TBB_LIBRARIES ${_TBB_LIBSET1_DIRS})
-IF(ENABLE_TBBMALLOC)
- LIST(APPEND TBB_LIBRARIES ${_TBB_LIBSET2_DIRS} )
-ENDIF()
-
-# print for debug
-IF(_VERB)
- foreach(LIB ${TBB_LIBRARIES})
- MESSAGE(STATUS "lib=${LIB}")
- endforeach()
-ENDIF()
-
-# ----------------------------------------------------------------------------
-# TBB_INCLUDE_DIRS: search include dir
-# ----------------------------------------------------------------------------
-
-SET(_TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIRS})
-IF( (NOT _TBB_INCLUDE_DIRS) AND (TBB_LIB_PATH))
- SET(_VAR1 ${TBB_LIB_PATH})
- SET(_BASENAME ${_VAR1})
- SET(_TBB_TBBROOT "_TBB_TBBROOT-NOTFOUND")
- WHILE( (NOT _TBB_TBBROOT) AND (_BASENAME) )
- get_filename_component(_DIRNAME ${_VAR1} PATH)
- #MESSAGE(STATUS "_DIRNAME=${_DIRNAME}")
- get_filename_component(_BASENAME ${_VAR1} NAME)
- #MESSAGE(STATUS "_BASENAME=${_BASENAME}") # on remonte jusqu'Ã un "lib" ou "build"
-
- IF( ("${_BASENAME}" STREQUAL "lib") OR ("${_BASENAME}" STREQUAL "build") OR ("${_BASENAME}" STREQUAL "bin") )
- SET(_TBB_TBBROOT ${_DIRNAME})
- ELSE()
- SET(_VAR1 ${_DIRNAME})
- ENDIF()
- ENDWHILE()
- #MESSAGE(STATUS "_TBB_TBBROOT=${_TBB_TBBROOT}")
-
- FIND_PATH(_TBB_INCLUDE_DIRS
- NAMES tbb/parallel_for.h
- PATHS "${_TBB_TBBROOT}" "$ENV{TBBROOT}"
- PATH_SUFFIXES include
- )
- #MESSAGE(STATUS "_TBB_INCLUDE_DIRS=${_TBB_INCLUDE_DIRS}")
-ENDIF()
-IF(NOT TBB_INCLUDE_DIRS) # set cache if needed
- SET(TBB_INCLUDE_DIRS ${_TBB_INCLUDE_DIRS} CACHE PATH "where the tbb/*.h are" FORCE)
-ENDIF()
-unset(_TBB_INCLUDE_DIRS CACHE)
-
-# ----------------------------------------------------------------------------
-# Versions
-# ----------------------------------------------------------------------------
-
-SET(_TBB_VERSION_INTERFACE ${TBB_VERSION_INTERFACE})
-IF( (NOT TBB_VERSION_INTERFACE) AND TBB_INCLUDE_DIRS AND NOT DEFINED ENV{ONEAPI_ROOT})
- FILE(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _FILE)
- set(_TBB_VERSION_MAJOR 0)
- set(_TBB_VERSION_MINOR 0)
- STRING(REGEX REPLACE ".*#define TBB_INTERFACE_VERSION ([0-9]+).*" "\\1" _TBB_VERSION_INTERFACE "${_FILE}")
- STRING(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1" _TBB_VERSION_MAJOR "${_FILE}")
- STRING(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1" _TBB_VERSION_MINOR "${_FILE}")
- set(_TBB_VERSION_STRING "${_TBB_VERSION_MAJOR}.${_TBB_VERSION_MINOR}")
- unset(_FILE)
-ENDIF()
-IF(NOT TBB_VERSION_INTERFACE)
- SET(TBB_VERSION_INTERFACE ${_TBB_VERSION_INTERFACE} CACHE STRING "" FORCE)
- SET(TBB_VERSION_MAJOR ${_TBB_VERSION_MAJOR} CACHE INTERNAL "" FORCE)
- SET(TBB_VERSION_MINOR ${_TBB_VERSION_MINOR} CACHE INTERNAL "" FORCE)
- SET(TBB_VERSION_STRING ${_TBB_VERSION_STRING} CACHE STRING "" FORCE)
- mark_as_advanced(TBB_VERSION_INTERFACE)
- mark_as_advanced(TBB_VERSION_MAJOR)
- mark_as_advanced(TBB_VERSION_MINOR)
- mark_as_advanced(TBB_VERSION_STRING)
-ENDIF()
-# ----------------------------------------------------------------------------
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
-# if all listed variables are TRUE
-find_package_handle_standard_args(TBB DEFAULT_MSG
- TBB_LIBRARIES TBB_INCLUDE_DIRS
- TBB_LIB_PATH TBB_LIB_PATH_DEBUG)
-
-#MESSAGE(STATUS "TBB_FOUND = ${TBB_FOUND}")
-# ----------------------------------------------------------------------------
-
-unset(_VERB)
diff --git a/CMake/codeblocks.cmake b/CMake/codeblocks.cmake
deleted file mode 100644
index 9462769b..00000000
--- a/CMake/codeblocks.cmake
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-#SET(CMAKE_GENERATOR "CodeBlocks - Unix Makefiles" CACHE INTERNAL "" FORCE)
-
-SET(MKL_LIB_PATH "/opt/intel/mkl/lib/intel64;/opt/intel/lib/intel64" CACHE PATH "" FORCE)
-SET(MKL_INCLUDE_PATH "/opt/intel/mkl/include" CACHE PATH "" FORCE)
-
diff --git a/CMake/fwkMacros.cmake b/CMake/fwkMacros.cmake
deleted file mode 100644
index 306c0f2b..00000000
--- a/CMake/fwkMacros.cmake
+++ /dev/null
@@ -1,63 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# useful macros/fcts
-
-
-MACRO(MACRO_AddTest srcDir)
- #message(STATUS "Adding test directory ${srcDir}")
-
- #Extract the number of MPI processes used to
- #launch one test.
- #If no extra arguments are given, the number
- #is set to 1.
- set (extra_macro_args ${ARGN})
- list(LENGTH extra_macro_args num_extra_args)
- if (${num_extra_args} GREATER 0)
- list(GET extra_macro_args 0 nProcs)
- else()
- set(nProcs 1)
- endif ()
-
- file(GLOB tfiles RELATIVE ${srcDir} ${srcDir}/*)
- #message(STATUS "tfiles=${tfiles}")
- foreach(tfile ${tfiles})
- set(spath ${srcDir}/${tfile})
- if(NOT IS_DIRECTORY ${spath} AND
- ${spath} MATCHES ".+\\.py$" AND
- NOT ${tfile} STREQUAL "__init__.py")
- string(REPLACE "${PROJECT_SOURCE_DIR}/" "" strip ${spath})
- message(STATUS "Adding test ${strip}")
- if (${nProcs} GREATER 1)
- add_test(NAME "${strip}-MPI${nProcs}"
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- COMMAND mpirun -np ${nProcs} --allow-run-as-root ${PYTHON_EXECUTABLE} run.py --nogui --clean ${strip})
- # (mpi is run as root in docker)
- else()
- add_test(NAME ${strip}
- WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}
- COMMAND ${PYTHON_EXECUTABLE} run.py --nogui --clean ${strip})
- endif ()
- else()
- MACRO_AddTest(${srcDir}/${tfile} ${nProcs})
- endif()
- endforeach()
-ENDMACRO()
-
-
-MACRO(MACRO_DebugPostfix libname)
- IF(MSVC)
- SET_TARGET_PROPERTIES(${libname} PROPERTIES DEBUG_POSTFIX "_d")
- ENDIF(MSVC)
-ENDMACRO()
diff --git a/CMake/spring.cmake b/CMake/spring.cmake
deleted file mode 100644
index 776f28b8..00000000
--- a/CMake/spring.cmake
+++ /dev/null
@@ -1,24 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-FIND_PROGRAM(CMAKE_CXX_COMPILER NAMES icpc)
-FIND_PROGRAM(CMAKE_C_COMPILER NAMES icc)
-
-# force to look for mkl
-SET(BLA_VENDOR "Intel10_64lp" CACHE STRING "" FORCE)
-
-# Trilinos not available on spring
-LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_LIST_DIR})
-INCLUDE(disable-trilinos)
-
diff --git a/CMake/ubuntu.cmake b/CMake/ubuntu.cmake
deleted file mode 100644
index e6e3eea8..00000000
--- a/CMake/ubuntu.cmake
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-#FIND_PROGRAM(CMAKE_CXX_COMPILER NAMES icpc)
-#FIND_PROGRAM(CMAKE_C_COMPILER NAMES icc)
-
-#SET(CMAKE_BUILD_TYPE "Debug" CACHE FILEPATH "" FORCE)
-
-#SET(BLA_VENDOR "Intel10_64lp" CACHE STRING "" FORCE) # useless for cmake 3.5 (xenial)
-#SET(SWIG_EXECUTABLE "/home/boman/local/swig3/bin/swig" CACHE FILEPATH "" FORCE)
-
diff --git a/CMakeLists.txt b/CMakeLists.txt
index aa76b306..c25b2e47 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -1,4 +1,4 @@
-# Copyright 2020 University of Liège
+# Copyright 2022 University of Liège
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
@@ -21,27 +21,25 @@ IF(${CMAKE_VERSION} VERSION_GREATER "3.14.0") # we might want to update the proj
cmake_policy(SET CMP0086 OLD)
ENDIF()
+# -- I/O
+# Lib/Exe dir
SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH
"Single output directory for building all libraries.")
SET(EXECUTABLE_OUTPUT_PATH ${PROJECT_BINARY_DIR}/bin CACHE PATH
"Single output directory for building all executables.")
MARK_AS_ADVANCED(LIBRARY_OUTPUT_PATH EXECUTABLE_OUTPUT_PATH)
+# Build type
IF(NOT CMAKE_BUILD_TYPE)
SET( CMAKE_BUILD_TYPE "Release" CACHE STRING
"Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel."
FORCE)
ENDIF(NOT CMAKE_BUILD_TYPE)
-MESSAGE(STATUS "CMAKE_BUILD_TYPE: ${CMAKE_BUILD_TYPE}")
LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/CMake")
# -- GENERAL OPTIONS
-# print OS
-MESSAGE(STATUS "CMAKE_SYSTEM_NAME=\"${CMAKE_SYSTEM_NAME}\"")
-MESSAGE(STATUS "CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
-
# (de)activate modules
OPTION(WAVES_USE_FLOW "Compile flow module" ON)
OPTION(WAVES_USE_HEAT "Compile heat module" ON)
@@ -50,11 +48,6 @@ OPTION(WAVES_USE_KATOPTRON "Compile katoptron module" ON)
OPTION(WAVES_USE_PARAMS "Compile params module" ON)
OPTION(WAVES_USE_TLNOS "Compile tlnos module" ON)
OPTION(WAVES_USE_WAVES "Compile waves module" ON)
-# (de)activate extensions
-OPTION(WAVES_USE_TBOXVTK "Compile tboxVtk module" ON)
-# (de)activate external packages
-OPTION(WAVES_USE_MKL "Compile with Intel MKL" ON)
-OPTION(WAVES_USE_MUMPS "Compile with MUMPS" ON)
# --- Disable some Options on Windows
IF(WIN32)
@@ -65,7 +58,7 @@ IF(WIN32)
ENDIF()
# macros/fcts
-INCLUDE(fwkMacros)
+# INCLUDE(fwkMacros)
# -- C++11
SET(CMAKE_CXX_STANDARD 11) # newer way to set C++11 (requires cmake>=3.1)
@@ -98,7 +91,7 @@ IF (CMAKE_VERSION VERSION_LESS 3.12.0)
FIND_PACKAGE(PythonInterp 3.6 REQUIRED)
FIND_PACKAGE(PythonLibs 3.6 REQUIRED)
ELSE()
- find_package (Python3 COMPONENTS Interpreter Development)
+ FIND_PACKAGE(Python3 COMPONENTS Interpreter Development)
# use Python3_ROOT_DIR if wrong python found (e.g. anaconda)
SET(PYTHON_EXECUTABLE ${Python3_EXECUTABLE})
SET(PYTHON_LIBRARIES ${Python3_LIBRARIES})
@@ -127,11 +120,8 @@ IF(DOXYGEN_FOUND)
# set input and output files
SET(DOXYGEN_IN ${PROJECT_SOURCE_DIR}/Doxyfile.in)
SET(DOXYGEN_OUT ${PROJECT_BINARY_DIR}/Doxyfile)
-
# request to configure the file
CONFIGURE_FILE(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
- #message("Doxygen build started")
-
# note the option ALL which allows to build the docs together with the application
# "make dox" rebuilds the doc
ADD_CUSTOM_TARGET( dox #ALL
@@ -140,25 +130,27 @@ IF(DOXYGEN_FOUND)
COMMENT "Generating API documentation with Doxygen"
VERBATIM )
ELSE()
- MESSAGE("Doxygen need to be installed to generate the doxygen documentation")
+ MESSAGE("Doxygen needs to be installed to generate the doxygen documentation")
ENDIF()
-# -- Configure file (for SWIG to detect definitions)
-CONFIGURE_FILE(${PROJECT_SOURCE_DIR}/waves_config.h.in
- ${PROJECT_BINARY_DIR}/waves_config.h)
-INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}) # to find "waves_config.h"
+INCLUDE_DIRECTORIES(${PROJECT_BINARY_DIR}) # to find "amfe_def.h"
# -- CTest
ENABLE_TESTING()
-# -- Sub directories
+# -- INSTALL
+IF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+ EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -m site --user-site OUTPUT_VARIABLE PY_SITE OUTPUT_STRIP_TRAILING_WHITESPACE)
+ SET(CMAKE_INSTALL_PREFIX "${PY_SITE}/waves" CACHE STRING "Install location" FORCE)
+ SET(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT FALSE)
+ENDIF()
+IF(UNIX AND NOT APPLE)
+ SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}")
+ENDIF()
-ADD_SUBDIRECTORY( fwk )
-ADD_SUBDIRECTORY( tbox )
+# -- Sub directories
-IF(WAVES_USE_TBOXVTK)
- ADD_SUBDIRECTORY( tboxVtk )
-ENDIF()
+ADD_SUBDIRECTORY( ext )
IF(WAVES_USE_FLOW)
ADD_SUBDIRECTORY( flow )
@@ -188,12 +180,13 @@ IF(WAVES_USE_WAVES)
ADD_SUBDIRECTORY( waves )
ENDIF()
-# -- Packaging
-# set paths and target names
-SET(WAVES_INCLUDE_DIRS "${PROJECT_SOURCE_DIR}/fwk/src" "${PROJECT_SOURCE_DIR}/tbox/src" "${PROJECT_BINARY_DIR}")
-SET(WAVES_SWIG_DIRS "${PROJECT_SOURCE_DIR}/fwk/_src" "${PROJECT_SOURCE_DIR}/tbox/_src")
-SET(WAVES_LIBRARIES fwk tbox)
-# export target config
-EXPORT(TARGETS ${WAVES_LIBRARIES} FILE "${PROJECT_BINARY_DIR}/wavesTargets.cmake")
-# generate configuration file with absolute paths
-CONFIGURE_FILE(waves-config.cmake.in "${PROJECT_BINARY_DIR}/waves-config.cmake" @ONLY)
+# -- FINAL
+MESSAGE(STATUS "PROJECT: ${CMAKE_PROJECT_NAME}")
+MESSAGE(STATUS "* SYSTEM NAME=\"${CMAKE_SYSTEM_NAME}\"")
+MESSAGE(STATUS "* CXX COMPILER: ${CMAKE_CXX_COMPILER_ID}")
+MESSAGE(STATUS "* CXX STANDARD: ${CMAKE_CXX_STANDARD}")
+MESSAGE(STATUS "* INSTALL DIR: ${CMAKE_INSTALL_PREFIX}")
+MESSAGE(STATUS "* BUILD TYPE: ${CMAKE_BUILD_TYPE}")
+MESSAGE(STATUS "* VTK SUPPORT: ${USE_VTK}")
+MESSAGE(STATUS "* MKL SUPPORT: ${USE_MKL}")
+MESSAGE(STATUS "* MUMPS SUPPORT: ${USE_MUMPS}")
diff --git a/README.md b/README.md
index 7829bbab..93754a57 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,6 @@ Waves is a collection of general utilities and finite element tools for solving
## Features
Set of python/C++ modules:
- - [fwk](/fwk): general utilities (timers, ...)
- - [tbox](/tbox): general finite element utilities (mesh handler, nodes/elements handler, ...)
- - [tboxVtk](/tboxVtk): VTK extensions for tbox
- [waves](/waves): 3D(Hex8) transient wave equation solver (FEM)
- [flow](/flow): 2D(Tri3) and 3D(Tetra4) steady full potential equation solver (FEM)
- [heat](/heat): 2D(Tri3) steady nonlinear heat equation solver (multiscale FE²M)
@@ -17,8 +14,8 @@ Set of python/C++ modules:
- [tlnos](/tlnos): basic Trilinos examples
Additional features:
- - [x] [gmsh](http://geuz.org/gmsh/) support for mesh and post-processing
- - [x] [vtk](http://www.vtk.org/)/[PyQt](https://riverbankcomputing.com/software/pyqt/intro) support for post processing and basic GUI
+ - [x] [Gmsh](http://geuz.org/gmsh/) support for mesh and post-processing
+ - [x] [VTK](http://www.vtk.org/)/[PyQt](https://riverbankcomputing.com/software/pyqt/intro) support for post processing and basic GUI
- [x] [OpenBLAS](http://www.openblas.net/) or [Intel MKL](https://software.intel.com/en-us/intel-mkl) support
- [x] [Eigen3](http://eigen.tuxfamily.org/index.php?title=Main_Page) support for linear algebra
- [Intel Pardiso](https://software.intel.com/content/www/us/en/develop/documentation/mkl-developer-reference-c/top/sparse-solver-routines/intel-mkl-pardiso-parallel-direct-sparse-solver-interface/pardiso.html) support
diff --git a/ext/CMakeLists.txt b/ext/CMakeLists.txt
new file mode 100644
index 00000000..3c75cd07
--- /dev/null
+++ b/ext/CMakeLists.txt
@@ -0,0 +1 @@
+ADD_SUBDIRECTORY(amfe)
diff --git a/ext/amfe b/ext/amfe
new file mode 160000
index 00000000..054ba00c
--- /dev/null
+++ b/ext/amfe
@@ -0,0 +1 @@
+Subproject commit 054ba00c327e4f2745ff9c559832247f90c3cec9
diff --git a/flow/_src/CMakeLists.txt b/flow/_src/CMakeLists.txt
index 12e3f6ed..98d7f823 100644
--- a/flow/_src/CMakeLists.txt
+++ b/flow/_src/CMakeLists.txt
@@ -24,10 +24,10 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/flow/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
)
SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
@@ -39,11 +39,14 @@ endif()
MACRO_DebugPostfix(_floww)
TARGET_INCLUDE_DIRECTORIES(_floww PRIVATE ${PROJECT_SOURCE_DIR}/flow/_src
- ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${PYTHON_INCLUDE_PATH}
)
SWIG_LINK_LIBRARIES(floww
flow tbox fwk ${PYTHON_LIBRARIES}
)
+
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/floww.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _floww DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/flow/default.py b/flow/default.py
index 50b4bb56..500ce6be 100644
--- a/flow/default.py
+++ b/flow/default.py
@@ -119,8 +119,7 @@ def meshMorpher(msh, dim, mov, fxd = ['upstream', 'farfield', 'downstream'], fld
'''Initialize mesh morpher
'''
args = parseargs()
- mshDef = tbox.MshDeform(msh, dim)
- mshDef.nthreads = args.k
+ mshDef = tbox.MshDeform(msh, dim, args.k)
mshDef.setField(fld)
mshDef.addFixed(fxd)
mshDef.addMoving(mov)
diff --git a/flow/src/CMakeLists.txt b/flow/src/CMakeLists.txt
index 2fd589db..d6a008ce 100644
--- a/flow/src/CMakeLists.txt
+++ b/flow/src/CMakeLists.txt
@@ -22,5 +22,7 @@ TARGET_INCLUDE_DIRECTORIES(flow PUBLIC ${PROJECT_SOURCE_DIR}/flow/src)
TARGET_LINK_LIBRARIES(flow tbox)
+INSTALL(TARGETS flow DESTINATION ${CMAKE_INSTALL_PREFIX})
+
SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
diff --git a/fwk/CMakeLists.txt b/fwk/CMakeLists.txt
deleted file mode 100644
index 156e07c4..00000000
--- a/fwk/CMakeLists.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# Add source dir
-ADD_SUBDIRECTORY( src )
-ADD_SUBDIRECTORY( _src )
-
-# Add test dir
-MACRO_AddTest(${CMAKE_CURRENT_SOURCE_DIR}/tests)
diff --git a/fwk/__init__.py b/fwk/__init__.py
deleted file mode 100644
index fe2254ff..00000000
--- a/fwk/__init__.py
+++ /dev/null
@@ -1,8 +0,0 @@
-# -*- coding: utf-8 -*-
-# fwk MODULE initialization file
-
-from . import wutils
-wutils.findbins('fwk')
-
-from fwkw import *
-
diff --git a/fwk/_src/CMakeLists.txt b/fwk/_src/CMakeLists.txt
deleted file mode 100644
index 7e59712e..00000000
--- a/fwk/_src/CMakeLists.txt
+++ /dev/null
@@ -1,43 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake file for the SWIG interface of fwk.so
-
-INCLUDE(${SWIG_USE_FILE})
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.swg)
-FILE(GLOB ISRCS *.i)
-
-SET(CMAKE_SWIG_FLAGS "")
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
-
-SET(SWINCFLAGS
--I${PROJECT_SOURCE_DIR}/fwk/src
-)
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
-
-if (${CMAKE_VERSION} VERSION_LESS "3.8.0")
- SWIG_ADD_MODULE(fwkw python ${ISRCS} ${SRCS})
-else()
- SWIG_ADD_LIBRARY(fwkw LANGUAGE python SOURCES ${ISRCS} ${SRCS})
-endif()
-MACRO_DebugPostfix(_fwkw)
-
-TARGET_INCLUDE_DIRECTORIES(_fwkw PRIVATE ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PYTHON_INCLUDE_PATH}
-)
-
-SWIG_LINK_LIBRARIES(fwkw
- fwk ${PYTHON_LIBRARIES}
-)
diff --git a/fwk/_src/fwkw.h b/fwk/_src/fwkw.h
deleted file mode 100644
index 8d6ee8b7..00000000
--- a/fwk/_src/fwkw.h
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCppBuf2Py.h"
-#include "wExtract.h"
-#include "wHMSTime.h"
-#include "wObject.h"
-#include "wTime.h"
-#include "wTimer.h"
-#include "wTimers.h"
-#include "wTimes.h"
\ No newline at end of file
diff --git a/fwk/_src/fwkw.i b/fwk/_src/fwkw.i
deleted file mode 100644
index 3f3b930f..00000000
--- a/fwk/_src/fwkw.i
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// fwk.i: SWIG input file of the fwk python interface
-
-%feature("autodoc","1");
-
-%module(docstring=
-"'fwkw' module: base framework
-(c) ULg - A&M",
-directors="1",
-threads="1"
-) fwkw
-%{
-
-//#if defined(_WIN32) && defined(__GNUC__)
-#undef _hypot
-#include <cmath>
-//#endif
-
-#include <memory>
-#include <string>
-#include <sstream>
-#include <typeinfo>
-
-#include "fwk.h"
-#include "fwkw.h"
-
-%}
-
-%include "fwkw.swg"
-
-%include "fwk.h"
-
-//%#define SHARED_PTR_DISOWN $disown
-%include <std_shared_ptr.i>
-
-%shared_ptr(fwk::wSharedObject);
-
-%include "wObject.h"
-%include "wHMSTime.h"
-%include "wTime.h"
-%include "wTimes.h"
-%include "wTimer.h"
-%include "wTimers.h"
-
-namespace fwk {
-
-%extend wObject {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-
-%extend wSharedObject {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-
-%extend HMSTime {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-
-%extend Timer {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-
-%extend Time {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-
-%extend Times {
- std::string __str__() {
- std::stringstream str; str << *self;
- return str.str();
- }
-}
-};
-
-%include "wExtract.h"
-
-%warnfilter(401); //Nothing known about base class 'std::basic_streambuf< char >'
-%include "wCppBuf2Py.h"
-%warnfilter(+401);
-
-// --------------------------------------------------------------------
-namespace fwk {
-%extend Timers {
- Timer &getitem(std::string const &name)
- {
- return (*self)[name];
- }
-
- %pythoncode {
-def __getitem__(self, name):
- return self.getitem(name)
- }
-}
-};
diff --git a/fwk/_src/fwkw.swg b/fwk/_src/fwkw.swg
deleted file mode 100644
index 0add1dde..00000000
--- a/fwk/_src/fwkw.swg
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
- // common includes
-
-// !! mingw + c++11 + python:
-// cmath doit être inclus AVANT Python.h (et en particulier pyconfig.h)
-// car il renomme hypot en _hypoth (bidouille liée au visual)
-%begin %{
-#if defined(_WIN32) && defined(__GNUC__)
-#include <cmath>
-#endif
-%}
-
-// petite bidouille pour pouvoir compiler avec "threads=1" et iterer sur des std_vector
-// (sinon ca explose � la destruction de l'iterateur)
-%nothread swig::SwigPyIterator::~SwigPyIterator();
-
-%include "std_string.i"
-%include "exception.i"
-%include "std_vector.i"
-%include "std_list.i"
-%include "std_map.i"
-
-/*
-%exception {
- try {
- $action
- }
- catch(std::exception &e)
- {
- std::stringstream txt;
- txt << e.what(); // << ' ' << typeid(e).name();
- SWIG_exception(SWIG_RuntimeError, txt.str().c_str());
- }
- catch (Swig::DirectorException &)
- {
- SWIG_exception(SWIG_RuntimeError, "DirectorException!");
- }
- catch(...)
- {
- SWIG_exception(SWIG_RuntimeError, "Unknown C++ Runtime Error");
- }
-}
-*/
-
-// from: http://swig.10945.n7.nabble.com/Trapping-Swig-DirectorException-td6013.html
-// le code suivant permet de voir la call stack dans les appels C++ => python
-
-%{
- static void handle_exception(void) {
- try {
- throw;
- } catch (std::exception &e) {
- std::stringstream txt;
- txt << e.what(); // << ' ' << typeid(e).name();
- PyErr_SetString(PyExc_RuntimeError, e.what());
- }
- catch(...)
- {
- PyErr_SetString(PyExc_RuntimeError, "Unknown C++ Runtime Error");
- }
- }
-%}
-
-%exception {
- try {
- $action
- } catch (...) {
- // Note that if a director method failed, the Python error indicator
- // already contains full details of the exception, and it will be
- // reraised when we go to SWIG_fail; so no need to convert the C++
- // exception back to a Python one
- if (!PyErr_Occurred()) {
- handle_exception();
- }
- SWIG_fail;
- }
-}
-
-%feature("director:except") {
- if ($error != NULL) {
- throw Swig::DirectorMethodException();
- }
-}
-
-
-%ignore operator<<;
-
-
-
-
diff --git a/fwk/_src/wCppBuf2Py.cpp b/fwk/_src/wCppBuf2Py.cpp
deleted file mode 100644
index d4d4d0ee..00000000
--- a/fwk/_src/wCppBuf2Py.cpp
+++ /dev/null
@@ -1,102 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include <Python.h>
-#include "wCppBuf2Py.h"
-#include <stdio.h>
-#include <algorithm>
-
-CppBuf2Py::CppBuf2Py(std::ostream &o1, bool err) : stream(o1), errstream(err)
-{
- oldbuf = stream.rdbuf();
- stream.rdbuf(this);
- verb = false;
-}
-
-CppBuf2Py::~CppBuf2Py()
-{
- stream.rdbuf(oldbuf); // restore the ostream
-}
-
-std::streamsize
-CppBuf2Py::xsputn(const char *s, std::streamsize n)
-{
- if (verb)
- printf("CppBuf2Py::xsputn(%ld)\n", static_cast<long>(n));
- // PySys_WriteStdout truncates to 1000 chars
- static const std::streamsize MAXSIZE = 1000;
- std::streamsize written = std::min(n, MAXSIZE);
- if (verb)
- printf("written=%ld\n", static_cast<long>(written));
- std::string str(s, n);
- if (verb)
- printf("string=%s\n", str.c_str());
-
- PyGILState_STATE gstate = PyGILState_Ensure();
- if (errstream)
- PySys_WriteStderr("%s", str.c_str());
- else
- PySys_WriteStdout("%s", str.c_str());
- PyGILState_Release(gstate);
-
- return written;
-}
-
-int CppBuf2Py::overflow(int c)
-{
- if (verb)
- printf("CppBuf2Py::overflow(%d)\n", c);
-
- if (c != EOF)
- {
- PyGILState_STATE gstate = PyGILState_Ensure();
- if (errstream)
- PySys_WriteStderr("%c", c);
- else
- PySys_WriteStdout("%c", c);
- PyGILState_Release(gstate);
- }
- return c;
-}
-
-void CppBuf2Py::test()
-{
- CppBuf2Py buf(std::cout);
- for (int i = 0; i < 1000; ++i)
- std::cout << "(" << i << ")"
- << " this is a test - ";
-}
-
-// =============================================================================
-
-StdOutErr2Py::StdOutErr2Py() : out(std::cout), err(std::cerr, true)
-{
-}
-
-void StdOutErr2Py::test()
-{
- StdOutErr2Py redirector;
-
- for (int i = 0; i < 50; ++i)
- {
- std::cout << "(" << i << ")"
- << " this is a test - ";
- std::cerr << "(" << i << ")"
- << " error - ";
- }
- std::cout << '\n';
- std::cerr << '\n';
-}
diff --git a/fwk/_src/wCppBuf2Py.h b/fwk/_src/wCppBuf2Py.h
deleted file mode 100644
index 7dafad98..00000000
--- a/fwk/_src/wCppBuf2Py.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef CPPBUF2PY_H
-#define CPPBUF2PY_H
-
-#include "fwk.h"
-#include <iostream>
-
-// http://bo-peng.blogspot.be/2004/10/how-to-re-direct-cout-to-python_05.html
-// https://docs.python.org/2/c-api/sys.html#system-functions
-
-/**
- * @brief redirect a std::stream to python
- */
-#ifndef SWIG
-class CppBuf2Py : public std::basic_streambuf<char>
-{
-public:
- typedef std::char_traits<char> traits_type;
- typedef traits_type::int_type int_type;
-
-private:
- std::ostream &stream;
- std::streambuf *oldbuf;
- bool verb;
- bool errstream;
-
-public:
- CppBuf2Py(std::ostream &o1, bool err = false);
- ~CppBuf2Py();
-
- static void test();
-
-protected:
- virtual std::streamsize xsputn(const char *s, std::streamsize n);
- virtual int_type overflow(int c);
-};
-#endif //SWIG
-
-/**
- * @brief redirect std::cout/std::cerr to python sys.stdout/sys.stderr
- */
-
-class StdOutErr2Py
-{
- CppBuf2Py out;
- CppBuf2Py err;
-
-public:
- StdOutErr2Py();
-
- static void test();
-};
-
-#endif //CPPBUF2PY_H
diff --git a/fwk/coloring.py b/fwk/coloring.py
deleted file mode 100644
index a57b1b5a..00000000
--- a/fwk/coloring.py
+++ /dev/null
@@ -1,24 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# custom color class
-
-class ccolors:
- ANSI_RED = '\x1b[1;31m'
- ANSI_GREEN = '\x1b[1;32m'
- ANSI_YELLOW = '\x1b[1;33m'
- ANSI_BLUE = '\x1b[1;34m'
- ANSI_RESET = '\x1b[0m'
diff --git a/fwk/src/CMakeLists.txt b/fwk/src/CMakeLists.txt
deleted file mode 100644
index 02e45112..00000000
--- a/fwk/src/CMakeLists.txt
+++ /dev/null
@@ -1,26 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake input file of fwk.so
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.hpp)
-
-ADD_LIBRARY(fwk SHARED ${SRCS})
-MACRO_DebugPostfix(fwk)
-
-TARGET_INCLUDE_DIRECTORIES(fwk PUBLIC ${PROJECT_SOURCE_DIR}/fwk/src)
-
-# ---
-SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
-SOURCE_GROUP(timer REGULAR_EXPRESSION ".+(Time).+")
diff --git a/fwk/src/fwk.cpp b/fwk/src/fwk.cpp
deleted file mode 100644
index 9f54df7c..00000000
--- a/fwk/src/fwk.cpp
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "fwk.h"
-#include <iostream>
-
-#if defined(WIN32)
-#include <float.h>
-#elif defined(__GNUC__)
-#include <fenv.h>
-#endif
-
-#define ANSI_COLOR_YELLOW "\x1b[1;33m"
-#define ANSI_COLOR_BLUE "\x1b[1;34m"
-#define ANSI_COLOR_RESET "\x1b[0m"
-
-FWK_API void testswig(bool i) // testswig(3.0) displays 1 (no error and cast float=>bool)
-{
- std::cout << "testswig received i = " << i << '\n';
-}
-
-/**
- * @brief Enable Floating Point Exception
- *
- * Imported from Metafor
- * @authors Adrien Crovato
- */
-FWK_API void enableFpe()
-{
-#if !defined(__MINGW32__) // MinGW: 2 "float.h" and the wrong one is included by default...
- std::cout << ANSI_COLOR_BLUE << "Enabling Floating-Point Exceptions..." << ANSI_COLOR_RESET << std::endl;
-#if defined(WIN32)
- // doc https://msdn.microsoft.com/en-us/library/e9b52ceh(v=vs.110).aspx
- // _EM_INVALID | _EM_DENORMAL | _EM_ZERODIVIDE | _EM_OVERFLOW | _EM_UNDERFLOW | _EM_INEXACT
- _clear87(); // doc : "clearing the mask sets the exceptions"
- _control87(_EM_INVALID | _EM_DENORMAL | _EM_UNDERFLOW | _EM_INEXACT, _MCW_EM); // doc : "setting the _MCW_EM mask hides the exception"
-#elif defined(__APPLE__)
- // we should try feraiseexcept (c++11)
-#elif defined(__GNUC__)
- // FE_ALL_EXCEPT|FE_DIVBYZERO|FE_INEXACT|FE_INVALID|FE_OVERFLOW|FE_UNDERFLOW
- feenableexcept(FE_OVERFLOW | FE_DIVBYZERO | FE_INVALID);
-#else // defined(WIN32)
- std::cout << ANSI_COLOR_YELLOW << "Floating-Point Exceptions not implemented for this compiler!" << ANSI_COLOR_RESET << std::endl;
-#endif
-#endif //!defined(__MINGW32__)
-}
-
-/**
- * @brief Disable Floating Point Exception
- * @authors Adrien Crovato
- */
-FWK_API void disableFpe()
-{
-#if defined(__GNUC__) && !defined(__clang__) && !defined(__MINGW32__)
- std::cout << ANSI_COLOR_BLUE << "Disabling Floating-Point Exceptions..." << ANSI_COLOR_RESET << std::endl;
- fedisableexcept(FE_ALL_EXCEPT);
-#else
- std::cout << "disableFpe() is not implemented" << std::endl;
-#endif
-}
diff --git a/fwk/src/fwk.h b/fwk/src/fwk.h
deleted file mode 100644
index 85c99132..00000000
--- a/fwk/src/fwk.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// fwk global header
-
-#ifndef FWK_H
-#define FWK_H
-
-#if defined(WIN32)
-#ifdef fwk_EXPORTS
-#define FWK_API __declspec(dllexport)
-#else
-#define FWK_API __declspec(dllimport)
-#endif
-#else
-#define FWK_API
-#endif
-
-#ifdef _MSC_VER
-#if !defined(_CRT_SECURE_NO_WARNINGS)
-#define _CRT_SECURE_NO_WARNINGS 1
-#endif
-
-#pragma warning(disable : 4251) // DLL/templates non exportes
-#pragma warning(disable : 4275) // non - DLL-interface classkey 'identifier' used as base for DLL-interface classkey 'identifier'
-
-#define NOMINMAX // avoids the definition of "min/max" macro in <minwindef.h> (which could shadow std::max)
-
-#endif //_MSC_VER
-
-#include "waves_config.h"
-
-namespace fwk
-{
-
-class wObject;
-class Extract;
-class Observer;
-
-class HMSTime;
-class Time;
-class Timer;
-class Timers;
-class Times;
-
-} // namespace fwk
-
-// global fcts
-
-FWK_API void testswig(bool i);
-FWK_API void enableFpe();
-FWK_API void disableFpe();
-
-#endif //FWK_H
diff --git a/fwk/src/wExtract.cpp b/fwk/src/wExtract.cpp
deleted file mode 100644
index e8068b89..00000000
--- a/fwk/src/wExtract.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wExtract.h"
-
-using namespace fwk;
-
-Extract::Extract()
-{
-}
-
-void Extract::write(std::ostream &out) const
-{
- out << "Extract";
-}
-
-std::vector<double>
-Extract::execute()
-{
- std::vector<double> ret;
- return ret;
-}
diff --git a/fwk/src/wExtract.h b/fwk/src/wExtract.h
deleted file mode 100644
index d6ee0031..00000000
--- a/fwk/src/wExtract.h
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WEXTRACT_H
-#define WEXTRACT_H
-
-#include "fwk.h"
-#include "wObject.h"
-#include <vector>
-
-namespace fwk
-{
-
-/**
- * @brief an object able to extract scalar results from the model
- */
-
-class FWK_API Extract : public wObject
-{
-public:
- Extract();
- virtual std::vector<double> execute();
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace fwk
-
-#endif //WEXTRACT_H
diff --git a/fwk/src/wHMSTime.cpp b/fwk/src/wHMSTime.cpp
deleted file mode 100644
index 4aa47a56..00000000
--- a/fwk/src/wHMSTime.cpp
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wHMSTime.h"
-#include <iomanip>
-#include <sstream>
-
-using namespace fwk;
-
-HMSTime::HMSTime(double time)
-{
- double secinmins = 60;
- double secinhours = 60 * secinmins;
- double secindays = 24 * secinhours;
- double secinmonths = 30 * secindays;
- double secinyears = 365 * secinmonths;
-
- years = static_cast<int>(time / secinyears);
- time -= years * secinyears;
-
- months = static_cast<int>(time / secinmonths);
- time -= months * secinmonths;
-
- days = static_cast<int>(time / secindays);
- time -= days * secindays;
-
- hours = static_cast<int>(time / secinhours);
- time -= hours * secinhours;
-
- mins = static_cast<int>(time / secinmins);
- secs = time - mins * secinmins;
-}
-
-std::string
-HMSTime::str() const
-{
- std::ostringstream st;
- if (years)
- st << years << "y";
- if (years || months)
- st << months << "mo";
- if (years || months || days)
- st << days << "d";
- if (years || months || days || hours)
- st << hours << "h";
- if (years || months || days || hours || mins)
- st << mins << "m";
- st << std::fixed << std::setprecision(2) << secs << "s";
-
- return st.str();
-}
-namespace fwk
-{
-FWK_API std::ostream &
-operator<<(std::ostream &out, HMSTime const &obj)
-{
- out << obj.str();
- return out;
-}
-}; // namespace fwk
diff --git a/fwk/src/wHMSTime.h b/fwk/src/wHMSTime.h
deleted file mode 100644
index 6af798d6..00000000
--- a/fwk/src/wHMSTime.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WHMSTIME_H
-#define WHMSTIME_H
-
-#include "fwk.h"
-#include <iostream>
-
-namespace fwk
-{
-
-/**
- * @brief Convert seconds to a HMS string
- */
-
-class FWK_API HMSTime
-{
- int years;
- int months;
- int days;
- int hours;
- int mins;
- double secs;
-
-public:
- explicit HMSTime(double sec = 0.0);
- friend FWK_API std::ostream &operator<<(std::ostream &out, HMSTime const &obj);
- std::string str() const;
-};
-} // namespace fwk
-
-#endif //WHMSTIME_H
diff --git a/fwk/src/wObject.cpp b/fwk/src/wObject.cpp
deleted file mode 100644
index 5ae407c5..00000000
--- a/fwk/src/wObject.cpp
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wObject.h"
-
-namespace fwk
-{
-
-FWK_API std::ostream &
-operator<<(std::ostream &out, wObject const &obj)
-{
- obj.write(out);
- return out;
-}
-
-void wObject::write(std::ostream &out) const
-{
-}
-
-FWK_API std::ostream &
-operator<<(std::ostream &out, wSharedObject const &obj)
-{
- obj.write(out);
- return out;
-}
-
-void wSharedObject::write(std::ostream &out) const
-{
-}
-
-} // namespace fwk
diff --git a/fwk/src/wObject.h b/fwk/src/wObject.h
deleted file mode 100644
index 663a8b98..00000000
--- a/fwk/src/wObject.h
+++ /dev/null
@@ -1,74 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WOBJECT_H
-#define WOBJECT_H
-
-#include "fwk.h"
-#include <iostream>
-
-namespace fwk
-{
-
-/**
- * @brief Base class of all virtual objects
- *
- * The only purpose of this class is that it avoids many copy/paste for
- * the print function (__str__() fct) in SWIG/python
- */
-
-class FWK_API wObject
-{
-public:
- wObject() = default;
- virtual ~wObject() {}
- wObject(const wObject &) = delete;
- wObject &operator=(const wObject &) = delete;
-
-#ifndef SWIG
- friend FWK_API std::ostream &operator<<(std::ostream &out, wObject const &obj);
- virtual void write(std::ostream &out) const;
-#endif
-};
-
-/**
- * @brief Base class of smart-pointed objects (shared_ptr)
- *
- * This base class is only required for "print" in SWIG/python.
- * std::cout << *o works from C++ (it calls "write") even if the object inherits from wObject
- * which is not defined in SWIG as shared_ptr-managed object
- * However "print o" fails in python if the shared object inherits from wObject.
- * This class also avoids a warning in SWIG telling that some derived or base classes are not
- * managed by shared_ptr.
- */
-
-class FWK_API wSharedObject
-{
-public:
- wSharedObject() = default;
- virtual ~wSharedObject() {}
- wSharedObject(const wSharedObject &) = delete;
- wSharedObject &operator=(const wSharedObject &) = delete;
-
-#ifndef SWIG
- friend FWK_API std::ostream &operator<<(std::ostream &out, wSharedObject const &obj);
- virtual void write(std::ostream &out) const;
-#endif
-};
-
-} // namespace fwk
-
-#endif //WOBJECT_H
diff --git a/fwk/src/wObserver.cpp b/fwk/src/wObserver.cpp
deleted file mode 100644
index 0162b4a3..00000000
--- a/fwk/src/wObserver.cpp
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wObserver.h"
-#include <stdexcept>
-
-using namespace fwk;
-
-void Observer::update(double data)
-{
- throw std::runtime_error("fwk::Observer::update() not implemented!\n");
-}
\ No newline at end of file
diff --git a/fwk/src/wObserver.h b/fwk/src/wObserver.h
deleted file mode 100644
index cabc058c..00000000
--- a/fwk/src/wObserver.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WOBSERVER_H
-#define WOBSERVER_H
-
-#include "fwk.h"
-
-namespace fwk
-{
-
-/**
- * @brief Base class that obsverves another class, and that updates accordingly
- */
-
-class FWK_API Observer
-{
-public:
- Observer() {}
- virtual ~Observer() {}
- virtual void update(double data);
-};
-
-} // namespace fwk
-
-#endif //WOBSERVER_H
diff --git a/fwk/src/wTime.cpp b/fwk/src/wTime.cpp
deleted file mode 100644
index 9ee5a2c4..00000000
--- a/fwk/src/wTime.cpp
+++ /dev/null
@@ -1,73 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WIN32
-#include <unistd.h>
-#endif
-#include "wTime.h"
-#include "wHMSTime.h"
-
-using namespace fwk;
-
-namespace fwk
-{
-
-FWK_API std::ostream &
-operator<<(std::ostream &out, Time const &obj)
-{
- out << obj.hms();
- return out;
-}
-
-} // namespace fwk
-
-std::string
-Time::hms() const
-{
- return HMSTime(sec()).str();
-}
-
-#ifdef WIN32
-
-double
-Int64Time::sec() const
-{
- static __int64 freq = 10000000U;
- return time / static_cast<double>(freq);
-}
-#else
-
-double
-UnixClockTime::sec() const
-{
- static clock_t freq = sysconf(_SC_CLK_TCK);
- return time / static_cast<double>(freq);
-}
-
-#endif
-
-double
-ClockTime::sec() const
-{
- static clock_t freq = CLOCKS_PER_SEC;
- return time / static_cast<double>(freq);
-}
-
-double
-DblTime::sec() const
-{
- return time;
-}
diff --git a/fwk/src/wTime.h b/fwk/src/wTime.h
deleted file mode 100644
index c782967c..00000000
--- a/fwk/src/wTime.h
+++ /dev/null
@@ -1,115 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTIME_H
-#define WTIME_H
-
-#include "fwk.h"
-#include <time.h>
-#include <string>
-#include <iostream>
-
-namespace fwk
-{
-
-/**
- * @brief Portable base class handling a time
- */
-class FWK_API Time
-{
-public:
- virtual double sec() const = 0;
- std::string hms() const;
-#ifndef SWIG
- friend FWK_API std::ostream &operator<<(std::ostream &out, Time const &obj);
-#endif
-};
-
-//-----------------------------------------------------------------------------------------
-
-#ifndef SWIG
-
-#ifdef WIN32
-
-/**
- * @brief Time as a __int64 (MS Windows only)
- */
-class FWK_API Int64Time : public Time
-{
- __int64 time;
-
-public:
- explicit Int64Time(__int64 t = 0) : time(t) {}
- virtual double sec() const override;
- operator bool() const { return time != 0; }
- Int64Time operator+(Int64Time const &obj) const { return Int64Time(time + obj.time); }
- Int64Time operator-(Int64Time const &obj) const { return Int64Time(time - obj.time); }
-};
-
-#else //WIN32
-
-class FWK_API UnixClockTime : public Time
-{
- clock_t time;
-
-public:
- explicit UnixClockTime(clock_t t = 0) : time(t) {}
- virtual double sec() const override;
- operator bool() const { return time != 0; }
- UnixClockTime operator+(UnixClockTime const &obj) const { return UnixClockTime(time + obj.time); }
- UnixClockTime operator-(UnixClockTime const &obj) const { return UnixClockTime(time - obj.time); }
-};
-
-#endif //WIN32
-
-//-----------------------------------------------------------------------------------------
-
-/**
- * @brief Time as a clock_t (freq = CLOCKS_PER_SEC)
- */
-class FWK_API ClockTime : public Time
-{
- clock_t time;
-
-public:
- explicit ClockTime(clock_t t = 0) : time(t) {}
- virtual double sec() const override;
- operator bool() const { return time != 0; }
- ClockTime operator+(ClockTime const &obj) const { return ClockTime(time + obj.time); }
- ClockTime operator-(ClockTime const &obj) const { return ClockTime(time - obj.time); }
-};
-
-//-----------------------------------------------------------------------------------------
-
-/**
- * @brief Time as a double
- */
-class FWK_API DblTime : public Time
-{
- double time;
-
-public:
- explicit DblTime(double t = 0.0) : time(t) {}
- virtual double sec() const override;
- operator bool() const { return time != 0.0; }
- DblTime operator+(DblTime const &obj) const { return DblTime(time + obj.time); }
- DblTime operator-(DblTime const &obj) const { return DblTime(time - obj.time); }
-};
-
-#endif //SWIG
-
-}; // namespace fwk
-#endif //WTIME_H
diff --git a/fwk/src/wTimer.cpp b/fwk/src/wTimer.cpp
deleted file mode 100644
index 2242c0e1..00000000
--- a/fwk/src/wTimer.cpp
+++ /dev/null
@@ -1,78 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTimer.h"
-
-using namespace fwk;
-
-Timer::Timer()
-{
- reset();
-}
-
-/**
- * @brief reset the timer
- */
-
-void Timer::reset()
-{
- tStart = Times();
- tElaps = Times();
- isOn = false;
-}
-
-/**
- * @brief Start the timer from last "elapsed time"
- */
-
-void Timer::start()
-{
- isOn = true;
- tStart.read();
-}
-
-/**
- * @brief stop the timer
- */
-
-void Timer::stop()
-{
- tElaps = read();
- tStart = Times();
- isOn = false;
-}
-
-/**
- * @brief read current time (without stopping the timer)
- */
-
-Times Timer::read() const
-{
- if (isOn)
- return tElaps + Times().read() - tStart;
- else
- return tElaps;
-}
-
-namespace fwk
-{
-FWK_API std::ostream &
-operator<<(std::ostream &out, Timer const &obj)
-{
- out << obj.read();
- return out;
-}
-} // namespace fwk
diff --git a/fwk/src/wTimer.h b/fwk/src/wTimer.h
deleted file mode 100644
index 2a960587..00000000
--- a/fwk/src/wTimer.h
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTIMER_H
-#define WTIMER_H
-
-#include "fwk.h"
-#include "wTimes.h"
-
-namespace fwk
-{
-
-/**
- * @brief Un simple chronometre
- */
-
-class FWK_API Timer
-{
- Times tStart;
- Times tElaps;
-
- bool isOn;
-
-public:
- Timer();
-
- void start();
- void stop();
- void reset();
- Times read() const;
-
- friend FWK_API std::ostream &operator<<(std::ostream &out, Timer const &obj);
-
-#ifndef SWIG
- void setTStart(Times times)
- {
- tStart = times;
- };
- void setTElaps(Times times) { tElaps = times; };
-#endif
-};
-}; // namespace fwk
-#endif //TIMER_H
diff --git a/fwk/src/wTimers.cpp b/fwk/src/wTimers.cpp
deleted file mode 100644
index 69ae39ba..00000000
--- a/fwk/src/wTimers.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTimers.h"
-#include <iomanip>
-
-using namespace fwk;
-
-Timers::Timers()
-{
-}
-
-Timer &
-Timers::operator[](std::string const &name)
-{
- return timers[name];
-}
-
-void Timers::reset()
-{
- for (auto it = timers.begin(); it != timers.end(); ++it)
- it->second.reset();
-}
-
-void Timers::write(std::ostream &out) const
-{
- out << std::fixed << std::setprecision(1);
- out << std::setw(15) << std::left << " "
- << std::setw(10) << std::right << "user"
- << std::setw(10) << std::right << "real"
- << std::setw(10) << std::right << "kernel"
- << '\n';
-
- for (auto it = timers.begin(); it != timers.end(); ++it)
- {
- Times tm = it->second.read();
- out << std::setw(15) << std::left << it->first
- << std::setw(10) << std::right << tm.getUser().sec()
- << std::setw(10) << std::right << tm.getReal().sec()
- << std::setw(10) << std::right << tm.getKernel().sec()
- << '\n';
- }
-}
diff --git a/fwk/src/wTimers.h b/fwk/src/wTimers.h
deleted file mode 100644
index 779994be..00000000
--- a/fwk/src/wTimers.h
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTIMERS_H
-#define WTIMERS_H
-
-#include "fwk.h"
-#include "wObject.h"
-#include "wTimer.h"
-#include <map>
-
-namespace fwk
-{
-
-/**
- * @brief list of named timers
- */
-
-class FWK_API Timers : public wObject
-{
- std::map<std::string, Timer> timers;
-
-public:
- Timers();
- void reset();
-
-#ifndef SWIG
-
- Timer &operator[](std::string const &name);
- virtual void write(std::ostream &out) const override;
-#endif
-};
-}; // namespace fwk
-#endif //TIMERS_H
diff --git a/fwk/src/wTimes.cpp b/fwk/src/wTimes.cpp
deleted file mode 100644
index 1ee97deb..00000000
--- a/fwk/src/wTimes.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTimes.h"
-
-#ifdef WIN32
-#include <windows.h>
-#else
-#include <unistd.h> // needed by Linux 32-bit only!
-#include <sys/times.h>
-#endif
-
-using namespace fwk;
-
-Times Times::read()
-{
-#ifdef WIN32
- HANDLE hProcess = GetCurrentProcess();
- FILETIME ftCreation, ftExit, ftKernel, ftUser;
- GetProcessTimes(hProcess, &ftCreation, &ftExit, &ftKernel, &ftUser);
- user = Int64Time(*(reinterpret_cast<__int64 *>(&ftUser)));
- kernel = Int64Time(*(reinterpret_cast<__int64 *>(&ftKernel)));
- real = ClockTime(clock());
-#else
- struct tms tm;
- real = UnixClockTime(times(&tm));
- user = UnixClockTime(tm.tms_utime);
- kernel = UnixClockTime(tm.tms_stime);
-#endif
- return *this;
-}
-
-namespace fwk
-{
-FWK_API std::ostream &
-operator<<(std::ostream &out, Times const &obj)
-{
- out << "usr:" << obj.getUser();
- out << " kern:" << obj.getKernel();
- out << " real:" << obj.getReal();
- return out;
-}
-} // namespace fwk
diff --git a/fwk/src/wTimes.h b/fwk/src/wTimes.h
deleted file mode 100644
index 42c17ce8..00000000
--- a/fwk/src/wTimes.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTIMES_H
-#define WTIMES_H
-
-#include "fwk.h"
-#include "wTime.h"
-
-namespace fwk
-{
-/**
- * @brief Class containing user, kernel, real (wall clock) CPU time counters
- */
-
-class FWK_API Times
-{
-#ifdef WIN32
- Int64Time user;
- Int64Time kernel;
- ClockTime real;
-#else
- UnixClockTime user;
- UnixClockTime kernel;
- UnixClockTime real;
-#endif
-
-public:
- Times read();
-
- Time const &getUser() const;
- Time const &getKernel() const;
- Time const &getReal() const;
-
-#ifndef SWIG
- // [RB] the following 3 routines looks like a dirty hack from Kim
- // to display Trilinos timers as waves ones
- // @todo remove these calls or replace them by an appropriate (copy) constructor
-#ifdef WIN32
- void setUser(Int64Time time)
- {
- user = time;
- }
- void setKernel(Int64Time time) { kernel = time; }
- void setReal(ClockTime time) { real = time; }
-#else
- void setUser(UnixClockTime time)
- {
- user = time;
- }
- void setKernel(UnixClockTime time) { kernel = time; }
- void setReal(UnixClockTime time) { real = time; }
-#endif
- Times operator+(Times const &obj) const;
- Times operator-(Times const &obj) const;
- friend FWK_API std::ostream &operator<<(std::ostream &out, Times const &obj);
-#endif
-};
-
-#include "wTimes.inl"
-}; // namespace fwk
-#endif //WTIMES_H
diff --git a/fwk/src/wTimes.inl b/fwk/src/wTimes.inl
deleted file mode 100644
index 1c339839..00000000
--- a/fwk/src/wTimes.inl
+++ /dev/null
@@ -1,53 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-inline Time const &
-Times::getUser() const
-{
- return user;
-}
-
-inline Time const &
-Times::getKernel() const
-{
- return kernel;
-}
-
-inline Time const &
-Times::getReal() const
-{
- return real;
-}
-
-inline Times
-Times::operator+(Times const &obj) const
-{
- Times ret;
- ret.user = user + obj.user;
- ret.kernel = kernel + obj.kernel;
- ret.real = real + obj.real;
- return ret;
-}
-
-inline Times
-Times::operator-(Times const &obj) const
-{
- Times ret;
- ret.user = user - obj.user;
- ret.kernel = kernel - obj.kernel;
- ret.real = real - obj.real;
- return ret;
-}
diff --git a/fwk/testing.py b/fwk/testing.py
deleted file mode 100644
index e6de9e76..00000000
--- a/fwk/testing.py
+++ /dev/null
@@ -1,80 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# testing classes (for ctest)
-
-from .coloring import ccolors
-
-class CTest:
- def __init__(self, name, val, expected, maxdiff=1e-10, refval=0.0, forceabs=False):
- self.name = name # name of the test
- self.val = float(val) # calculated value
- self.expected = float(expected) # expected value
- self.maxdiff = abs(float(maxdiff)) # tolerance on max difference
- self.refval = abs(float(refval)) # optional value used as denominator
- # if the expected one is close to 0
- self.forceabs = forceabs # force the calculation of an absolute diff
-
- def run(self):
- ok = True
- adiff = abs(self.val-self.expected) # absolute diff
-
- # the ref value is the largest among the expected value and
- # the one provided by the user
- denom = max(abs(self.refval), abs(self.expected))
-
- if not self.forceabs and denom>self.maxdiff:
- diff = adiff / denom # relative diff
- typ='rel'
- percent = '%3.1f%%' % (self.maxdiff*100)
- else:
- diff = adiff # absolute diff
- typ='abs'
- percent = '%f' % self.maxdiff
-
- print("[CTest] %s = %f (expected %f +/- %s)" % \
- (self.name, self.val, self.expected, percent))
-
- if diff<=self.maxdiff:
- sgn = '<='
- info = "ok"
- else:
- sgn = '>'
- ok = False
- info = "wrong!"
- print("\t%s diff = %e %s %e [%s]" % (typ, diff, sgn, self.maxdiff, info))
- return ok
-
-class CTests:
- def __init__(self):
- self.tests = []
- def add(self, t):
- self.tests.append(t)
- def run(self):
- ok = True
- for i,t in enumerate(self.tests):
- #print "running test %d/%d..." % (i+1,len(self.tests))
- ok = t.run() and ok
-
- if ok:
- print(ccolors.ANSI_GREEN + '** All tests are OK!' + ccolors.ANSI_RESET)
- else:
- print('\n\n')
- raise Exception(ccolors.ANSI_RED + '** Some tests failed!' + ccolors.ANSI_RESET)
-
-
-
diff --git a/fwk/tests/timers.py b/fwk/tests/timers.py
deleted file mode 100644
index 5df6f545..00000000
--- a/fwk/tests/timers.py
+++ /dev/null
@@ -1,71 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# basic test of timers
-
-import fwk
-from time import sleep
-
-
-delay = 0.2
-
-print('-'*79)
-print("Timer - a simple Timer")
-print('-'*79)
-
-timer = fwk.Timer()
-timer.start()
-for i in range(3):
- sleep(delay)
- print(timer)
-timer.stop()
-sleep(delay)
-print(timer)
-
-print('-'*79)
-print("Times - a cpu time (usr, real, kernel)")
-print('-'*79)
-
-times = timer.read()
-print("it lasted %f secs" % times.getReal().sec())
-print("CPU time = %f secs" % times.getUser().sec())
-
-print("once again...")
-#print "it lasted %f secs" % timer.read().getReal().sec() # plante car retour de read() desalloue lors de sec().
-#print "CPU time = %f secs" % timer.read().getUser().sec()
-
-
-print('-'*79)
-print("HMSTime - conversion from sec to HMS")
-print('-'*79)
-
-nsec = 100000
-print("%s secs equals to %s" % (nsec, fwk.HMSTime(nsec)))
-
-print('-'*79)
-print("Timers - list of Timers")
-print('-'*79)
-
-timers = fwk.Timers()
-timers['cpu1'].start()
-sleep(delay)
-timers['cpu2'].start()
-sleep(delay)
-timers['cpu3'].start()
-sleep(delay)
-print(timers)
-
diff --git a/fwk/wutils.py b/fwk/wutils.py
deleted file mode 100644
index 7383760e..00000000
--- a/fwk/wutils.py
+++ /dev/null
@@ -1,270 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# Python utilities
-
-try: # permet d'importer les .so de mkl à partir d'un module python
- import sys,DLFCN
- sys.setdlopenflags(DLFCN.RTLD_NOW|DLFCN.RTLD_GLOBAL)
-except:
- pass
-
-# ------------------------------------------------------------------------------
-
-def findbins(modname, dirB=['build','wavesB'], verb=False): # changer wavesB en autre chose !
- """
- try to find where the binaries related to a python module are
- if modname='fwk' => look for 'fwkw.[so|pyd]'
- """
-
- modwrap = modname+'w' # assumption: SWIG-generated module = module+'w'
-
- # are we lucky?
- try:
- __import__(modwrap) #import fwkw
- if verb:
- print("[findbins] module %s already in the PYTHONPATH!" % modwrap)
- return # nothing to do
- except:
- pass
- if verb:
- print("[findbins] module %s is not in the PYTHONPATH!" % modwrap)
-
- # the module is not in the pythonpath
- # let's look for a folder called "dirB" in parent directories
- # result in "spath"
- import sys, os, os.path
- path = os.path.abspath(sys.modules[modname].__file__)
- found = False
- while True:
- for dir in dirB:
- spath = os.path.join(path,dir)
- if verb:
- print("[findbins] path = ", path)
- print("[findbins] spath = ", spath)
- print("[findbins] os.path.isdir(spath) = ", os.path.isdir(spath))
- if(os.path.isdir(spath)):
- found = True
- if verb:
- print("[findbins] break with ",dir)
- break
- uppath = os.path.split(path)[0]
- if(path==uppath):
- raise Exception('[findbins] binary dir not found in '+repr(dirB)+' !')
- path=uppath
-
- if found == True : # to break the while ...
- break
- if verb:
- print("[findbins] spath=", spath)
-
-
- # build a list of possible directories (libpath)
- # according to the system and the runtime environment
-
- pyexe = os.path.basename(sys.executable)
- if verb:
- print("[findbins] pyexe=", pyexe)
-
- libpath = []
- if pyexe.find('_d.exe')>=0:
- print("[findbins] looking for win/debug libs")
- libpath.append(os.path.join(spath, 'bin/Debug'.replace('/',os.sep)))
- if 'GCC' in sys.version: # windows+gcc = mingw => needs to append lib dir to PATH
- os.environ['PATH'] += ';' + os.path.join(spath, 'bin')
- elif pyexe.find('.exe')>=0:
- print("[findbins] looking for win/release libs")
- libpath.append(os.path.join(spath, 'bin/Release'.replace('/',os.sep)))
- libpath.append(os.path.join(spath, 'bin/RelWithDebInfo'.replace('/',os.sep)))
- if 'GCC' in sys.version: # windows+gcc = mingw => needs to append lib dir to PATH
- os.environ['PATH'] += ';' + os.path.join(spath, 'bin')
- else:
- print("[findbins] looking for linux/mingw libs")
- libpath.append( os.path.join(spath, 'bin') ) # also for win-mingw
-
- # check the paths one by one
- for p in libpath:
- if os.path.isdir(p):
- if verb:
- print("[findbins] adding %s to sys.path" % p)
- sys.path.append(p)
- if verb:
- print("[findbins] sys.path =", sys.path)
- break
- else:
- raise Exception("[findbins] '%s' not found!" % libpath)
-
- #exec("import %s" % modwrap)
- #mod = sys.modules[modwrap]
- mod = __import__(modwrap)
- print('[findbins] loading ', mod.__file__)
-
- # initialisations
- initDLL()
- initMKL(parseargs().k)
-
-# attention! si waves and heat possedent des classes de mêmes noms,
-# c'est celle du premier module qui sera chargée!
-# => ne pas charger waves et heat en même temps tant qu'il n'y a pas de namespaces
-# distingant les 2 ensembles de classes
-
-#-------------------------------------------------------------------------------
-
-def initDLL():
- # For new versions of python, DLLs must be loaded via a specific command
- import platform, os, sys
- if 'Windows' in platform.uname() and sys.version_info.minor >= 8:
- lookfor = ['tbb', 'mkl', 'vtk']
- for k in lookfor:
- for v in os.environ['path'].split(';'):
- if k in v.lower():
- os.add_dll_directory(v)
- break
-
-# ------------------------------------------------------------------------------
-
-def initMKL(nthreads):
- import os
- # we try to have full control over the threading environment
- # => set MKL/OMP variables if (and only if) they are not set!
- # number of "default" threads for MKL (available MKL domains: ALL, BLAS, VML, PARDISO)
- if not 'MKL_NUM_THREADS' in os.environ:
- os.environ['MKL_NUM_THREADS'] = '%d' % nthreads
- os.environ['MKL_DOMAIN_NUM_THREADS'] = 'MKL_DOMAIN_ALL=%d' % nthreads
- # threading interface
- if not 'MKL_THREADING_LAYER' in os.environ:
- if nthreads == 1:
- os.environ['MKL_THREADING_LAYER'] = 'SEQUENTIAL'
- else:
- os.environ['MKL_THREADING_LAYER'] = 'TBB'
- # interface (32 or 64 bits)
- if not 'MKL_INTERFACE_LAYER' in os.environ:
- os.environ['MKL_INTERFACE_LAYER'] = 'LP64' # 32 bits (default), ILP64 for 64 bits
- # we do not want to use OpenMP
- if not 'OMP_NUM_THREADS' in os.environ:
- os.environ['OMP_NUM_THREADS'] = '1'
- if not 'MKL_DYNAMIC' in os.environ:
- os.environ['MKL_DYNAMIC'] = 'FALSE'
- if not 'OMP_DYNAMIC' in os.environ:
- os.environ['OMP_DYNAMIC'] = 'FALSE'
- # display variables
- for s in ['OMP_', 'MKL', 'KMP']:
- print('* %s environment:' % s)
- for key, value in os.environ.items():
- if s in key:
- print('\t%s = %s' % (key, value))
-
-# ------------------------------------------------------------------------------
-
-def setupwdir(testname):
- """
- creates a single working folder for the given test
- """
- try:
- # are we using MPI?
- import mpi4py.MPI as mpi
- comm = mpi.COMM_WORLD
- rank = comm.rank
- siz = comm.size
- name = mpi.Get_processor_name()
- status = mpi.Status()
- except:
- comm = None
- rank = 0
- siz = 1
- name = "noname"
- import os, os.path
-
- # builds the name of the workspace folder
- #print "__file__=",__file__
- dir1 = os.path.abspath(os.path.dirname(__file__)+os.sep+"..")+os.sep
- print("dir1=",dir1)
- print("testname=",testname)
- common = os.path.commonprefix( (testname, dir1) )
- #print "common=", common
- resdir = testname[len(common):].replace(os.sep,"_")
- resdir = os.path.splitext(resdir)[0] # remove ".py"
- if siz>1:
- # append the mpi size if mpi is used
- # (so that the same test can be run concurrently with
- # sevral mpi sizes in ctest)
- resdir += "_mpi%d" % siz
- #print "resdir=", resdir
- wdir = os.path.join('workspace', resdir)
-
- if rank == 0:
- # rank0 is in charge of creating the folder...
- args = parseargs()
- if not os.path.isdir(wdir):
- print("creating", wdir)
- os.makedirs(wdir)
- elif os.path.isdir(wdir) and args.clean:
- print('cleaning', wdir)
- import shutil
- for f in os.listdir(wdir):
- fpth = os.path.join(wdir, f)
- if os.path.isfile(fpth):
- os.remove(fpth)
- elif os.path.isdir(fpth):
- shutil.rmtree(fpth)
-
- if siz>1: # if multiple process => send sync to slaves.
- comm.Barrier()
-
- # we can now safely go into the new folder
- os.chdir(wdir)
-
-# ------------------------------------------------------------------------------
-
-def parseargs():
- """
- parses command line arguments
- """
- import argparse
- parser = argparse.ArgumentParser()
- parser.add_argument("-v", "--verb", help="increase output verbosity", action="count", default=0)
- parser.add_argument("--nogui", help="disable any graphical output", action="store_true")
- parser.add_argument("--fpe", help="enable floating point exceptions", action="store_true")
- parser.add_argument("--clean", help="clean workspace", action="store_true")
- parser.add_argument("-k", help="nb of threads", type=int, default=1)
- parser.add_argument('file', nargs='*', help='python files')
- args = parser.parse_args()
- return args
-
-# ------------------------------------------------------------------------------
-
-def pth(filename, caller=''):
- import os, os.path
- retname = filename
- # try to build the name of the file if a caller file or dir is given
- if not os.path.isabs(filename):
- if caller:
- #print "caller=",caller
- if os.path.isfile(caller):
- dirname = os.path.split(caller)[0]
- elif os.path.isdir(caller):
- dirname = caller
- else:
- raise Exception("neither a file nor a dir (%s)" %caller)
- f = os.path.join(dirname, filename)
- if os.path.isfile(f):
- retname = f
- # check if the file exist
- if not os.path.isfile(retname):
- raise Exception("path to a non-existent file! (%s)" % filename)
- #print "retname=",retname
- return retname
diff --git a/heat/_src/CMakeLists.txt b/heat/_src/CMakeLists.txt
index c74b28c7..8784cebd 100644
--- a/heat/_src/CMakeLists.txt
+++ b/heat/_src/CMakeLists.txt
@@ -25,10 +25,10 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/heat/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
)
SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
@@ -39,11 +39,14 @@ else()
endif()
MACRO_DebugPostfix(_heatw)
-TARGET_INCLUDE_DIRECTORIES(_heatw PRIVATE ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+TARGET_INCLUDE_DIRECTORIES(_heatw PRIVATE ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${PYTHON_INCLUDE_PATH}
)
SWIG_LINK_LIBRARIES(heatw
heat tbox fwk ${PYTHON_LIBRARIES}
)
+
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/heatw.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _heatw DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/heat/src/CMakeLists.txt b/heat/src/CMakeLists.txt
index 3fc96b69..31b8dffa 100644
--- a/heat/src/CMakeLists.txt
+++ b/heat/src/CMakeLists.txt
@@ -22,4 +22,6 @@ TARGET_INCLUDE_DIRECTORIES(heat PUBLIC ${PROJECT_SOURCE_DIR}/heat/src)
TARGET_LINK_LIBRARIES(heat tbox)
+INSTALL(TARGETS heat DESTINATION ${CMAKE_INSTALL_PREFIX})
+
SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
diff --git a/katoptron/_src/CMakeLists.txt b/katoptron/_src/CMakeLists.txt
index fec7116b..d7fd03c0 100644
--- a/katoptron/_src/CMakeLists.txt
+++ b/katoptron/_src/CMakeLists.txt
@@ -14,7 +14,6 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
# -- Search for Trilinos
FIND_PACKAGE(Trilinos REQUIRED)
FIND_PACKAGE(MPI4PY REQUIRED)
-#FIND_PACKAGE(PYTEUCHOS REQUIRED)
#FIND_PACKAGE(NUMPY REQUIRED)
set (_VERB 1) # set to 1 for debugging
@@ -54,10 +53,10 @@ endif()
IF(1)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/katoptron/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
-I${MPI4PY_INCLUDE_DIR}
-I${Trilinos_INCLUDE_DIRS}
-I${TRILINOS_SOURCE_DIR}/packages/PyTrilinos/src
@@ -67,10 +66,10 @@ SET(SWINCFLAGS
ELSE()
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/katoptron/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
-I${MPI4PY_INCLUDE_DIR}
-I${Trilinos_INCLUDE_DIRS}
)
@@ -88,10 +87,10 @@ MACRO_DebugPostfix(_katoptronw)
IF(1)
INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/katoptron/src
- ${PROJECT_SOURCE_DIR}/tbox/src
- ${PROJECT_SOURCE_DIR}/fwk/src
- ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${Trilinos_INCLUDE_DIRS}
${Trilinos_TPL_INCLUDE_DIRS}
${MPI_INCLUDE_PATH}
@@ -102,8 +101,8 @@ INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/katoptron/src
${NUMPY_INCLUDE_DIR})
ELSE()
INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/katoptron/src
- ${PROJECT_SOURCE_DIR}/tbox/src
- ${PROJECT_SOURCE_DIR}/fwk/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
${Trilinos_INCLUDE_DIRS}
${Trilinos_TPL_INCLUDE_DIRS}
${MPI_INCLUDE_PATH}
@@ -113,3 +112,6 @@ ENDIF()
SWIG_LINK_LIBRARIES(katoptronw
katoptron tbox fwk ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES} ${PYTHON_LIBRARIES}
)
+
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/katoptronw.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _katoptronw DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/katoptron/exe/CMakeLists.txt b/katoptron/exe/CMakeLists.txt
index 14cc3cd0..d69d7975 100644
--- a/katoptron/exe/CMakeLists.txt
+++ b/katoptron/exe/CMakeLists.txt
@@ -73,8 +73,8 @@ list(REMOVE_ITEM Trilinos_LIBRARIES pytrilinos)
INCLUDE_DIRECTORIES( ${MPI_INCLUDE_PATH}
${PROJECT_SOURCE_DIR}/katoptron/src
- ${PROJECT_SOURCE_DIR}/tbox/src
- ${PROJECT_SOURCE_DIR}/fwk/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
${Trilinos_INCLUDE_DIRS}
${Trilinos_TPL_INCLUDE_DIRS}
)
diff --git a/katoptron/src/CMakeLists.txt b/katoptron/src/CMakeLists.txt
index 4e275939..5c97361a 100644
--- a/katoptron/src/CMakeLists.txt
+++ b/katoptron/src/CMakeLists.txt
@@ -84,8 +84,8 @@ IF(_VERB)
MESSAGE(" Trilinos_LIBRARIES = ${Trilinos_LIBRARIES}")
ENDIF()
-INCLUDE_DIRECTORIES ( ${PROJECT_SOURCE_DIR}/tbox/src
- ${PROJECT_SOURCE_DIR}/fwk/src
+INCLUDE_DIRECTORIES ( ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
${Trilinos_INCLUDE_DIRS}
${Trilinos_TPL_INCLUDE_DIRS}
${MPI_INCLUDE_PATH})
@@ -94,5 +94,4 @@ LINK_DIRECTORIES (${Trilinos_LIBRARY_DIRS} ${Trilinos_TPL_LIBRARY_DIRS})
TARGET_LINK_LIBRARIES(katoptron tbox tboxVtk fwk ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES} ${MPI_LIBRARIES})
-#SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
-
+INSTALL(TARGETS katoptron DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/tboxVtk/src/wVtkExport_KIM2CLEAN.cpp b/katoptron/src/wVtkExport_KIM2CLEAN.cpp
similarity index 100%
rename from tboxVtk/src/wVtkExport_KIM2CLEAN.cpp
rename to katoptron/src/wVtkExport_KIM2CLEAN.cpp
diff --git a/tboxVtk/src/wVtkExport_KIM2CLEAN.h b/katoptron/src/wVtkExport_KIM2CLEAN.h
similarity index 97%
rename from tboxVtk/src/wVtkExport_KIM2CLEAN.h
rename to katoptron/src/wVtkExport_KIM2CLEAN.h
index 6c4e10c0..e47a29e8 100644
--- a/tboxVtk/src/wVtkExport_KIM2CLEAN.h
+++ b/katoptron/src/wVtkExport_KIM2CLEAN.h
@@ -17,7 +17,7 @@
#ifndef WVTKEXPORT_KIM2CLEAN_H
#define WVTKEXPORT_KIM2CLEAN_H
-#include "tboxVtk.h"
+#include "katoptron.h"
#include <string>
#include <memory>
#include <vector>
@@ -42,7 +42,7 @@ namespace tboxVtk
* and finalization will have to be used. Those can be done using some unwanted #ifdef VTK_HAS_MPI or using more
* elegant strategies or requiring VTK binaries that support MPI.
*/
-class TBOXVTK_API VtkExport_KIM2CLEAN
+class KATOPTRON_API VtkExport_KIM2CLEAN
{
public:
std::shared_ptr<tbox::MshData> msh;
diff --git a/mirrors/_src/CMakeLists.txt b/mirrors/_src/CMakeLists.txt
index 8ef37374..fe6600e3 100644
--- a/mirrors/_src/CMakeLists.txt
+++ b/mirrors/_src/CMakeLists.txt
@@ -24,10 +24,10 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/mirrors/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
)
SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
@@ -38,11 +38,14 @@ else()
endif()
MACRO_DebugPostfix(_mirrorsw)
-TARGET_INCLUDE_DIRECTORIES(_mirrorsw PRIVATE ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+TARGET_INCLUDE_DIRECTORIES(_mirrorsw PRIVATE ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${PYTHON_INCLUDE_PATH}
)
SWIG_LINK_LIBRARIES(mirrorsw
mirrors tbox fwk ${PYTHON_LIBRARIES}
)
+
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/mirrorsw.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _mirrorsw DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/mirrors/src/CMakeLists.txt b/mirrors/src/CMakeLists.txt
index 359324c6..a7689259 100644
--- a/mirrors/src/CMakeLists.txt
+++ b/mirrors/src/CMakeLists.txt
@@ -22,5 +22,7 @@ TARGET_INCLUDE_DIRECTORIES(mirrors PUBLIC ${PROJECT_SOURCE_DIR}/mirrors/src)
TARGET_LINK_LIBRARIES(mirrors tbox)
+INSTALL(TARGETS mirrors DESTINATION ${CMAKE_INSTALL_PREFIX})
+
SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
diff --git a/run.py b/run.py
index 76b9a05b..1f4e1109 100755
--- a/run.py
+++ b/run.py
@@ -16,85 +16,21 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-
-#
-# runs a test as if it was installed
-# - fixes the python path in a dev environment
-# - creates a workspace folder
-
-
-class DupStream:
- def __init__(self, stream1, stream2):
- self.stream1 = stream1
- self.stream2 = stream2
-
- def write(self, data):
- self.stream1.write(data)
- self.stream2.write(data)
-
- def flush(self):
- self.stream1.flush()
- self.stream2.flush()
-
-
-class Tee:
- def __init__(self, name):
- import sys
- self.file = open(name, 'w')
- self.stdoutbak = sys.stdout
- self.stderrbak = sys.stderr
- sys.stdout = DupStream(sys.stdout, self.file)
- sys.stderr = DupStream(sys.stderr, self.file)
-
- def __del__(self):
- import sys
- sys.stdout = self.stdoutbak
- sys.stderr = self.stderrbak
- self.file.close()
-
-
-def main(thisfile):
- global __file__ # required for run_pfem.py
- global __name__ # required for run_pfem.py
- import sys, os
+# Calls fwk.wutils.run to execute a script as if dartflo was installed
+
+def main():
+ import os.path, sys
+ # adds fwk/tbox to the python path
+ thisdir = os.path.split(os.path.abspath(__file__))[0]
+ fwkdir = os.path.abspath(os.path.join(thisdir, 'ext', 'amfe'))
+ if not os.path.isdir(fwkdir):
+ raise Exception('waves/ext/amfe not found!\n')
+ sys.path.append(fwkdir)
# adds "." to the pythonpath
- sys.path.append(os.path.dirname(os.path.realpath(__file__)))
- import fwk.wutils as wu
- from fwk.coloring import ccolors
- import fwk.testing # [AC]tmp fix for win-msys, to be removed once we understand why python cannot import this module outside run.py
-
- # redirect C++ streams to Python
- import fwk
- redirect = fwk.StdOutErr2Py()
-
- # parse args
- args = wu.parseargs()
- if args.fpe:
- fwk.enableFpe() # enables floating point exceptions at runtime
- print(ccolors.ANSI_YELLOW + 'Floating point exceptions will cause numpy to overflow!' + ccolors.ANSI_RESET)
+ sys.path.append(thisdir)
- # run all tests sequentially
- for testname in args.file:
- testname = os.path.abspath(testname)
- if not os.path.isfile(testname):
- raise Exception("file not found: %s" % testname)
-
- wu.setupwdir(testname)
-
- __file__ = testname
- __name__ = "__main__"
- print("[run.py] __file__", __file__)
- # split streams
- tee = Tee('stdout.txt')
-
- # start test
- import time, socket
- print('-' * 80)
- print(ccolors.ANSI_BLUE + 'PyStarting...' + ccolors.ANSI_RESET)
- print("starting test", testname)
- print("time:", time.strftime("%c"))
- print("hostname:", socket.gethostname())
- exec(open(testname, 'r', encoding='utf8').read(), globals(), globals()) # exec at global level!!
+ import fwk.wutils as wu
+ wu.run()
if __name__ == "__main__":
- main(__file__)
+ main()
diff --git a/tbox/CMakeLists.txt b/tbox/CMakeLists.txt
deleted file mode 100644
index 156e07c4..00000000
--- a/tbox/CMakeLists.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# Add source dir
-ADD_SUBDIRECTORY( src )
-ADD_SUBDIRECTORY( _src )
-
-# Add test dir
-MACRO_AddTest(${CMAKE_CURRENT_SOURCE_DIR}/tests)
diff --git a/tbox/__init__.py b/tbox/__init__.py
deleted file mode 100644
index 9ee55c94..00000000
--- a/tbox/__init__.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# -*- coding: utf-8 -*-
-# tbox MODULE initialization file
-
-# Copyright 2018 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import fwk
-from tboxw import *
-
diff --git a/tbox/_src/CMakeLists.txt b/tbox/_src/CMakeLists.txt
deleted file mode 100644
index dca92118..00000000
--- a/tbox/_src/CMakeLists.txt
+++ /dev/null
@@ -1,47 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake file for the SWIG interface of tbox.so
-
-INCLUDE(${SWIG_USE_FILE})
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.swg)
-FILE(GLOB ISRCS *.i)
-
-SET(CMAKE_SWIG_FLAGS "")
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
-
-SET(SWINCFLAGS
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
-)
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
-
-if (${CMAKE_VERSION} VERSION_LESS "3.8.0")
- SWIG_ADD_MODULE(tboxw python ${ISRCS} ${SRCS})
-else()
- SWIG_ADD_LIBRARY(tboxw LANGUAGE python SOURCES ${ISRCS} ${SRCS})
-endif()
-MACRO_DebugPostfix(_tboxw)
-
-TARGET_INCLUDE_DIRECTORIES(_tboxw PRIVATE ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
- ${PYTHON_INCLUDE_PATH}
-)
-
-SWIG_LINK_LIBRARIES(tboxw
- tbox fwk ${PYTHON_LIBRARIES}
-)
diff --git a/tbox/_src/tboxw.h b/tbox/_src/tboxw.h
deleted file mode 100644
index b9feacda..00000000
--- a/tbox/_src/tboxw.h
+++ /dev/null
@@ -1,67 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "tbox.h"
-#include "eigen_extra.h"
-#include "std_extra.h"
-
-#include "wCache.h"
-#include "wCacheHex8.h"
-#include "wCacheLine2.h"
-#include "wCachePoint1.h"
-#include "wCacheQuad4.h"
-#include "wCacheTetra4.h"
-#include "wCacheTri3.h"
-#include "wElement.h"
-#include "wFct0.h"
-#include "wFct1.h"
-#include "wFct2.h"
-#include "wGaussHex8.h"
-#include "wGaussLine2.h"
-#include "wGaussQuad4.h"
-#include "wGaussTetra4.h"
-#include "wGaussTri3.h"
-#include "wGmres.h"
-#include "wGmshExport.h"
-#include "wGmshImport.h"
-#include "wGroup.h"
-#include "wGroups.h"
-#include "wHex8.h"
-#include "wLazy.h"
-#include "wLine2.h"
-#include "wLinearSolver.h"
-#include "wMshConvert.h"
-#include "wMshCrack.h"
-#include "wMshData.h"
-#include "wMshDeform.h"
-#include "wMshExport.h"
-#include "wMshImport.h"
-#include "wMumps.h"
-#include "wNode.h"
-#include "wPardiso.h"
-#include "wPoint1.h"
-#include "wQuad4.h"
-#include "wResults.h"
-#include "wSfHex8.h"
-#include "wSfLine2.h"
-#include "wSfQuad4.h"
-#include "wSfTetra4.h"
-#include "wSfTri3.h"
-#include "wSparseLu.h"
-#include "wTag.h"
-#include "wTetra4.h"
-#include "wTri3.h"
-#include "wUnitTest.h"
\ No newline at end of file
diff --git a/tbox/_src/tboxw.i b/tbox/_src/tboxw.i
deleted file mode 100644
index 58f05923..00000000
--- a/tbox/_src/tboxw.i
+++ /dev/null
@@ -1,268 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// tbox.i: SWIG input file of the tbox python interface
-
-%feature("autodoc","1");
-
-%module(docstring=
-"'tboxw' module: shared tools
-(c) ULg - A&M",
-directors="1",
-threads="1"
-) tboxw
-%{
-
-//#if defined(_WIN32) && defined(__GNUC__)
-#undef _hypot
-#include <cmath>
-//#endif
-
-#include <memory>
-#include <string>
-#include <sstream>
-#include <typeinfo>
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-// ---fwk---
-#include "fwkw.h"
-
-// ---tbox---
-#include "tboxw.h"
-
-%}
-
-%include "waves_config.h"
-%include "fwkw.swg"
-
-// ----------- MODULES UTILISES ------------
-%import "fwkw.i"
-
-// ----------- TBOX CLASSES ----------------
-%include "tbox.h"
-
-// Instantiate some std templates
-namespace std {
- %template(std_vector_int) std::vector<int>;
- %template(std_vector_double) std::vector<double>;
- %template(std_vector_vector_double) std::vector<std::vector<double>>;
- %template(std_vector_string) std::vector<std::string>;
-}
-
-// %nodefault: for pure virtual (abstract) class
-// %feature("director"): allows C++ to see inherited classe extensions implemented in python
-// %pythonappend ... self.__disown__(): set thisown=0, which directly increments the python reference count by 1 (only for directors)
-%feature("director") tbox::Fct0XYZ;
-%pythonappend tbox::Fct0XYZ::Fct0XYZ "self.__disown__()"
-%shared_ptr(tbox::Fct0);
-%shared_ptr(tbox::Fct0C);
-%shared_ptr(tbox::Fct0XYZ);
-%shared_ptr(tbox::Fct0U);
-%shared_ptr(tbox::PwLf)
-%nodefault tbox::Fct0; // Fct0 is pure virtual but swig doesn't know it.
-%include "wFct0.h"
-
-%shared_ptr(tbox::Fct1);
-%shared_ptr(tbox::Fct1C);
-%nodefault tbox::Fct1; // Fct1 is pure virtual but swig doesn't know it.
-%include "wFct1.h"
-
-%feature("director") tbox::Fct2;
-%feature("director") tbox::Fct2XYZ;
-%feature("director") tbox::Fct2U;
-%feature("director") tbox::Fct2UdU;
-%shared_ptr(tbox::Fct2);
-%shared_ptr(tbox::Fct2C);
-%shared_ptr(tbox::Fct2XYZ);
-%shared_ptr(tbox::Fct2U);
-%shared_ptr(tbox::Fct2UdU);
-%shared_ptr(tbox::Fct2PwLf);
-%nodefault tbox::Fct2; // Fct2 is pure virtual but swig doesn't know it.
-%include "wFct2.h"
-
-%include "wNode.h"
-%nodefault tbox::Element; // Element is pure virtual but swig doesn't know it.
-%warnfilter(509); // Shadowed overloaded method MATTYPE. Code compiling and running.
-%include "wElement.h"
-%warnfilter(+509);
-%include "wTag.h"
-%include "wQuad4.h"
-%include "wTetra4.h"
-%include "wHex8.h"
-%include "wLine2.h"
-%include "wPoint1.h"
-
-%shared_ptr(tbox::MshData);
-%include "wMshData.h"
-
-%shared_ptr(tbox::MshImport)
-%nodefault tbox::MshImport;
-%include "wMshImport.h"
-%shared_ptr(tbox::MshExport)
-%nodefault tbox::MshExport;
-%include "wMshExport.h"
-%shared_ptr(tbox::GmshImport)
-%include "wGmshImport.h"
-%shared_ptr(tbox::GmshExport)
-%include "wGmshExport.h"
-
-%shared_ptr(tbox::MshConvert)
-%include "wMshConvert.h"
-
-// Instantiate some std templates
-%template(std_vector_Nodep) std::vector<tbox::Node *>;
-%template(std_vector_Elementp) std::vector<tbox::Element *>;
-%template(std_vector_pair_Nodep) std::vector<std::pair<tbox::Node *, tbox::Node *>>;
-%template(std_map_Nodep) std::map<tbox::Node *, tbox::Node *>;
-%template(std_vector_Tagp) std::vector<tbox::Tag*>;
-%template(std_map_int_Tagp) std::map<int, tbox::Tag*>;
-%template(std_map_string_Tagp) std::map<std::string, tbox::Tag*>;
-
-%shared_ptr(tbox::Group);
-%include "wGroup.h"
-%shared_ptr(tbox::Groups);
-%warnfilter(509); // Shadowed constructor. Code compiling and running.
-%include "wGroups.h"
-%warnfilter(+509);
-%shared_ptr(tbox::MshDeform);
-%include "wMshDeform.h" // included after std templates because it needs them
-%shared_ptr(tbox::MshCrack);
-%include "wMshCrack.h"
-
-// Instantiate some std templates
-%template(std_vector_Groupp) std::vector<tbox::Group*>;
-
-%shared_ptr(tbox::LinearSolver);
-%nodefault tbox::LinearSolver;
-%include "wLinearSolver.h"
-%shared_ptr(tbox::Pardiso);
-%include "wPardiso.h"
-%shared_ptr(tbox::Mumps);
-%include "wMumps.h"
-%shared_ptr(tbox::SparseLu);
-%include "wSparseLu.h"
-%shared_ptr(tbox::Gmres);
-%include "wGmres.h"
-
-%include "wUnitTest.h"
-
-// --------------------------------------------------------------------
-// Minimal interface for Eigen
-// TODO add interface to numpy
-// --------------------------------------------------------------------
-namespace Eigen
-{
-class MatrixXd
-{
-};
-class VectorXd
-{
-};
-class Vector3d
-{
-public:
- Vector3d();
-};
-}
-
-%extend Eigen::MatrixXd {
- void resize(int nR, int nC)
- {
- (*self).resize(nR, nC);
- }
- double getitem(int i, int j)
- {
- return (*self)(i,j);
- }
- void setitem(int i, int j, double a)
- {
- (*self)(i,j) = a;
- }
- std::string __str__()
- {
- std::ostringstream out; out << *self; return out.str();
- }
-
- %pythoncode {
-def __resize__(self, nR, nC):
- self.resize(nR, nC)
-def __getitem__(self, idx):
- return self.getitem(idx[0],idx[1])
-def __setitem__(self, idx, v):
- return self.setitem(idx[0],idx[1], v)
- }
-}
-
-%extend Eigen::VectorXd {
- double getitem(int i)
- {
- return (*self)(i);
- }
- std::string __str__()
- {
- std::ostringstream out; out << *self; return out.str();
- }
-
- %pythoncode {
-def __getitem__(self, idx):
- return self.getitem(idx)
- }
-}
-
-%extend Eigen::Vector3d {
- Vector3d(double x, double y, double z)
- {
- Eigen::Vector3d *v = new Eigen::Vector3d();
- *v << x,y,z;
- return v;
- }
- double getitem(int i)
- {
- return (*self)(i);
- }
- void setitem(int i, double a)
- {
- (*self)(i) = a;
- }
- std::string __str__()
- {
- std::ostringstream out; out << *self; return out.str();
- }
-
- Vector3d operator-(const Vector3d &v) const
- {
- return Eigen::Vector3d((*self)(0) - v(0), (*self)(1) - v(1), (*self)(2) - v(2));
- }
- double norm()
- {
- return sqrt((*self)(0) * (*self)(0) + (*self)(1) * (*self)(1) + (*self)(2) * (*self)(2));
- }
- int size()
- {
- return 3;
- }
-
- %pythoncode {
-def __getitem__(self, idx):
- return self.getitem(idx)
-def __setitem__(self, idx, v):
- return self.setitem(idx, v)
- }
-}
-
-%template(std_vector_V3d) std::vector<Eigen::Vector3d>;
diff --git a/tbox/gmsh.py b/tbox/gmsh.py
deleted file mode 100644
index 40bc9cf6..00000000
--- a/tbox/gmsh.py
+++ /dev/null
@@ -1,136 +0,0 @@
-# -*- coding: utf8 -*-
-# gmsh utilities
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import os, os.path, sys
-import fwk.wutils as wu
-
-class MeshLoader:
- """
- Chargement d'un fichier 'geo' (execute gmsh si nécessaire)
- gmsh doit être dans le PATH
- """
- def __init__(self, filename, caller=''):
- self.filename = wu.pth(filename, caller)
- self.verb = False
-
- def convert_from_APDL(self, oldfilename):
- import tbox
- msh = tbox.MshData()
- mshConv = tbox.MshConvert(msh)
- mshConv.ansys_gmsh(oldfilename, self.filename)
-
- def execute(self, myrank=-1, **pars):
- print(" [%s] processing %s" % (self.__class__, self.filename))
- ext = os.path.splitext(self.filename)[1]
- if ext == '.msh':
- return self.__loadMSH(self.filename, myrank)
- elif ext == '.geo':
- self.__execGMSH(self.filename, pars)
- return self.__loadMSH(os.path.basename(self.filename.replace('.geo','.msh')), myrank)
- else:
- raise Exception("Error %s: bad gmsh extension")
-
- def __buildParList(self, pars):
- parcmd=""
- for k,v in pars.items():
- if k[0] == '-':
- parcmd += "%s %s " % (k,v) # option
- else:
- parcmd += "-setnumber %s %s " % (k,v) # parameter
- return parcmd
-
- def __execGMSH(self, geofile, pars):
- mshfile=os.path.basename(geofile.replace('.geo','.msh'))
-
- parnew=str(pars)
- if self.verb: print(" [%s] new set of pars=%s" % (self.__class__, parnew))
-
- # force rebuild if pars have changed although .msh exists
- parfile=os.path.basename(geofile.replace('.geo','.par'))
- rebuild=True
- if os.path.isfile(mshfile):
- if self.verb: print(" [%s] an older version of .msh has been found" %self.__class__)
- if os.path.getmtime(mshfile) < os.path.getmtime(geofile):
- if self.verb: print(" [%s] .geo has been modified => gmsh should be rerun" %self.__class__)
- else:
- if self.verb: print(" [%s] .geo and .msh match" %self.__class__)
- if os.path.isfile(parfile):
- # a parfile exists
- f = open(parfile,'r')
- parold = f.readline()
- f.close()
- if self.verb: print(" [%s] old set of pars=%s" % (self.__class__, parold))
- if parold==parnew:
- rebuild=False
- if self.verb: print(" [%s] pars are the same => gmsh run avoided" %self.__class__)
- else:
- if self.verb: print(" [%s] pars are different => gmsh should be rerun" %self.__class__)
- else:
- if self.verb: print(" [%s] %s not found" % (self.__class__, parfile))
-
- if rebuild:
- print(' [%s] running gmsh on "%s"...' % (self.__class__, geofile))
- parcmd = self.__buildParList(pars)
- # TEMPORARY FIX: force gmsh to produce meshes in v2 format [RB]
- cmd = 'gmsh -3 -format msh2 %s -o "%s" "%s"'% (parcmd, mshfile, geofile)
- if self.verb: print(" [%s] cmd= %s" % (self.__class__, cmd))
-
- import shlex
- args=shlex.split(cmd)
-
- # lance gmsh et réagit si "gmsh" n'est pas trouvé
- import subprocess
- try:
- sproc = subprocess.Popen(args, stdout=subprocess.PIPE, stderr=subprocess.PIPE, env=os.environ)
- out, err = sproc.communicate()
- except Exception as e:
- print("Error:", e)
- print("\n** Check that gmsh in your PATH!!\n")
- raise e
-
- # redirige la sortie de gmsh vers le stdout (eventuellement GUI) via un PIPE
- # (evite d'imprimer hors de la fenetre)
- for l in out.splitlines():
- print(" [gmsh-out] ", l)
- for l in err.splitlines():
- print(" [gmsh-err] ", l)
-
- if not os.path.isfile(mshfile):
- raise Exception("Problem during gmsh run")
-
- # write pars
- if self.verb: print(" [%s] writing parameters to %s" % (self.__class__, parfile))
- f = open(parfile,'w')
- f.write(parnew)
- f.close()
-
- else:
- print(' [%s] "%s" up-to-date' % (self.__class__, mshfile))
- self.mshfile = mshfile
-
- def __loadMSH(self, mshfile, myrank):
- import tbox
- msh = tbox.MshData()
- gmshLoader = tbox.GmshImport(msh)
- gmshLoader.load(mshfile, myrank)
- msh.name = os.path.basename(os.path.splitext(mshfile)[0])
- return msh
-
-# ------------------------------------------------------------------------------
-
-
diff --git a/tbox/solvers.py b/tbox/solvers.py
deleted file mode 100644
index 8e3e8b42..00000000
--- a/tbox/solvers.py
+++ /dev/null
@@ -1,38 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from fwk.coloring import ccolors
-import tbox
-
-## Check and set linear (inner) third-party solver
-#
-# Adrien Crovato
-class LinearSolver:
- def __init__(self):
- pass
- def pardiso(self):
- try:
- return tbox.Pardiso()
- except:
- print(ccolors.ANSI_YELLOW + 'Intel MKL Pardiso not found, using SparseLU (Eigen) instead!' + ccolors.ANSI_RESET)
- return tbox.SparseLu()
- def mumps(self):
- try:
- return tbox.Mumps()
- except:
- print(ccolors.ANSI_YELLOW + 'MUMPS not found, using SparseLU (Eigen) instead!' + ccolors.ANSI_RESET)
- return tbox.SparseLu()
diff --git a/tbox/src/CMakeLists.txt b/tbox/src/CMakeLists.txt
deleted file mode 100644
index 51a04a10..00000000
--- a/tbox/src/CMakeLists.txt
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake input file of tboxw.so
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.hpp)
-
-ADD_LIBRARY(tbox SHARED ${SRCS})
-MACRO_DebugPostfix(tbox)
-
-TARGET_INCLUDE_DIRECTORIES(tbox PUBLIC ${PROJECT_SOURCE_DIR}/tbox/src)
-
-# -- TBB --
-FIND_PACKAGE(TBB REQUIRED)
-SET(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} ${TBB_CXX_FLAGS_DEBUG}")
-TARGET_INCLUDE_DIRECTORIES(tbox PUBLIC ${TBB_INCLUDE_DIRS})
-IF(TBB_VERSION_INTERFACE LESS 11004)
- TARGET_COMPILE_DEFINITIONS(tbox PUBLIC TBB_PREVIEW_GLOBAL_CONTROL)
-ENDIF()
-TARGET_LINK_LIBRARIES(tbox ${TBB_LIBRARIES})
-
-# -- MKL/BLAS/LAPACK --
-# Do not forget to set your environement variables using: (default path)
-# - "C:\Program Files (x86)\Intel\Composer XE\mkl\bin\intel64\mklvars_intel64.bat" (windows, check that VS is in x64 mode)
-# - source /opt/intel/mkl/bin/mklvars.sh intel64 (linux)
-
-# Find MKL
-IF(WAVES_USE_MKL)
- # header (mkl.h) searched using INCLUDE or MKLROOT
- FIND_PATH(MKL_INCLUDE_DIRS NAMES "mkl.h" PATHS "$ENV{MKLROOT}/include")
- MESSAGE(STATUS "MKL_INCLUDE_DIRS=${MKL_INCLUDE_DIRS}")
- # library (mkl_rt.so) searched using LIBRARY_PATH (Linux/macOS) or LIB (windows)
- FIND_LIBRARY(MKL_LIBRARIES mkl_rt PATHS ENV LIBRARY_PATH)
- MESSAGE(STATUS "MKL_LIBRARIES=${MKL_LIBRARIES}")
- IF(MKL_INCLUDE_DIRS AND MKL_LIBRARIES)
- MESSAGE(STATUS "Found Intel MKL")
- SET(FOUND_MKL TRUE)
- SET(LAPACK_INCLUDE_DIRS ${MKL_INCLUDE_DIRS})
- SET(LAPACK_LIBRARIES ${MKL_LIBRARIES})
- ELSE()
- MESSAGE(FATAL_ERROR "Intel MKL not found!")
- ENDIF()
-# Find BLAS
-ELSE()
- IF(${BLA_VENDOR} MATCHES "OpenBlas")
- FIND_LIBRARY(LAPACK_LIBRARIES openblas)
- ELSE()
- FIND_PACKAGE(LAPACK REQUIRED) #FIND_LAPACK calls FIND_BLAS
- ENDIF()
- IF(NOT LAPACK_LIBRARIES)
- MESSAGE(FATAL_ERROR "BLAS/LAPACK not found!")
- ENDIF()
- MESSAGE(STATUS "LAPACK_LIBRARIES=${LAPACK_LIBRARIES}")
- MESSAGE(STATUS "LAPACK_LINKER_FLAGS=${LAPACK_LINKER_FLAGS}")
- MESSAGE(STATUS "BLA_VENDOR=${BLA_VENDOR}")
- MESSAGE(STATUS "BLA_STATIC=${BLA_STATIC}")
-ENDIF()
-
-# -- Eigen --
-FIND_PACKAGE(EIGEN 3.3.4 REQUIRED)
-TARGET_INCLUDE_DIRECTORIES(tbox PUBLIC ${EIGEN_INCLUDE_DIRS} ${LAPACK_INCLUDE_DIRS})
-TARGET_COMPILE_DEFINITIONS(tbox PUBLIC EIGEN_DONT_PARALLELIZE)
-IF(FOUND_MKL)
- MESSAGE(STATUS "Linking Eigen with MKL")
- TARGET_COMPILE_DEFINITIONS(tbox PUBLIC EIGEN_USE_MKL_ALL)
-ELSE()
- MESSAGE(STATUS "Linking Eigen with BLAS ${BLA_VENDOR}")
- TARGET_COMPILE_DEFINITIONS(tbox PUBLIC EIGEN_USE_BLAS)
-ENDIF()
-TARGET_LINK_LIBRARIES(tbox ${LAPACK_LIBRARIES})
-
-# -- MUMPS --
-IF (WAVES_USE_MUMPS)
- FIND_PACKAGE(MUMPS REQUIRED)
- TARGET_INCLUDE_DIRECTORIES(tbox PUBLIC ${MUMPS_INCLUDE_DIRS})
- TARGET_LINK_LIBRARIES(tbox ${MUMPS_LIBRARIES})
-ENDIF()
-
-TARGET_LINK_LIBRARIES(tbox fwk)
-
-SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
-SOURCE_GROUP(timer REGULAR_EXPRESSION ".+(Time).+")
-SOURCE_GROUP(hex8 REGULAR_EXPRESSION ".+(Hex8).+")
-SOURCE_GROUP(quad4 REGULAR_EXPRESSION ".+(Quad4).+")
-SOURCE_GROUP(tri3 REGULAR_EXPRESSION ".+(Tri3).+")
-SOURCE_GROUP(line2 REGULAR_EXPRESSION ".+(Line2).+")
-SOURCE_GROUP(point1 REGULAR_EXPRESSION ".+(Point1).+")
diff --git a/tbox/src/eigen_extra.cpp b/tbox/src/eigen_extra.cpp
deleted file mode 100644
index 845994f0..00000000
--- a/tbox/src/eigen_extra.cpp
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "eigen_extra.h"
-#include <fstream>
-
-using namespace tbox;
-
-/**
- * @brief save CSR matrix to a file
- *
- * matlab usage: load K.txt; K=spconvert(K)
- */
-
-TBOX_API void
-tomatlab(std::string const &fname, Eigen::SparseMatrix<double> const &A)
-{
- std::ofstream f(fname.c_str());
-
- for (int k = 0; k < A.outerSize(); ++k)
- for (Eigen::SparseMatrix<double>::InnerIterator it(A, k); it; ++it)
- f << it.row() + 1 << ' ' << it.col() + 1 << ' ' << it.value() << '\n';
-
- f.close();
-}
diff --git a/tbox/src/eigen_extra.h b/tbox/src/eigen_extra.h
deleted file mode 100644
index 09559a73..00000000
--- a/tbox/src/eigen_extra.h
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef EIGEN_EXTRA_H
-#define EIGEN_EXTRA_H
-
-#include "tbox.h"
-#include <string>
-#include <Eigen/Sparse>
-
-namespace tbox
-{
-
-TBOX_API void
-tomatlab(std::string const &fname, Eigen::SparseMatrix<double> const &A);
-}
-
-#endif //EIGEN_EXTRA_H
diff --git a/tbox/src/std_extra.h b/tbox/src/std_extra.h
deleted file mode 100644
index 16b70c1a..00000000
--- a/tbox/src/std_extra.h
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef STD_EXTRA_H
-#define STD_EXTRA_H
-
-#include "tbox.h"
-#include <iostream>
-#include <vector>
-
-namespace std
-{
-
-template <typename T>
-ostream &operator<<(ostream &out, vector<T> const &v)
-{
- out << '[';
- for (size_t i = 0; i < v.size(); ++i)
- {
- out << v[i];
- if (i != v.size() - 1)
- out << ", ";
- }
- out << ']';
- return out;
-}
-
-} // namespace std
-
-#endif //STD_EXTRA_H
diff --git a/tbox/src/tbox.h b/tbox/src/tbox.h
deleted file mode 100644
index b6814d4c..00000000
--- a/tbox/src/tbox.h
+++ /dev/null
@@ -1,111 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// tbox global header
-
-#ifndef TBOX_H
-#define TBOX_H
-
-#if defined(WIN32)
-#ifdef tbox_EXPORTS
-#define TBOX_API __declspec(dllexport)
-#else
-#define TBOX_API __declspec(dllimport)
-#endif
-#else
-#define TBOX_API
-#endif
-
-#include "fwk.h"
-
-namespace tbox
-{
-
-// Mesh handling
-class MshData;
-class Node;
-class Element;
-class Group;
-class Groups;
-class Tag;
-
-// Element handling
-class Cache;
-
-// Point1
-class Point1;
-class CachePoint1;
-
-// Line2
-class SfLine2;
-class CacheLine2;
-class GaussLine2;
-class Line2;
-
-// Tri3
-class SfTri3;
-class CacheTri3;
-class GaussTri3;
-class Tri3;
-
-// Quad4
-class SfQuad4;
-class CacheQuad4;
-class GaussQuad4;
-class Quad4;
-
-// Tetra4
-class SfTetra4;
-class CacheTetra4;
-class GaussTetra4;
-class Tetra4;
-
-// Hex8
-class SfHex8;
-class CacheHex8;
-class GaussHex8;
-class Hex8;
-
-// Mesh utilities
-class MshImport;
-class MshExport;
-class GmshImport;
-class GmshExport;
-class MshDeform;
-class MshCrack;
-class MshConvert;
-
-// Utilities
-class PwLf;
-class Fct0;
-class Fct1;
-class Fct2;
-class Results;
-class Linesearch;
-
-// Linear solvers
-class LinearSolver;
-class Pardiso;
-class Mumps;
-class SparseLu;
-class Gmres;
-
-// Testing
-class UnitTest;
-
-} // namespace tbox
-
-#endif //TBOX_H
diff --git a/tbox/src/wCache.cpp b/tbox/src/wCache.cpp
deleted file mode 100644
index 1ad82077..00000000
--- a/tbox/src/wCache.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCache.h"
-
-using namespace tbox;
-
-Cache::Cache(int _n) : n(_n)
-{
-}
-
-Gauss &Cache::getVGauss()
-{
- throw std::runtime_error("Cache::getGauss not implemented!\n");
-}
\ No newline at end of file
diff --git a/tbox/src/wCache.h b/tbox/src/wCache.h
deleted file mode 100644
index f20921ce..00000000
--- a/tbox/src/wCache.h
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHE_H
-#define WCACHE_H
-
-#include "tbox.h"
-#include "wGauss.h"
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Base cache for element
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API Cache
-{
-protected:
- int n; ///< degree of element
- std::vector<Eigen::MatrixXd> dff; ///< derivative of shape functions
- std::vector<Eigen::VectorXd> ff; ///< shape functions
-
-public:
- explicit Cache(int _n);
- virtual ~Cache() {}
-
- inline Eigen::MatrixXd const &getDsf(size_t k);
- inline Eigen::VectorXd const &getSf(size_t k);
- virtual Gauss &getVGauss();
-};
-
-#include "wCache.inl"
-
-} // namespace tbox
-
-#endif //WCACHE_H
diff --git a/tbox/src/wCache.inl b/tbox/src/wCache.inl
deleted file mode 100644
index eb7b8608..00000000
--- a/tbox/src/wCache.inl
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return the shape function derivatives at Gauss point k
- *
- * dff[k](i, j) contains the ith derivative of the shape function associated to node j
- */
-inline Eigen::MatrixXd const &Cache::getDsf(size_t k)
-{
- return dff[k];
-}
-
-/**
- * @brief Return the shape functions at Gauss point k
- *
- * ff[k](i) contains the shape function associated to node i
- */
-inline Eigen::VectorXd const &Cache::getSf(size_t k)
-{
- return ff[k];
-}
diff --git a/tbox/src/wCacheHex8.cpp b/tbox/src/wCacheHex8.cpp
deleted file mode 100644
index 1d1293d3..00000000
--- a/tbox/src/wCacheHex8.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCacheHex8.h"
-
-using namespace tbox;
-
-CacheHex8::CacheHex8(int _n) : Cache(_n), gauss(_n)
-{
- // get number of gauss points
- size_t ngp = gauss.getN();
-
- // pre-compute dff and ff
- dff.resize(ngp);
- ff.resize(ngp);
- for (size_t k = 0; k < ngp; ++k)
- {
- Eigen::Vector3d const &ksi = gauss.getP(k);
- sf.evalD(ksi, dff[k]);
- sf.eval(ksi, ff[k]);
- }
-}
-
-Gauss &CacheHex8::getVGauss()
-{
- return gauss;
-}
diff --git a/tbox/src/wCacheHex8.h b/tbox/src/wCacheHex8.h
deleted file mode 100644
index 212dba30..00000000
--- a/tbox/src/wCacheHex8.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHEHEX8_H
-#define WCACHEHEX8_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfHex8.h"
-#include "wGaussHex8.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Hex8 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CacheHex8 : public Cache
-{
-public:
- SfHex8 sf;
- GaussHex8 gauss;
-
- explicit CacheHex8(int _n = 2);
-
- virtual Gauss &getVGauss() override;
-};
-
-} // namespace tbox
-
-#endif //WCACHEHEX8_H
diff --git a/tbox/src/wCacheLine2.cpp b/tbox/src/wCacheLine2.cpp
deleted file mode 100644
index 779ea413..00000000
--- a/tbox/src/wCacheLine2.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCacheLine2.h"
-
-using namespace tbox;
-
-CacheLine2::CacheLine2(int _n) : Cache(_n), gauss(_n)
-{
- // get number of gauss points
- size_t ngp = gauss.getN();
-
- // pre-compute dff and ff
- dff.resize(ngp);
- ff.resize(ngp);
- for (size_t k = 0; k < ngp; ++k)
- {
- Eigen::Vector3d const &ksi = gauss.getP(k);
- sf.evalD(ksi, dff[k]);
- sf.eval(ksi, ff[k]);
- }
-}
-
-Gauss &CacheLine2::getVGauss()
-{
- return gauss;
-}
diff --git a/tbox/src/wCacheLine2.h b/tbox/src/wCacheLine2.h
deleted file mode 100644
index a912013a..00000000
--- a/tbox/src/wCacheLine2.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHELINE2_H
-#define WCACHELINE2_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfLine2.h"
-#include "wGaussLine2.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Line2 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CacheLine2 : public Cache
-{
-public:
- SfLine2 sf;
- GaussLine2 gauss;
-
- explicit CacheLine2(int _n = 2);
-
- virtual Gauss &getVGauss() override;
-};
-
-} // namespace tbox
-
-#endif //WCACHELINE2_H
diff --git a/tbox/src/wCachePoint1.cpp b/tbox/src/wCachePoint1.cpp
deleted file mode 100644
index 51364dcc..00000000
--- a/tbox/src/wCachePoint1.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCachePoint1.h"
-
-using namespace tbox;
-
-CachePoint1::CachePoint1(int _npg) : Cache(_npg)
-{
-}
diff --git a/tbox/src/wCachePoint1.h b/tbox/src/wCachePoint1.h
deleted file mode 100644
index 9d5f290b..00000000
--- a/tbox/src/wCachePoint1.h
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHEPOINT1_H
-#define WCACHEPOINT1_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfLine2.h"
-#include "wGaussLine2.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Point1 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CachePoint1 : public Cache
-{
-public:
- explicit CachePoint1(int _n = 0);
-};
-
-} // namespace tbox
-
-#endif //WCACHEPOINT1_H
diff --git a/tbox/src/wCacheQuad4.cpp b/tbox/src/wCacheQuad4.cpp
deleted file mode 100644
index 3a70e5b0..00000000
--- a/tbox/src/wCacheQuad4.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCacheQuad4.h"
-
-using namespace tbox;
-
-CacheQuad4::CacheQuad4(int _n) : Cache(_n), gauss(_n)
-{
- // get number of gauss points
- size_t ngp = gauss.getN();
-
- // pre-compute dff and ff
- dff.resize(ngp);
- ff.resize(ngp);
- for (size_t k = 0; k < ngp; ++k)
- {
- Eigen::Vector3d const &ksi = gauss.getP(k);
- sf.evalD(ksi, dff[k]);
- sf.eval(ksi, ff[k]);
- }
-}
-
-Gauss &CacheQuad4::getVGauss()
-{
- return gauss;
-}
\ No newline at end of file
diff --git a/tbox/src/wCacheQuad4.h b/tbox/src/wCacheQuad4.h
deleted file mode 100644
index 49a2fb1e..00000000
--- a/tbox/src/wCacheQuad4.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHEQUAD4_H
-#define WCACHEQUAD4_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfQuad4.h"
-#include "wGaussQuad4.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Quad4 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CacheQuad4 : public Cache
-{
-public:
- SfQuad4 sf;
- GaussQuad4 gauss;
-
- explicit CacheQuad4(int _n = 2);
-
- virtual Gauss &getVGauss() override;
-};
-
-} // namespace tbox
-
-#endif //WCACHEQUAD4_H
diff --git a/tbox/src/wCacheTetra4.cpp b/tbox/src/wCacheTetra4.cpp
deleted file mode 100644
index e9d8dace..00000000
--- a/tbox/src/wCacheTetra4.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCacheTetra4.h"
-
-using namespace tbox;
-
-CacheTetra4::CacheTetra4(int _n) : Cache(_n), gauss(_n)
-{
- // get number of gauss points
- size_t ngp = gauss.getN();
-
- // pre-compute dff and ff
- dff.resize(ngp);
- ff.resize(ngp);
- for (size_t k = 0; k < ngp; ++k)
- {
- Eigen::Vector3d const &ksi = gauss.getP(k);
- sf.evalD(ksi, dff[k]);
- sf.eval(ksi, ff[k]);
- }
-}
-
-Gauss &CacheTetra4::getVGauss()
-{
- return gauss;
-}
diff --git a/tbox/src/wCacheTetra4.h b/tbox/src/wCacheTetra4.h
deleted file mode 100644
index 4d1062ff..00000000
--- a/tbox/src/wCacheTetra4.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHETETRA4_H
-#define WCACHETETRA4_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfTetra4.h"
-#include "wGaussTetra4.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Tetra4 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CacheTetra4 : public Cache
-{
-public:
- SfTetra4 sf;
- GaussTetra4 gauss;
-
- explicit CacheTetra4(int _n = 2);
-
- virtual Gauss &getVGauss() override;
-};
-
-} // namespace tbox
-
-#endif //WCACHETETRA4_H
diff --git a/tbox/src/wCacheTri3.cpp b/tbox/src/wCacheTri3.cpp
deleted file mode 100644
index fd638428..00000000
--- a/tbox/src/wCacheTri3.cpp
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wCacheTri3.h"
-
-using namespace tbox;
-
-CacheTri3::CacheTri3(int _n) : Cache(_n), gauss(_n)
-{
- // get number of gauss points
- size_t ngp = gauss.getN();
-
- // pre-compute dff and ff
- dff.resize(ngp);
- ff.resize(ngp);
- for (size_t k = 0; k < ngp; ++k)
- {
- Eigen::Vector3d const &ksi = gauss.getP(k);
- sf.evalD(ksi, dff[k]);
- sf.eval(ksi, ff[k]);
- }
-}
-
-Gauss &CacheTri3::getVGauss()
-{
- return gauss;
-}
\ No newline at end of file
diff --git a/tbox/src/wCacheTri3.h b/tbox/src/wCacheTri3.h
deleted file mode 100644
index c7491eb7..00000000
--- a/tbox/src/wCacheTri3.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WCACHETRI3_H
-#define WCACHETRI3_H
-
-#include "tbox.h"
-#include "wCache.h"
-#include "wSfTri3.h"
-#include "wGaussTri3.h"
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief Cache handling Tri3 shape functions and gauss points
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API CacheTri3 : public Cache
-{
-public:
- SfTri3 sf;
- GaussTri3 gauss;
-
- explicit CacheTri3(int _n = 2);
-
- virtual Gauss &getVGauss() override;
-};
-
-} // namespace tbox
-
-#endif //WCACHETRI3_H
diff --git a/tbox/src/wElement.cpp b/tbox/src/wElement.cpp
deleted file mode 100644
index f2755ff8..00000000
--- a/tbox/src/wElement.cpp
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wElement.h"
-#include "wNode.h"
-#include "wTag.h"
-#include "wCache.h"
-#include "std_extra.h"
-
-using namespace tbox;
-
-namespace tbox
-{
-
-TBOX_API std::ostream &
-operator<<(std::ostream &out, ELTYPE const &obj)
-{
- switch (obj)
- {
- case ELTYPE::LINE2:
- out << "LINE2";
- break;
- case ELTYPE::TRI3:
- out << "TRI3";
- break;
- case ELTYPE::QUAD4:
- out << "QUAD4";
- break;
- case ELTYPE::TETRA4:
- out << "TETRA4";
- break;
- case ELTYPE::HEX8:
- out << "HEX8";
- break;
- case ELTYPE::POINT1:
- out << "POINT1";
- break;
- default:
- out << "UNKNOWN-" << static_cast<int>(obj);
- break;
- }
- return out;
-}
-
-} // namespace tbox
-
-Element::Element(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods)
- : wObject(), order(0), hasVals(false), hasGrads(false), isVol(false),
- no(n), ptag(_ptag), etag(_etag), parts(_parts), nodes(nods)
-{
- if (ptag)
- ptag->elems.push_back(this);
- if (etag)
- etag->elems.push_back(this);
-
- for (auto p : parts)
- p->elems.push_back(this);
-}
-
-void Element::initValues(bool isvol, int ordr)
-{
- throw std::runtime_error("Element::initValues() not implemented!\n");
-}
-void Element::initGradients()
-{
- throw std::runtime_error("Element::initGradients() not implemented!\n");
-}
-void Element::update()
-{
- throw std::runtime_error("Element::update() not implemented!\n");
-}
-
-/**
- * @brief Check that determinant of Jacobian is positive
- */
-void Element::checkJac(size_t k) const
-{
- if (detJs[k] <= 0)
- {
- std::stringstream err;
- err << "Negative jacobian detected for element: " << *this << "\n";
- throw std::runtime_error(err.str());
- }
-}
-
-void Element::buildJ()
-{
- throw std::runtime_error("Element::buildJ not implemented\n");
-}
-void Element::buildSurfaceJ()
-{
- throw std::runtime_error("Element::buildSurfaceJ not implemented\n");
-}
-void Element::buildGradientJ()
-{
- throw std::runtime_error("Element::buildGradientJ not implemented\n");
-}
-void Element::buildGradientSurfaceJ()
-{
- throw std::runtime_error("Element::buildGradientSurfaceJ not implemented\n");
-}
-
-void Element::computeV()
-{
- throw std::runtime_error("Element::computeV not implemented\n");
-}
-void Element::buildGradientV(int dim)
-{
- throw std::runtime_error("Element::buildGradientV not implemented\n");
-}
-
-/**
- * @brief Compute center of gravity of element
- */
-void Element::computeCg()
-{
- cg = Eigen::Vector3d::Zero();
- for (auto n : nodes)
- cg += n->pos;
- cg /= static_cast<double>(nodes.size());
-}
-
-std::vector<Eigen::Vector3d> Element::computeTangents() const
-{
- throw std::runtime_error("Element::computeTangents not implemented\n");
-}
-std::vector<Eigen::Vector3d> Element::buildTangents(size_t k) const
-{
- throw std::runtime_error("Element::buildTangents not implemented\n");
-}
-
-void Element::computeNormal()
-{
- throw std::runtime_error("Element::computeNormal not implemented\n");
-}
-void Element::computeGradientNormal()
-{
- throw std::runtime_error("Element::computeGradientNormal not implemented\n");
-}
-
-/**
- * @brief Return the values extrapolated at all the element nodes
- * based on the values at Gauss points
- */
-Eigen::MatrixXd Element::gp2node(Eigen::MatrixXd &values_at_gp) const
-{
- Cache &cache = getVCache();
- size_t ngp = cache.getVGauss().getN();
-
- Eigen::MatrixXd A(ngp, nodes.size());
- for (size_t i = 0; i < ngp; ++i)
- A.row(i) = cache.getSf(i).transpose();
-
- return (A.transpose() * A).inverse() * A.transpose() * values_at_gp; // nodes.size() * 18
-}
-
-Eigen::VectorXd Element::computeGradient(std::vector<double> const &u, size_t k) const
-{
- throw std::runtime_error("Element::computeGradient not implemented\n");
-}
-
-void Element::write(std::ostream &out) const
-{
- out << type() << " #" << no << ":";
-
- out << " nodes=[ ";
- for (auto n : nodes)
- out << "#" << n->no << ' ';
- out << "]";
-
- if (ptag)
- out << " ptag #" << ptag->no;
- if (etag)
- out << " etag #" << etag->no;
- if (!parts.empty())
- {
- out << " parts=[ ";
- for (auto p : parts)
- out << "#" << p->no << ' ';
- out << "]";
- }
-}
diff --git a/tbox/src/wElement.h b/tbox/src/wElement.h
deleted file mode 100644
index 3c02267a..00000000
--- a/tbox/src/wElement.h
+++ /dev/null
@@ -1,137 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WELEMENT_H
-#define WELEMENT_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief element types (from gmsh)
- * @authors Romain Boman
- */
-enum class ELTYPE
-{
- UNKNOWN = 0,
- LINE2 = 1,
- TRI3 = 2,
- QUAD4 = 3,
- TETRA4 = 4,
- HEX8 = 5,
- POINT1 = 15
-};
-#ifndef SWIG
-TBOX_API std::ostream &operator<<(std::ostream &out, ELTYPE const &obj);
-#endif
-
-/**
- * @brief Base finite element class
- * @authors Romain Boman, Kim Liegeois, Adrien Crovato
- */
-class TBOX_API Element : public fwk::wObject
-{
- friend class MshCrack; // so that MshCrack can access normal and cg before update
-protected:
- int order; ///< order of integration (Gauss quadrature)
- // Flags
- bool hasVals; ///< true if (precomputed) values have been initialized
- bool hasGrads; ///< true if (precomputed) gradients have been initialized
- bool isVol; ///< true if element is a volume element
- // Jacobian
- std::vector<double> detJs; ///< determinant of Jacobian matrix
- std::vector<Eigen::MatrixXd> Js; ///< Jacobian matrix
- std::vector<Eigen::MatrixXd> iJs; ///< inverse of Jacobian matrix
- std::vector<std::vector<double>> gradDetJs; ///< gradient of Jacobian determinant wrt to nodes position
- std::vector<std::vector<Eigen::MatrixXd>> gradJs; ///< gradient of Jacobian matrix wrt to nodes position
- // Volume and CG
- double vol; ///< element volume
- Eigen::Vector3d cg; ///< element center of gravity
- std::vector<double> gradVol; ///< gradient of volume wrt to nodes position
- // Normal vectors
- Eigen::Vector3d normal; ///< unit normal vector
- std::vector<Eigen::Vector3d> gradNormal; ///< graident of unit normal vector wrt to nodes position
-
-public:
- int no; ///< label
- Tag *ptag; ///< physical tag (group)
- Tag *etag; ///< elementary tag (geometry)
- std::vector<Tag *> parts; ///< partitions
- std::vector<Node *> nodes; ///< nodes
-
-#ifndef SWIG
- Element(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Element() {}
-#endif
- virtual ELTYPE type() const
- {
- return ELTYPE::UNKNOWN;
- }
-
-#ifndef SWIG
-protected:
- // Jacobian
- void checkJac(size_t k) const;
- virtual void buildJ();
- virtual void buildSurfaceJ();
- virtual void buildGradientJ();
- virtual void buildGradientSurfaceJ();
- // CG and Volume
- void computeCg();
- virtual void computeV();
- virtual void buildGradientV(int dim);
- // Tangent and normal vectors
- virtual std::vector<Eigen::Vector3d> computeTangents() const;
- virtual std::vector<Eigen::Vector3d> buildTangents(size_t k) const;
- virtual void computeNormal();
- virtual void computeGradientNormal();
-
-public:
- // Initialize and update precomputed values
- virtual void initValues(bool isvol, int ordr = 2);
- virtual void initGradients();
- virtual void update();
- // Getters
- virtual Cache &getVCache() const = 0;
- inline bool hasValues() const;
- inline bool hasGradients() const;
- inline double getDetJ(size_t k) const;
- inline Eigen::MatrixXd const &getJ(size_t k) const;
- inline Eigen::MatrixXd const &getJinv(size_t k) const;
- inline std::vector<double> const &getGradDetJ(size_t k) const;
- inline std::vector<Eigen::MatrixXd> const &getGradJ(size_t k) const;
- inline double getVol() const;
- inline Eigen::Vector3d const &getCg() const;
- inline std::vector<double> const &getGradVol() const;
- inline Eigen::Vector3d const &getNormal() const;
- inline std::vector<Eigen::Vector3d> const &getGradNormal() const;
- // Utilities
- virtual Eigen::VectorXd computeGradient(std::vector<double> const &u, size_t k) const;
- Eigen::MatrixXd gp2node(Eigen::MatrixXd &values_at_gp) const;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-#include "wElement.inl"
-
-} // namespace tbox
-
-#endif //WELEMENT_H
diff --git a/tbox/src/wElement.inl b/tbox/src/wElement.inl
deleted file mode 100644
index 9bed1207..00000000
--- a/tbox/src/wElement.inl
+++ /dev/null
@@ -1,166 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return wether the element values have been initialized or not
- */
-inline bool Element::hasValues() const
-{
- return hasVals;
-}
-
-/**
- * @brief Return wether the element gradients have been initialized or not
- */
-inline bool Element::hasGradients() const
-{
- return hasGrads;
-}
-
-/**
- * @brief Return the determinant of the Jacobian at Gauss point k
- */
-inline double Element::getDetJ(size_t k) const
-{
- if (hasVals)
- return detJs[k];
- else
- throw std::runtime_error("Element::getDetJ is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the the Jacobian matrix at Gauss point k
- */
-inline Eigen::MatrixXd const &Element::getJ(size_t k) const
-{
- if (hasVals)
- {
- if (isVol)
- return Js[k];
- else
- throw std::runtime_error("Element::getJ Jacobian matrix is not available for surface element!\n");
- }
- else
- throw std::runtime_error("Element::getJ is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the inverse of the Jacobian matrix at Gauss point k
- */
-inline Eigen::MatrixXd const &Element::getJinv(size_t k) const
-{
- if (hasVals)
- {
- if (isVol)
- return iJs[k];
- else
- throw std::runtime_error("Element::getJinv inverse Jacobian matrix is not available for surface element!\n");
- }
- else
- throw std::runtime_error("Element::getJinv is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the volume of the element
- */
-inline double Element::getVol() const
-{
- if (hasVals)
- return vol;
- else
- throw std::runtime_error("Mem::getVol is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the center of gravity of the element
- */
-inline Eigen::Vector3d const &Element::getCg() const
-{
- if (hasVals)
- return cg;
- else
- throw std::runtime_error("Element::getCg is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the unit normal vector of the element
- */
-inline Eigen::Vector3d const &Element::getNormal() const
-{
- if (hasVals)
- {
- if (!isVol)
- return normal;
- else
- throw std::runtime_error("Element::getNormal normal vector is not available for volume element!\n");
- }
- else
- throw std::runtime_error("Element::getNormal is invalid because element memory is not up-to-date!\n");
-}
-
-/**
- * @brief Return the gradient of determinant of the Jacobian with respect to node positions at Gauss point k
- */
-inline std::vector<double> const &Element::getGradDetJ(size_t k) const
-{
- if (hasGrads)
- return gradDetJs[k];
- else
- throw std::runtime_error("Element::getGradDetJ is invalid because element memory (gradient) is not up-to-date!\n");
-}
-
-/**
- * @brief Return the gradient of the Jacobian matrix with respect to node positions at Gauss point k
- */
-inline std::vector<Eigen::MatrixXd> const &Element::getGradJ(size_t k) const
-{
- if (hasGrads)
- {
- if (isVol)
- return gradJs[k];
- else
- throw std::runtime_error("Element::getGradJ gradient of Jacobian matrix is not available for surface element!\n");
- }
- else
- throw std::runtime_error("Element::getGradJ is invalid because element memory (gradient) is not up-to-date!\n");
-}
-
-/**
- * @brief Return the gradient of the volume with respect to node positions
- */
-inline std::vector<double> const &Element::getGradVol() const
-{
- if (hasGrads)
- return gradVol;
- else
- throw std::runtime_error("Element::getGradVol is invalid because element memory (gradient) is not up-to-date!\n");
-}
-
-/**
- * @brief Return the gradient of the unit normal vector with respect to node positions
- */
-inline std::vector<Eigen::Vector3d> const &Element::getGradNormal() const
-{
- if (hasGrads)
- {
- if (!isVol)
- return gradNormal;
- else
- throw std::runtime_error("Element::getGradNormal normal vector gradient is not available for volume element!\n");
- }
- else
- throw std::runtime_error("Element::getGradNormal is invalid because element memory (gradient) is not up-to-date!\n");
-}
diff --git a/tbox/src/wFct0.cpp b/tbox/src/wFct0.cpp
deleted file mode 100644
index 2f4618d3..00000000
--- a/tbox/src/wFct0.cpp
+++ /dev/null
@@ -1,114 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wFct0.h"
-#include "wElement.h"
-#include "wNode.h"
-#include "wCache.h"
-
-using namespace tbox;
-
-void PwLf::add(double x, double y)
-{
- auto it = pts.find(x);
- if (it != pts.end())
- {
- std::ostringstream str;
- str << "PwLf: value at " << x << " already exist!\n";
- throw std::runtime_error(str.str());
- }
- pts[x] = y;
-}
-
-double PwLf::eval(double x) const
-{
- auto it1 = pts.begin();
- if (it1 == pts.end())
- throw std::runtime_error("PwLf is empty!");
- auto it2 = it1;
- ++it2;
- if (it2 == pts.end())
- return it1->second; //fct is a constant
- auto it3 = it2;
- ++it3;
-
- for (; it3 != pts.end(); ++it1, ++it2, ++it3)
- if (x <= it2->first)
- break;
-
- // eval using it1-it2
- double x1 = it1->first;
- double y1 = it1->second;
- double x2 = it2->first;
- double y2 = it2->second;
- return y1 + (y2 - y1) / (x2 - x1) * (x - x1);
-}
-
-void PwLf::write(std::ostream &out) const
-{
- out << "PwLf=";
- for (auto &p : pts)
- out << "\tx=" << p.first << " y=" << p.second << '\n';
-}
-
-//-------------------------------------------------------------------------
-
-void Fct0C::write(std::ostream &out) const
-{
- out << "Fct0C=" << v;
-}
-
-//-------------------------------------------------------------------------
-
-double
-Fct0XYZ::eval(Element const &e, std::vector<double> const &u, size_t k) const
-{
- Cache &cache = e.getVCache();
- Eigen::VectorXd const &ff = cache.getSf(k);
-
- // position pg en x,y
- Eigen::Vector3d xpg(0, 0, 0);
- for (size_t i = 0; i < e.nodes.size(); ++i)
- xpg += ff(i) * e.nodes[i]->pos;
-
- return this->eval(xpg);
-}
-
-void Fct0XYZ::write(std::ostream &out) const
-{
- out << "Fct0XYZ";
-}
-
-//-------------------------------------------------------------------------
-
-double
-Fct0U::eval(Element const &e, std::vector<double> const &u, size_t k) const
-{
- Cache &cache = e.getVCache();
- Eigen::VectorXd const &ff = cache.getSf(k);
-
- // u au pg
- double upg = 0.0;
- for (size_t i = 0; i < e.nodes.size(); ++i)
- upg += ff(i) * u[e.nodes[i]->row];
-
- return this->eval(upg);
-}
-
-void Fct0U::write(std::ostream &out) const
-{
- out << "Fct0U";
-}
diff --git a/tbox/src/wFct0.h b/tbox/src/wFct0.h
deleted file mode 100644
index 591b6d51..00000000
--- a/tbox/src/wFct0.h
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WFCT0_H
-#define WFCT0_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <map>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-class TBOX_API PwLf : public fwk::wSharedObject
-{
- std::map<double, double> pts;
-
-public:
- PwLf() : wSharedObject() {}
- void add(double x, double y);
- double eval(double x) const;
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief Scalar functions to be integrated over an element
- *
- * eval() evaluates the function at kth Gauss point
- * @authors Romain Boman
- */
-class TBOX_API Fct0 : public fwk::wSharedObject
-{
-public:
-#ifndef SWIG
- Fct0() : wSharedObject()
- {
- }
-#endif
- virtual ~Fct0()
- {
- }
-
-#ifndef SWIG
- virtual double eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const = 0;
-#endif
-};
-
-/**
- * @brief Constant function
- * @authors Romain Boman
- */
-class TBOX_API Fct0C : public Fct0
-{
- double v;
-
-public:
- Fct0C(double _v) : Fct0(), v(_v) {}
-
-#ifndef SWIG
- virtual double eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const override
- {
- return v;
- }
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief Function depending on position
- * @authors Romain Boman
- */
-class TBOX_API Fct0XYZ : public Fct0
-{
-public:
- virtual double eval(Eigen::Vector3d const &pos) const = 0;
-
-#ifndef SWIG
- virtual double eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief function depending on element
- * @authors Romain Boman
- */
-class TBOX_API Fct0U : public Fct0
-{
-public:
- virtual double eval(double u) const = 0;
-
-#ifndef SWIG
- virtual double eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WFCT0_H
diff --git a/tbox/src/wFct1.cpp b/tbox/src/wFct1.cpp
deleted file mode 100644
index 5d90ba81..00000000
--- a/tbox/src/wFct1.cpp
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wFct1.h"
-
-using namespace tbox;
-
-void Fct1C::write(std::ostream &out) const
-{
- out << "Fct1C = " << v;
-}
diff --git a/tbox/src/wFct1.h b/tbox/src/wFct1.h
deleted file mode 100644
index f82320d1..00000000
--- a/tbox/src/wFct1.h
+++ /dev/null
@@ -1,82 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WFCT1_H
-#define WFCT1_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Vector functions to be integrated over an element
- *
- * eval() evaluates the function at kth Gauss point
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API Fct1 : public fwk::wSharedObject
-{
-public:
-#ifndef SWIG
- Fct1() : wSharedObject()
- {
- }
-#endif
- virtual ~Fct1()
- {
- }
-
-#ifndef SWIG
- virtual Eigen::Vector3d eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const = 0;
-#endif
-};
-
-/**
- * @brief Constant function
- * @authors Adrien Crovato
- */
-class TBOX_API Fct1C : public Fct1
-{
- Eigen::Vector3d v;
-
-public:
- Fct1C(double _v0, double _v1, double _v2) : Fct1()
- {
- v(0) = _v0;
- v(1) = _v1;
- v(2) = _v2;
- }
-
-#ifndef SWIG
- virtual Eigen::Vector3d eval(Element const &e,
- std::vector<double> const &u,
- size_t k) const override
- {
- return v;
- }
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WFCT1_H
diff --git a/tbox/src/wFct2.cpp b/tbox/src/wFct2.cpp
deleted file mode 100644
index 9abe21bc..00000000
--- a/tbox/src/wFct2.cpp
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wFct2.h"
-#include "wFct0.h"
-#include "wElement.h"
-#include "wNode.h"
-#include "wCache.h"
-#include <Eigen/Dense>
-
-using namespace tbox;
-
-Fct2C::Fct2C(double _v11, double _v22, double _v12) : Fct2()
-{
- v(0, 0) = _v11;
- v(1, 1) = _v22;
- v(1, 0) = _v12;
- v(0, 1) = _v12;
-
- double det = v.determinant();
- if (det <= 0.0)
- throw std::runtime_error("det(Fct2C)<0!");
-}
-
-void Fct2C::eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const
-{
- out = v; // Eigen resizes automatically
-}
-
-void Fct2C::write(std::ostream &out) const
-{
- out << "Fct2C=" << v;
-}
-
-//-------------------------------------------------------------------------
-
-void Fct2XYZ::eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const
-{
- Cache &cache = e.getVCache();
- Eigen::VectorXd const &ff = cache.getSf(k);
-
- // position pg en x,y
- Eigen::Vector3d xpg(0, 0, 0);
- for (size_t i = 0; i < e.nodes.size(); ++i)
- xpg += ff(i) * e.nodes[i]->pos;
-
- this->eval(xpg, out, fake);
-}
-
-void Fct2XYZ::write(std::ostream &out) const
-{
- out << "Fct2XYZ";
-}
-
-//-------------------------------------------------------------------------
-
-void Fct2U::eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const
-{
- Cache &cache = e.getVCache();
- Eigen::VectorXd const &ff = cache.getSf(k);
-
- // u au pg
- double upg = 0.0;
- for (size_t i = 0; i < e.nodes.size(); ++i)
- upg += ff(i) * u[e.nodes[i]->row];
-
- this->eval(upg, out, fake);
-}
-
-void Fct2U::write(std::ostream &out) const
-{
- out << "Fct2U";
-}
-
-//-------------------------------------------------------------------------
-
-void Fct2UdU::eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const
-{
- Cache &cache = e.getVCache();
- Eigen::VectorXd const &ff = cache.getSf(k);
-
- // u au pg => upg
- double upg = 0.0;
- for (size_t i = 0; i < e.nodes.size(); ++i)
- upg += ff(i) * u[e.nodes[i]->row];
-
- //gradU au pg => gradupg
- Eigen::VectorXd gradupg = e.computeGradient(u, k);
-
- this->eval(e, k, upg, gradupg, out, fake);
-}
-
-void Fct2UdU::write(std::ostream &out) const
-{
- out << "Fct2UdU";
-}
-
-//-------------------------------------------------------------------------
-
-void Fct2PwLf::eval(double u, Eigen::MatrixXd &v, bool fake) const
-{
- v.resize(2, 2);
- v(0, 0) = v11->eval(u);
- v(1, 1) = v22->eval(u);
- v(1, 0) = v(0, 1) = v12->eval(u);
-}
-
-void Fct2PwLf::write(std::ostream &out) const
-{
- out << "Fct2PwLf";
-}
diff --git a/tbox/src/wFct2.h b/tbox/src/wFct2.h
deleted file mode 100644
index ed200d74..00000000
--- a/tbox/src/wFct2.h
+++ /dev/null
@@ -1,141 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WFCT2_H
-#define WFCT2_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <memory>
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Matrix functions to be integrated over an element
- *
- * eval() evaluates the function at kth Gauss point
- * @authors Romain Boman
- */
-class TBOX_API Fct2 : public fwk::wSharedObject
-{
-public:
-#ifndef SWIG
- Fct2() : wSharedObject()
- {
- }
-#endif
- virtual ~Fct2()
- {
- }
-
- virtual void evalall() {}
-#ifndef SWIG
- virtual void eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const = 0;
-#endif
-};
-
-/**
- * @brief matrix function M = Cte
- */
-class TBOX_API Fct2C : public Fct2
-{
- Eigen::Matrix2d v;
-
-public:
- Fct2C(double _v11, double _v22, double _v12);
-
-#ifndef SWIG
- virtual void eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief matrix function M = fct(x,y,z)
- */
-class TBOX_API Fct2XYZ : public Fct2
-{
-public:
- virtual void eval(Eigen::Vector3d const &pos, Eigen::MatrixXd &v, bool fake) const = 0;
-
-#ifndef SWIG
- virtual void eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief matrix function M = fct(u)
- */
-class TBOX_API Fct2U : public Fct2
-{
-public:
- virtual void eval(double u, Eigen::MatrixXd &v, bool fake) const = 0;
-
-#ifndef SWIG
- virtual void eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-/**
- * @brief matrix function M = fct(u, gradU)
- */
-class TBOX_API Fct2UdU : public Fct2
-{
-public:
- virtual void eval(Element const &e, size_t k, double u, Eigen::VectorXd const &gradu,
- Eigen::MatrixXd &v, bool fake) const = 0;
-#ifndef SWIG
- virtual void eval(Element const &e,
- std::vector<double> const &u,
- size_t k, Eigen::MatrixXd &out, bool fake) const override;
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-/**
- * @brief matrix function M = fct(u)
- */
-class TBOX_API Fct2PwLf : public Fct2U
-{
- std::shared_ptr<PwLf> v11;
- std::shared_ptr<PwLf> v22;
- std::shared_ptr<PwLf> v12;
-
-public:
- Fct2PwLf(std::shared_ptr<PwLf> _v11, std::shared_ptr<PwLf> _v22, std::shared_ptr<PwLf> _v12) : Fct2U(), v11(_v11), v22(_v22), v12(_v12) {}
-
- virtual void eval(double u, Eigen::MatrixXd &v, bool fake) const override;
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WFCT2_H
diff --git a/tbox/src/wGauss.cpp b/tbox/src/wGauss.cpp
deleted file mode 100644
index 3bcadf2d..00000000
--- a/tbox/src/wGauss.cpp
+++ /dev/null
@@ -1,23 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGauss.h"
-
-using namespace tbox;
-
-Gauss::Gauss() : p(0), w(0)
-{
-}
diff --git a/tbox/src/wGauss.h b/tbox/src/wGauss.h
deleted file mode 100644
index 02409ad6..00000000
--- a/tbox/src/wGauss.h
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSS_H
-#define WGAUSS_H
-
-#include "tbox.h"
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Base class for Gauss points
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API Gauss
-{
-protected:
- size_t ngp; ///< number of Gauss points
- std::vector<Eigen::Vector3d> p; ///< positions
- std::vector<double> w; ///< weights
-
-public:
- explicit Gauss();
- virtual ~Gauss() {}
-
- inline size_t getN();
- inline Eigen::Vector3d const &getP(size_t k);
- inline double getW(size_t k);
-};
-
-#include "wGauss.inl"
-
-} // namespace tbox
-
-#endif //WGAUSS_H
diff --git a/tbox/src/wGauss.inl b/tbox/src/wGauss.inl
deleted file mode 100644
index 06fd2ce5..00000000
--- a/tbox/src/wGauss.inl
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return the number of Gauss points
- */
-inline size_t Gauss::getN()
-{
- return ngp;
-}
-
-/**
- * @brief Return the position in local coordinates of Gauss point k
- */
-inline Eigen::Vector3d const &Gauss::getP(size_t k)
-{
- return p[k];
-}
-
-/**
- * @brief Return the weight of Gauss point k
- */
-inline double Gauss::getW(size_t k)
-{
- return w[k];
-}
diff --git a/tbox/src/wGaussHex8.cpp b/tbox/src/wGaussHex8.cpp
deleted file mode 100644
index 226e1953..00000000
--- a/tbox/src/wGaussHex8.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGaussHex8.h"
-#include "wGaussLine2.h"
-#include <stdexcept>
-#include <cmath>
-
-using namespace tbox;
-
-GaussHex8::GaussHex8(int n) : Gauss()
-{
- GaussLine2 g(n);
-
- ngp = n * n * n;
- for (int i = 0; i < n; ++i)
- for (int j = 0; j < n; ++j)
- for (int k = 0; k < n; ++k)
- {
- p.push_back(Eigen::Vector3d(g.getP(i)(0), g.getP(j)(0), g.getP(k)(0)));
- w.push_back(g.getW(i) * g.getW(j) * g.getW(k));
- }
-}
diff --git a/tbox/src/wGaussHex8.h b/tbox/src/wGaussHex8.h
deleted file mode 100644
index 7208fca1..00000000
--- a/tbox/src/wGaussHex8.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSSHEX8_H
-#define WGAUSSHEX8_H
-
-#include "tbox.h"
-#include "wGauss.h"
-
-namespace tbox
-{
-
-/**
- * @brief Gauss points for Hex8
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API GaussHex8 : public Gauss
-{
-public:
- explicit GaussHex8(int n);
-};
-
-} // namespace tbox
-
-#endif //WGAUSSHEX8_H
diff --git a/tbox/src/wGaussLine2.cpp b/tbox/src/wGaussLine2.cpp
deleted file mode 100644
index fff3f28a..00000000
--- a/tbox/src/wGaussLine2.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGaussLine2.h"
-#include <stdexcept>
-#include <cmath>
-
-using namespace tbox;
-
-GaussLine2::GaussLine2(int n) : Gauss()
-{
- p.resize(n);
- w.resize(n);
- ngp = n;
- switch (n)
- {
- case 1:
- p[0] = Eigen::Vector3d(0.0, 0.0, 0.0);
- w[0] = 2.;
- break;
- case 2:
- p[0] = Eigen::Vector3d(-1.0 / sqrt(3.0), 0.0, 0.0);
- w[0] = 1.;
- p[1] = Eigen::Vector3d(+1.0 / sqrt(3.0), 0.0, 0.0);
- w[1] = 1.;
- break;
- case 3:
- p[0] = Eigen::Vector3d(-sqrt(3.0 / 5.0), 0.0, 0.0);
- w[0] = 5. / 9.;
- p[1] = Eigen::Vector3d(0.0, 0.0, 0.0);
- w[1] = 8. / 9.;
- p[2] = Eigen::Vector3d(+sqrt(3.0 / 5.0), 0.0, 0.0);
- w[2] = 5. / 9.;
- break;
- default:
- throw std::runtime_error("not implemented (GaussLine2)!");
- }
-}
diff --git a/tbox/src/wGaussLine2.h b/tbox/src/wGaussLine2.h
deleted file mode 100644
index f836fbad..00000000
--- a/tbox/src/wGaussLine2.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSSLINE2_H
-#define WGAUSSLINE2_H
-
-#include "tbox.h"
-#include "wGauss.h"
-
-namespace tbox
-{
-
-/**
- * @brief Gauss points for Line2
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API GaussLine2 : public Gauss
-{
-public:
- explicit GaussLine2(int n);
-};
-
-} // namespace tbox
-
-#endif //WGAUSSLINE2_H
diff --git a/tbox/src/wGaussQuad4.cpp b/tbox/src/wGaussQuad4.cpp
deleted file mode 100644
index b9b46e78..00000000
--- a/tbox/src/wGaussQuad4.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGaussQuad4.h"
-#include "wGaussLine2.h"
-#include <stdexcept>
-#include <cmath>
-
-using namespace tbox;
-
-GaussQuad4::GaussQuad4(int n) : Gauss()
-{
- GaussLine2 g(n);
-
- ngp = n * n;
- for (int i = 0; i < n; ++i)
- for (int j = 0; j < n; ++j)
- {
- p.push_back(Eigen::Vector3d(g.getP(i)(0), g.getP(j)(0), 0.0));
- w.push_back(g.getW(i) * g.getW(j));
- }
-}
diff --git a/tbox/src/wGaussQuad4.h b/tbox/src/wGaussQuad4.h
deleted file mode 100644
index e2a5c858..00000000
--- a/tbox/src/wGaussQuad4.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSSQUAD4_H
-#define WGAUSSQUAD4_H
-
-#include "tbox.h"
-#include "wGauss.h"
-
-namespace tbox
-{
-
-/**
- * @brief Gauss points for Quad4
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API GaussQuad4 : public Gauss
-{
-public:
- explicit GaussQuad4(int n);
-};
-
-} // namespace tbox
-
-#endif //WGAUSSQUAD4_H
diff --git a/tbox/src/wGaussTetra4.cpp b/tbox/src/wGaussTetra4.cpp
deleted file mode 100644
index 0e1a4e35..00000000
--- a/tbox/src/wGaussTetra4.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGaussTetra4.h"
-#include <stdexcept>
-#include <cmath>
-
-using namespace tbox;
-
-GaussTetra4::GaussTetra4(int n) : Gauss()
-{
- switch (n)
- {
- case 1:
- {
- p.resize(1);
- w.resize(1);
- ngp = 1;
- p[0] = Eigen::Vector3d(0.25, 0.25, 0.25);
- w[0] = 1. / 6.;
- break;
- }
- case 2:
- {
- p.resize(4);
- w.resize(4); // 4 pts !
- ngp = 4;
- double a = (5. - sqrt(5.)) / 20.;
- double b = (5. + 3. * sqrt(5.)) / 20.;
- p[0] = Eigen::Vector3d(a, a, a);
- w[0] = 1. / 4. / 6.;
- p[1] = Eigen::Vector3d(a, a, b);
- w[1] = 1. / 4. / 6.;
- p[2] = Eigen::Vector3d(a, b, a);
- w[2] = 1. / 4. / 6.;
- p[3] = Eigen::Vector3d(b, a, a);
- w[3] = 1. / 4. / 6.;
- break;
- }
- default:
- throw std::runtime_error("not implemented (GaussTetra4)!");
- }
-}
diff --git a/tbox/src/wGaussTetra4.h b/tbox/src/wGaussTetra4.h
deleted file mode 100644
index abc4daed..00000000
--- a/tbox/src/wGaussTetra4.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSSTETRA4_H
-#define WGAUSSTETRA4_H
-
-#include "tbox.h"
-#include "wGauss.h"
-
-namespace tbox
-{
-
-/**
- * @brief Gauss points for Tetra4
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API GaussTetra4 : public Gauss
-{
-public:
- explicit GaussTetra4(int n); // n is the degree (ngp can be higher!)
-};
-
-} // namespace tbox
-
-#endif //WGAUSSTETRA4_H
diff --git a/tbox/src/wGaussTri3.cpp b/tbox/src/wGaussTri3.cpp
deleted file mode 100644
index 39be394b..00000000
--- a/tbox/src/wGaussTri3.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGaussTri3.h"
-#include <stdexcept>
-#include <cmath>
-
-using namespace tbox;
-
-GaussTri3::GaussTri3(int n) : Gauss()
-{
- switch (n)
- {
- case 1:
- p.resize(1);
- w.resize(1);
- ngp = 1;
- p[0] = Eigen::Vector3d(1. / 3, 1. / 3, 0.0);
- w[0] = 1. / 2.; // ! sum=1/2
- break;
- case 2:
- p.resize(3);
- w.resize(3); // 3 pts !
- ngp = 3;
- p[0] = Eigen::Vector3d(1. / 6, 1. / 6, 0.0);
- w[0] = 1. / 3. / 2.;
- p[1] = Eigen::Vector3d(2. / 3, 1. / 6, 0.0);
- w[1] = 1. / 3. / 2.;
- p[2] = Eigen::Vector3d(1. / 6, 2. / 3, 0.0);
- w[2] = 1. / 3. / 2.;
- break;
- case 3:
- p.resize(4);
- w.resize(4);
- ngp = 4;
- p[0] = Eigen::Vector3d(1. / 3, 1. / 3, 0.0);
- w[0] = -27. / 48. / 2.;
- p[1] = Eigen::Vector3d(1. / 5, 3. / 5, 0.0);
- w[1] = 25. / 48. / 2.;
- p[2] = Eigen::Vector3d(1. / 5, 1. / 5, 0.0);
- w[2] = 25. / 48. / 2.;
- p[3] = Eigen::Vector3d(3. / 5, 1. / 5, 0.0);
- w[3] = 25. / 48. / 2.;
- break;
- default:
- throw std::runtime_error("not implemented (GaussTri3)!");
- }
-}
diff --git a/tbox/src/wGaussTri3.h b/tbox/src/wGaussTri3.h
deleted file mode 100644
index ee8291cc..00000000
--- a/tbox/src/wGaussTri3.h
+++ /dev/null
@@ -1,38 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGAUSSTRI3_H
-#define WGAUSSTRI3_H
-
-#include "tbox.h"
-#include "wGauss.h"
-
-namespace tbox
-{
-
-/**
- * @brief Gauss points for Tri3
- * @authors Adrien Crovato, Romain Boman, Kim Liegeois
- */
-class TBOX_API GaussTri3 : public Gauss
-{
-public:
- explicit GaussTri3(int n); // n is the degree (ngp can be higher!)
-};
-
-} // namespace tbox
-
-#endif //WGAUSSTRI3_H
diff --git a/tbox/src/wGmres.cpp b/tbox/src/wGmres.cpp
deleted file mode 100644
index b708c6e5..00000000
--- a/tbox/src/wGmres.cpp
+++ /dev/null
@@ -1,51 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGmres.h"
-using namespace tbox;
-
-Gmres::Gmres() : LinearSolver()
-{
- // set the preconditioner and solver parameters to "good" starting values
- solver.preconditioner().setFillfactor(1);
- solver.preconditioner().setDroptol(1e-6);
- solver.set_restart(50);
- solver.setTolerance(1e-8);
- solver.setMaxIterations(1000);
-}
-
-void Gmres::analyze(Eigen::SparseMatrix<double> const &A)
-{
- solver.analyzePattern(A);
-}
-void Gmres::factorize(Eigen::SparseMatrix<double> const &A)
-{
- solver.factorize(A);
-}
-void Gmres::solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- x = solver.solve(b);
-}
-void Gmres::compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- solver.compute(A);
- x = solver.solve(b);
-}
-
-void Gmres::write(std::ostream &out) const
-{
- out << "GMRES (Eigen)" << std::endl;
-}
diff --git a/tbox/src/wGmres.h b/tbox/src/wGmres.h
deleted file mode 100644
index b0a4a44c..00000000
--- a/tbox/src/wGmres.h
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGMRES_H
-#define WGMRES_H
-
-#include "tbox.h"
-#include "wLinearSolver.h"
-#include <unsupported/Eigen/IterativeSolvers>
-
-namespace tbox
-{
-
-/**
- * @brief GMRES interface
- * @authors Adrien Crovato
- */
-class TBOX_API Gmres : public LinearSolver
-{
- Eigen::GMRES<Eigen::SparseMatrix<double>, Eigen::IncompleteLUT<double>> solver;
-
-public:
- Gmres();
- virtual ~Gmres() {}
-
-#ifndef SWIG
- virtual void analyze(Eigen::SparseMatrix<double> const &A) override;
- virtual void factorize(Eigen::SparseMatrix<double> const &A) override;
- virtual void solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
- virtual void compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
-
- virtual double getError() override { return solver.error(); }
- virtual int getIterations() override { return solver.iterations(); }
-
- virtual void write(std::ostream &out) const override;
-#endif
-
- void setFillFactor(int f)
- {
- solver.preconditioner().setFillfactor(f);
- }
- void setDropTol(double t) { solver.preconditioner().setDroptol(t); }
- void setTolerance(double t) { solver.setTolerance(t); }
- void setRestart(int r) { solver.set_restart(r); }
- void setMaxIterations(int n) { solver.setMaxIterations(n); }
-};
-
-} // namespace tbox
-
-#endif // WGMRES_H
diff --git a/tbox/src/wGmshExport.cpp b/tbox/src/wGmshExport.cpp
deleted file mode 100644
index 6487d0db..00000000
--- a/tbox/src/wGmshExport.cpp
+++ /dev/null
@@ -1,304 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGmshExport.h"
-#include "wTag.h"
-#include "wElement.h"
-#include "wNode.h"
-#include "wResults.h"
-
-using namespace tbox;
-
-GmshExport::GmshExport(std::shared_ptr<MshData> _msh) : MshExport(_msh)
-{
-}
-
-GmshExport::~GmshExport()
-{
- std::cout << "~GmshExport()\n";
-}
-
-/**
- * @brief Save the mesh on disk
- */
-void GmshExport::save(std::string const &fname) const
-{
- std::string wname = fname + ".msh";
- std::cout << "writing file: " << wname << "... " << std::flush;
-
- // write gmsh .msh file with stdio commands
- FILE *file = fopen(wname.c_str(), "wt");
- if (!file)
- throw std::runtime_error("Error opening file (save)");
-
- // write format
- fprintf(file, "$MeshFormat\n");
- fprintf(file, "2.2 %d %d\n", 0, 8);
- fprintf(file, "$EndMeshFormat\n");
-
- // write physical names
- fprintf(file, "$PhysicalNames\n");
- std::vector<Tag *> named;
- for (auto &p : msh->ptags)
- if (p.second->name != Tag::defaultName())
- named.push_back(p.second);
- fprintf(file, "%lu\n", static_cast<unsigned long>(named.size()));
- for (auto t : named)
- fprintf(file, "%d %d \"%s\"\n", t->dim, t->no, t->name.c_str());
- fprintf(file, "$EndPhysicalNames\n");
-
- // nodes
- fprintf(file, "$Nodes\n");
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->nodes.size()));
- for (auto n : msh->nodes)
- fprintf(file, "%d %.16g %.16g %.16g\n", n->no, n->pos(0), n->pos(1), n->pos(2));
- fprintf(file, "$EndNodes\n");
-
- // elements
- fprintf(file, "$Elements\n");
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->elems.size()));
- for (auto e : msh->elems)
- {
- size_t ntag = 2;
- if (!e->parts.empty())
- ntag += 1 + e->parts.size();
- fprintf(file, "%d %d %lu", e->no, static_cast<int>(e->type()), static_cast<unsigned long>(ntag));
- if (e->ptag)
- fprintf(file, " %d", e->ptag->no);
- else
- fprintf(file, " 0");
- if (e->etag)
- fprintf(file, " %d", e->etag->no);
- else
- fprintf(file, " 0");
- if (!e->parts.empty())
- {
- fprintf(file, " %lu", static_cast<unsigned long>(e->parts.size()));
- for (auto p : e->parts)
- fprintf(file, " %d", p->no);
- }
- for (auto n : e->nodes)
- fprintf(file, " %d", n->no);
- fprintf(file, "\n");
- }
- fprintf(file, "$EndElements\n");
-
- // close file
- fclose(file);
- std::cout << "done" << std::endl;
-}
-
-/**
- * @brief Save results (associated to a mesh) on disk
- */
-void GmshExport::save(std::string const &fname, Results const &r) const
-{
- std::string wname = fname + ".pos";
- std::cout << "writing file: " << wname << "... " << std::flush;
-
- FILE *file;
- if (binary)
- file = fopen(wname.c_str(), "wb");
- else
- file = fopen(wname.c_str(), "wt");
- if (!file)
- throw std::runtime_error("Error opening file (save)");
-
- // write format
- fprintf(file, "$MeshFormat\n");
- fprintf(file, "2.2 %d %d\n", binary ? 1 : 0, 8);
- if (binary)
- {
- int one = 1;
- fwrite(&one, sizeof(int), 1, file);
- }
- fprintf(file, "$EndMeshFormat\n");
-
- // node data: scalars_at_nodes
- for (auto &p : r.scalars_at_nodes)
- {
- fprintf(file, "$NodeData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 1); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->nodes.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->nodes.size(); ++ii)
- {
- if (binary)
- {
- fwrite(&(msh->nodes[ii]->no), sizeof(int), 1, file);
- fwrite(&((*(p.second))[ii]), sizeof(double), 1, file);
- }
- else
- fprintf(file, "%d %.16g\n", msh->nodes[ii]->no, (*(p.second))[ii]);
- }
- fprintf(file, "$EndNodeData\n");
- }
-
- // element data: scalars_at_elems
- for (auto &p : r.scalars_at_elems)
- {
- fprintf(file, "$ElementData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 1); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->elems.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->elems.size(); ++ii)
- {
- if (binary)
- {
- fwrite(&msh->elems[ii]->no, sizeof(int), 1, file);
- fwrite(&(*(p.second))[ii], sizeof(double), 1, file);
- }
- else
- fprintf(file, "%d %.16g\n", msh->elems[ii]->no, (*(p.second))[ii]);
- }
- fprintf(file, "$EndElementData\n");
- }
-
- // node data: vectors_at_nodes
- for (auto &p : r.vectors_at_nodes)
- {
- fprintf(file, "$NodeData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 3); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->nodes.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->nodes.size(); ++ii)
- {
- Eigen::Vector3d const &v = (*(p.second))[ii];
- if (binary)
- {
- fwrite(&msh->nodes[ii]->no, sizeof(int), 1, file);
- fwrite(&(v(0)), sizeof(double), 3, file);
- }
- else
- fprintf(file, "%d %.16g %.16g %.16g\n", msh->nodes[ii]->no, v(0), v(1), v(2));
- }
- fprintf(file, "$EndNodeData\n");
- }
-
- // element data: vectors_at_elems
- for (auto &p : r.vectors_at_elems)
- {
- fprintf(file, "$ElementData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 3); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->elems.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->elems.size(); ++ii)
- {
- Eigen::Vector3d const &v = (*(p.second))[ii];
- if (binary)
- {
- fwrite(&(msh->elems[ii]->no), sizeof(int), 1, file);
- fwrite(&(v(0)), sizeof(double), 3, file);
- }
- else
- fprintf(file, "%d %.16g %.16g %.16g\n", msh->elems[ii]->no, v(0), v(1), v(2));
- }
- fprintf(file, "$EndElementData\n");
- }
-
- // node data: tensors_at_nodes
- for (auto &p : r.tensors_at_nodes)
- {
- fprintf(file, "$NodeData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 9); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->nodes.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->nodes.size(); ++ii)
- {
- Eigen::MatrixXd const &v = (*(p.second))[ii];
- if (binary)
- {
- fwrite(&msh->nodes[ii]->no, sizeof(int), 1, file);
- for (int i = 0; i < 3; ++i)
- for (int j = 0; j < 3; ++j)
- fwrite(&(v(i, j)), sizeof(double), 1, file);
- }
- else
- fprintf(file, "%d %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g\n",
- msh->nodes[ii]->no,
- v(0, 0), v(0, 1), v(0, 2),
- v(1, 0), v(1, 1), v(1, 2),
- v(2, 0), v(2, 1), v(2, 2));
- }
- fprintf(file, "$EndNodeData\n");
- }
-
- // element data: tensors_at_elems
- for (auto &p : r.tensors_at_elems)
- {
- fprintf(file, "$ElementData\n");
- fprintf(file, "%d\n", 1); // nb of string tags
- fprintf(file, "\"%s\"\n", p.first.c_str()); // the name of the view
- fprintf(file, "%d\n", 1); // nb of real tags (1)
- fprintf(file, "%.16g\n", r.time); // 1. the time value
- fprintf(file, "%d\n", 3); // nb of integer tags (3)
- fprintf(file, "%d\n", r.nt); // 1. time step index
- fprintf(file, "%d\n", 9); // 2. nb of field component (1, 3 or 9)
- fprintf(file, "%lu\n", static_cast<unsigned long>(msh->elems.size())); // 3. nb of entities in the view
- for (size_t ii = 0; ii < msh->elems.size(); ++ii)
- {
- Eigen::MatrixXd const &v = (*(p.second))[ii];
- if (binary)
- {
- fwrite(&(msh->elems[ii]->no), sizeof(int), 1, file);
- for (int i = 0; i < 3; ++i)
- for (int j = 0; j < 3; ++j)
- fwrite(&(v(i, j)), sizeof(double), 1, file);
- }
- else
- fprintf(file, "%d %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g %.16g\n",
- msh->elems[ii]->no,
- v(0, 0), v(0, 1), v(0, 2),
- v(1, 0), v(1, 1), v(1, 2),
- v(2, 0), v(2, 1), v(2, 2));
- }
- fprintf(file, "$EndElementData\n");
- }
-
- // close file
- fclose(file);
- std::cout << "done" << std::endl;
-}
-
-void GmshExport::write(std::ostream &out) const
-{
- out << "GmshExport on " << *msh << std::endl;
-}
\ No newline at end of file
diff --git a/tbox/src/wGmshExport.h b/tbox/src/wGmshExport.h
deleted file mode 100644
index eefcf447..00000000
--- a/tbox/src/wGmshExport.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGMSHEXPORT_H
-#define WGMSHEXPORT_H
-
-#include "tbox.h"
-#include "wMshExport.h"
-#include <vector>
-#include <map>
-
-namespace tbox
-{
-
-/**
- * @brief Write mesh in gmsh format
- * @authors Adrien Crovato, Romain Boman
- */
-class TBOX_API GmshExport : public MshExport
-{
-public:
- GmshExport(std::shared_ptr<MshData> _msh);
- virtual ~GmshExport();
-
- virtual void save(std::string const &fname) const override;
-#ifndef SWIG
- virtual void save(std::string const &fname, Results const &r) const override;
-#endif
-
- virtual void write(std::ostream &out) const override;
-};
-
-} // namespace tbox
-
-#endif //WGMSHUTILS_H
diff --git a/tbox/src/wGmshImport.cpp b/tbox/src/wGmshImport.cpp
deleted file mode 100644
index 3ea091dc..00000000
--- a/tbox/src/wGmshImport.cpp
+++ /dev/null
@@ -1,620 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGmshImport.h"
-#include "wTag.h"
-#include "wElement.h"
-#include "wNode.h"
-#include "wHex8.h"
-#include "wTetra4.h"
-#include "wQuad4.h"
-#include "wTri3.h"
-#include "wLine2.h"
-#include "wPoint1.h"
-#include "wResults.h"
-
-using namespace tbox;
-
-GmshImport::GmshImport(std::shared_ptr<MshData> _msh) : MshImport(_msh)
-{
-}
-
-GmshImport::~GmshImport()
-{
- std::cout << "~GmshImport()\n";
- nodemap.clear();
-}
-
-/**
- * @brief Load a mesh from a file
- */
-void GmshImport::load(std::string const &fname, int myrank)
-{
- // clear data structure
- msh->clear();
- nodemap.clear();
-
- std::cout << "reading file " << fname << "...\n";
-
- // read filename
- auto idx = fname.find(".msh");
- if (idx != std::string::npos)
- {
- msh->name = fname.substr(0, idx);
- std::cout << "\tsetting mesh name to \"" << msh->name << "\"\n";
- }
-
- // read gmsh .msh file with stdio commands
- FILE *file = fopen(fname.c_str(), "r");
- if (!file)
- throw std::runtime_error("Error opening file (load)");
-
- int skipped = 0;
- while (1)
- {
- // read next line
- char line[128];
- if (fgets(line, sizeof line, file) == NULL)
- break;
-
- // process code
- if (searchCode("$MeshFormat", line) == 0)
- readMshFormat(file);
- else if (searchCode("$Nodes", line) == 0)
- readMshNodes(file);
- else if (searchCode("$Elements", line) == 0)
- readMshElements(file, myrank);
- else if (searchCode("$PhysicalNames", line) == 0)
- readMshPhyNames(file);
- else
- {
- skipped += 1;
- if (verb)
- std::cout << "\t"
- << "[code] skipping line:\"" << line << "\"\n";
- }
- }
- if (verb)
- std::cout << skipped << " lines skipped\n";
-
- // close file
- fclose(file);
- nodemap.clear();
- std::cout << "done" << std::endl;
-}
-
-/**
- * @brief Read results from a file at time step index n
- */
-void GmshImport::load(std::string const &fname, Results &r, int n)
-{
- // Sanity checks
- if (msh == nullptr)
- throw std::runtime_error("tbox::GmshImport::load mesh data structure is empty. Please load a mesh before reading the results!\n");
-
- // Create index maps
- std::map<int, size_t> nimap, eimap;
- for (size_t i = 0; i < msh->nodes.size(); ++i)
- nimap[msh->nodes[i]->no] = i;
- for (size_t i = 0; i < msh->elems.size(); ++i)
- eimap[msh->elems[i]->no] = i;
-
- // Open file
- std::cout << "reading file " << fname << "...\n";
- FILE *file = fopen(fname.c_str(), "r");
- if (!file)
- throw std::runtime_error("Error opening file (load)");
-
- // Read results
- int skipped = 0;
- while (1)
- {
- // read next line
- char line[128];
- if (fgets(line, sizeof line, file) == NULL)
- break;
-
- // process code
- if (searchCode("$MeshFormat", line) == 0)
- readMshFormat(file);
- else if (searchCode("$NodeData", line) == 0)
- readResNodes(file, line, nimap, r, n);
- else if (searchCode("$ElementData", line) == 0)
- readResElements(file, line, eimap, r, n);
- else
- {
- skipped += 1;
- if (verb)
- std::cout << "\t"
- << "[code] skipping line:\"" << line << "\"\n";
- }
- }
- if (verb)
- std::cout << skipped << " lines skipped\n";
-
- // close file
- fclose(file);
- std::cout << "done" << std::endl;
-}
-
-/**
- * @brief Search for a line in a code
- */
-int GmshImport::searchCode(char const *code, char const *line) const
-{
- return strncmp(code, line, strlen(code));
-}
-
-/**
- * @brief Read mesh format type (version)
- */
-void GmshImport::readMshFormat(FILE *file)
-{
- double version = 0.0;
- int ftype = 0, dsize = 0;
- if (fscanf(file, "%lf %d %d\n", &version, &ftype, &dsize) != 3)
- throw std::runtime_error("Error reading file (readMshFormat)");
- if (ftype != 0)
- throw std::runtime_error("tbox::GmshImport::readMshFormat cannot read binary format!\n");
- double eps = 1e-5;
- if (version < 2.2 - eps || version > 2.2 + eps)
- {
- std::stringstream str;
- str << "bad .msh version: (" << version << ")";
- throw std::runtime_error(str.str());
- }
- else
- std::cout << "\treading .msh format " << version << "\n";
-}
-
-/**
- * @brief Read the nodes
- */
-void GmshImport::readMshNodes(FILE *file)
-{
- // read number of nodes
- int nbnod = 0;
- if (fscanf(file, "%d\n", &nbnod) != 1)
- throw std::runtime_error("Error reading number of nodes (readMshNodes)");
- std::cout << "\tcounted " << nbnod << " nodes\n";
-
- // allocate memory and read the nodes
- msh->nodes.reserve(nbnod);
- for (int i = 0; i < nbnod; ++i)
- {
- int no = 0;
- double x = 0.0, y = 0.0, z = 0.0;
- if (fscanf(file, "%d %lf %lf %lf\n", &no, &x, &y, &z) != 4)
- break;
- if (verb)
- std::cout << "\t" << no << ((i == nbnod - 1) ? ".\n" : ",");
- Node *nod = new Node(no, Eigen::Vector3d(x, y, z), i);
- msh->nodes.push_back(nod);
-
- nodemap[no] = nod;
- }
-}
-
-/**
- * @brief Read the elements
- */
-void GmshImport::readMshElements(FILE *file, int myrank)
-{
- // read number of elements
- int nbelm = 0;
- if (fscanf(file, "%d\n", &nbelm) != 1)
- throw std::runtime_error("Error reading number of elements (readMshElements)");
- std::cout << "\tcounted " << nbelm << " elements\n";
-
- // allocate memory and read the elements
- msh->elems.reserve(nbelm);
- for (int i = 0; i < nbelm; ++i)
- {
- // read number, type and nb of tags
- int no = 0, type = 0, nbtags = 0;
- if (fscanf(file, "%d %d %d", &no, &type, &nbtags) != 3)
- throw std::runtime_error("Error reading &no, &type, &nbtags (readMshElements)");
- if (verb)
- std::cout << "\t" << no << ((i == nbelm - 1) ? ".\n" : ",");
-
- // read/create/link tags
- // physical tag (group)
- Tag *ptag = nullptr;
- if (nbtags > 0)
- ptag = addTag(file, msh->ptags);
- // elementary tag (geometry)
- Tag *etag = nullptr;
- if (nbtags > 1)
- etag = addTag(file, msh->etags);
- // partitions
- bool belongsToPart = false;
- std::vector<Tag *> prts;
- if (nbtags > 2)
- {
- // read number of part
- int nbpart = 0;
- if (fscanf(file, "%d", &nbpart) != 1)
- throw std::runtime_error("Error reading &nbpart (readMshElements)");
- for (int j = 0; j < nbpart; ++j)
- {
- Tag *tag = addTag(file, msh->parts);
- prts.push_back(tag);
- if (myrank + 1 == tag->no || (myrank + 1 == -(tag->no)))
- belongsToPart = true;
- }
- }
- if (static_cast<ELTYPE>(type) == ELTYPE::POINT1)
- belongsToPart = true;
-
- bool skipline = true;
- // read/link nodes (if serial run or elements belong to partition)
- if (myrank < 0 || belongsToPart)
- {
- skipline = false;
- std::vector<Node *> nods;
- if (static_cast<ELTYPE>(type) == ELTYPE::HEX8) // 8-node hexa
- {
- readElNods(file, 8, nods);
- msh->elems.push_back(new Hex8(no, ptag, etag, prts, nods));
- }
- else if (static_cast<ELTYPE>(type) == ELTYPE::QUAD4) // 4-node quad
- {
- readElNods(file, 4, nods);
- msh->elems.push_back(new Quad4(no, ptag, etag, prts, nods));
- }
- else if (static_cast<ELTYPE>(type) == ELTYPE::TETRA4) // 4-node tetra
- {
- readElNods(file, 4, nods);
- msh->elems.push_back(new Tetra4(no, ptag, etag, prts, nods));
- }
- else if (static_cast<ELTYPE>(type) == ELTYPE::LINE2) // 2-node line
- {
- readElNods(file, 2, nods);
- msh->elems.push_back(new Line2(no, ptag, etag, prts, nods));
- }
- else if (static_cast<ELTYPE>(type) == ELTYPE::POINT1) // 1-node point
- {
- readElNods(file, 1, nods);
- msh->elems.push_back(new Point1(no, ptag, etag, prts, nods));
- }
- else if (static_cast<ELTYPE>(type) == ELTYPE::TRI3) // 3-node triangle
- {
- readElNods(file, 3, nods);
- msh->elems.push_back(new Tri3(no, ptag, etag, prts, nods));
- }
- else
- skipline = true;
- }
- if (skipline)
- {
- // skip line
- char line[128];
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("Error skipping line (readMshElements)");
- if (verb)
- std::cout << "[elm] skipping line:\"" << line << "\"\n";
- }
- }
-}
-
-/**
- * @brief Read physical group names
- */
-void GmshImport::readMshPhyNames(FILE *file)
-{
- // read number of names
- int nbtag = 0;
- if (fscanf(file, "%d\n", &nbtag) != 1)
- throw std::runtime_error("Error reading number of physical names (readMshPhyNames)");
-
- // read the names
- for (int i = 0; i < nbtag; ++i)
- {
- // read dimension, label and name
- int dim = 0, no = 0;
- char pname[128];
- if (fscanf(file, "%d %d \"%[^\"]\"", &dim, &no, pname) != 3)
- throw std::runtime_error("Error reading &dim, &no, &name (readMshPhyNames)");
- // add tag to gtag list
- auto it = msh->ptags.find(no);
- if (it == msh->ptags.end())
- msh->ptags[no] = new Tag(no, pname, dim);
- msh->ntags[pname] = msh->ptags[no];
- }
-}
-
-/**
- * @brief Read nodes of an element
- */
-void GmshImport::readElNods(FILE *file, int n, std::vector<Node *> &nods)
-{
- int nn;
- for (int j = 0; j < n; ++j)
- {
- if (fscanf(file, "%d", &nn) != 1)
- throw std::runtime_error("Error reading element/node links (readElNods)");
-
- auto it = nodemap.find(nn);
- if (it == nodemap.end())
- throw std::runtime_error("Unknown node label (readElNods)");
- nods.push_back(it->second);
- }
-}
-
-/**
- * @brief Create a tag for each physical group
- */
-Tag *GmshImport::addTag(FILE *file, std::map<int, Tag *> &tmap)
-{
- int tag;
- if (fscanf(file, "%d", &tag) != 1)
- throw std::runtime_error("Error reading tags (addtag)");
- auto it = tmap.find(tag);
- if (it == tmap.end())
- tmap[tag] = new Tag(tag);
- return tmap[tag];
-}
-
-/**
- * @brief Read header of results
- */
-void GmshImport::readResHeader(FILE *file, char *line, char *vname, unsigned long &nd, int &nc, int &nt, double &time)
-{
- // Read the header
- int nstrtags = 0, nrealtags = 0, ninttags = 0; // number of string, real and integer tags
- // get the number of string tags
- if (fscanf(file, "%d", &nstrtags) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the (first) name of the view (variable), and skip the others if any
- if (fscanf(file, " \"%[^\"]\"", vname) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- for (int i = 0; i < nstrtags - 1; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResHeader end-of-file reached before all lines could be read!\n");
- // get the number of real tags
- if (fscanf(file, "%d", &nrealtags) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- if (nrealtags != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the time
- if (fscanf(file, "%lg", &time) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the number of integer tags
- if (fscanf(file, "%d", &ninttags) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the time step index
- if (fscanf(file, "%d", &nt) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the number of components
- if (fscanf(file, "%d", &nc) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // get the number of data
- if (fscanf(file, "%lu", &nd) != 1)
- throw std::runtime_error("tbox::GmshImport::readResHeader error reading file!\n");
- // skip the number of partition, if given
- if (ninttags == 4)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResHeader end-of-file reached before all lines could be read!\n");
-}
-
-/**
- * @brief Read results at nodes
- */
-void GmshImport::readResNodes(FILE *file, char *line, std::map<int, size_t> &nimap, Results &r, int n)
-{
- // Read header
- char vname[128]; // name of view (variable to be read)
- int nc = 0, nt = 0; // number of components and time step index
- unsigned long nd = 0; // number of data points
- double time = 0.; // current time
- this->readResHeader(file, line, vname, nd, nc, nt, time);
-
- // Perform checks and read
- // check the number of nodes
- if (nd != static_cast<unsigned long>(msh->nodes.size()))
- throw std::runtime_error("tbox::GmshImport::readResNodes the number of data to be read does not match the number of nodes in the mesh!\n");
- // check if the view name matches a variable, and if the time step index matches the requested time step
- if (nc == 1)
- {
- auto resm = r.scalars_at_nodes;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading node data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da = 0.;
- if (fscanf(file, "%d %lg", &no, &da) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResNodes error reading file!\n");
- resm.at(vname)->at(nimap[no]) = da;
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping node data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else if (nc == 3)
- {
- auto resm = r.vectors_at_nodes;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading node data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da0 = 0., da1 = 0., da2 = 0.;
- if (fscanf(file, "%d %lg %lg %lg", &no, &da0, &da1, &da2) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResNodes error reading file!\n");
- resm.at(vname)->at(nimap[no]) = Eigen::Vector3d(da0, da1, da2);
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping node data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else if (nc == 9)
- {
- auto resm = r.tensors_at_nodes;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading node data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da0 = 0., da1 = 0., da2 = 0., da3 = 0., da4 = 0., da5 = 0., da6 = 0., da7 = 0., da8 = 0.;
- if (fscanf(file, "%d %lg %lg %lg %lg %lg %lg %lg %lg %lg", &no, &da0, &da1, &da2, &da3, &da4, &da5, &da6, &da7, &da8) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResNodes error reading file!\n");
- resm.at(vname)->at(nimap[no]) << da0, da1, da2, da3, da4, da5, da6, da7, da8;
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping node data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else
- throw std::runtime_error("tbox::GmshImport::readResNodes the number of components must be 1, 3, or 9!\n");
-}
-
-/**
- * @brief Read results at elements
- */
-void GmshImport::readResElements(FILE *file, char *line, std::map<int, size_t> &eimap, Results &r, int n)
-{
- // Read header
- char vname[128]; // name of view (variable to be read)
- int nc = 0, nt = 0; // number of components and time step index
- unsigned long nd = 0; // number of data points
- double time = 0.; // current time
- this->readResHeader(file, line, vname, nd, nc, nt, time);
-
- // Perform checks and read
- // check the number of elements
- if (nd != static_cast<unsigned long>(msh->elems.size()))
- throw std::runtime_error("tbox::GmshImport::readResElements the number of data to be read does not match the number of elements in the mesh!\n");
- // check if the view name matches a variable, and if the time step index matches the requested time step
- if (nc == 1)
- {
- auto resm = r.scalars_at_elems;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading element data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da = 0.;
- if (fscanf(file, "%d %lg", &no, &da) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResElements error reading file!\n");
- resm.at(vname)->at(eimap[no]) = da;
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping element data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else if (nc == 3)
- {
- auto resm = r.vectors_at_elems;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading element data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da0 = 0., da1 = 0., da2 = 0.;
- if (fscanf(file, "%d %lg %lg %lg", &no, &da0, &da1, &da2) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResElements error reading file!\n");
- resm.at(vname)->at(eimap[no]) = Eigen::Vector3d(da0, da1, da2);
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping element data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else if (nc == 9)
- {
- auto resm = r.tensors_at_elems;
- // set time and read data
- if (resm.find(vname) != resm.end() && nt == n)
- {
- std::cout << "\treading element data \"" << vname << "\" at time step #" << nt << std::endl;
- r.nt = nt;
- r.time = time;
- for (unsigned long i = 0; i < nd; ++i)
- {
- int no = 0;
- double da0 = 0., da1 = 0., da2 = 0., da3 = 0., da4 = 0., da5 = 0., da6 = 0., da7 = 0., da8 = 0.;
- if (fscanf(file, "%d %lg %lg %lg %lg %lg %lg %lg %lg %lg", &no, &da0, &da1, &da2, &da3, &da4, &da5, &da6, &da7, &da8) != nc + 1)
- throw std::runtime_error("tbox::GmshImport::readResElements error reading file!\n");
- resm.at(vname)->at(eimap[no]) << da0, da1, da2, da3, da4, da5, da6, da7, da8;
- }
- }
- // skip
- else
- {
- std::cout << "\tskipping element data \"" << vname << "\" at time step #" << nt << std::endl;
- for (unsigned long i = 0; i < nd; ++i)
- if (fgets(line, sizeof line, file) == NULL)
- throw std::runtime_error("tbox::GmshImport::readResNodes end-of-file reached before all data could be read!\n");
- }
- }
- else
- throw std::runtime_error("tbox::GmshImport::readResElements the number of components must be 1, 3, or 9!\n");
-}
-
-void GmshImport::write(std::ostream &out) const
-{
- out << "GmshImport on " << *msh << std::endl;
-}
diff --git a/tbox/src/wGmshImport.h b/tbox/src/wGmshImport.h
deleted file mode 100644
index 6afac564..00000000
--- a/tbox/src/wGmshImport.h
+++ /dev/null
@@ -1,62 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGMSHIMPORT_H
-#define WGMSHIMPORT_H
-
-#include "tbox.h"
-#include "wMshImport.h"
-#include <vector>
-#include <map>
-
-namespace tbox
-{
-
-/**
- * @brief Read and load gmsh mesh
- * @authors Adrien Crovato, Romain Boman
- * @todo only ASCII files are suported, extend to binary?
- * @todo upgrade to mesh format 4
- */
-class TBOX_API GmshImport : public MshImport
-{
- std::map<int, Node *> nodemap; ///< Map between node and its id number
-
- int searchCode(char const *code, char const *line) const;
- void readMshFormat(FILE *file);
- void readMshNodes(FILE *file);
- void readMshElements(FILE *file, int myrank);
- void readMshPhyNames(FILE *file);
- void readElNods(FILE *file, int n, std::vector<Node *> &nods);
- Tag *addTag(FILE *file, std::map<int, Tag *> &tmap);
-
- void readResHeader(FILE *file, char *line, char *vname, unsigned long &nd, int &nc, int &nt, double &time);
- void readResNodes(FILE *file, char *line, std::map<int, size_t> &nimap, Results &r, int n);
- void readResElements(FILE *file, char *line, std::map<int, size_t> &eimap, Results &r, int n);
-
-public:
- GmshImport(std::shared_ptr<MshData> _msh);
- virtual ~GmshImport();
-
- virtual void load(std::string const &fname, int myrank) override;
- virtual void load(std::string const &fname, Results &r, int n = 0) override;
-
- virtual void write(std::ostream &out) const override;
-};
-
-} // namespace tbox
-
-#endif //WGMSHIMPORT_H
diff --git a/tbox/src/wGroup.cpp b/tbox/src/wGroup.cpp
deleted file mode 100644
index c26634fd..00000000
--- a/tbox/src/wGroup.cpp
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGroup.h"
-#include "wMshData.h"
-#include <sstream>
-#include <stdexcept>
-#include <iterator>
-
-using namespace tbox;
-
-Group::Group(std::shared_ptr<MshData> _msh, int no) : wSharedObject(), msh(_msh), tag(NULL)
-{
- auto it = msh->ptags.find(no);
- if (it == msh->ptags.end())
- {
- std::stringstream out;
- out << "Physical Group #" << no << " not found among physical tags";
- throw std::out_of_range(out.str());
- }
- tag = it->second;
-}
-
-Group::Group(std::shared_ptr<MshData> _msh, std::string const &name) : wSharedObject(), msh(_msh)
-{
- auto it = msh->ntags.find(name);
- if (it == msh->ntags.end())
- {
- std::stringstream out;
- out << "Physical Group \"" << name << "\" not found among physical tags\n";
- out << "[info] available tags:\n\t";
- for (auto it = msh->ntags.begin(); it != msh->ntags.end(); ++it)
- {
- auto itn(it);
- ++itn;
- out << (it->first) << ((itn != msh->ntags.end()) ? ", " : "\n\n");
- //out << (it->first) << ((std::next(it)!=msh->ntags.end())? ", " : "\n\n");
- }
- throw std::out_of_range(out.str());
- }
- tag = it->second;
-}
diff --git a/tbox/src/wGroup.h b/tbox/src/wGroup.h
deleted file mode 100644
index fd3e155d..00000000
--- a/tbox/src/wGroup.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGROUP_H
-#define WGROUP_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <string>
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Group handling a set of elements
- * @authors Romain Boman
- */
-class TBOX_API Group : public fwk::wSharedObject
-{
-public:
-#ifndef SWIG
- std::shared_ptr<MshData> msh;
-#endif
- Tag *tag;
-
- Group(std::shared_ptr<MshData> _msh, int no);
- Group(std::shared_ptr<MshData> _msh, std::string const &name);
-};
-
-} // namespace tbox
-
-#endif //WGROUP_H
diff --git a/tbox/src/wGroups.cpp b/tbox/src/wGroups.cpp
deleted file mode 100644
index 217ac020..00000000
--- a/tbox/src/wGroups.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wGroups.h"
-#include "wGroup.h"
-#include "wMshData.h"
-#include <sstream>
-#include <stdexcept>
-#include <iterator>
-
-using namespace tbox;
-
-Groups::Groups(std::shared_ptr<MshData> _msh, std::vector<int> const &nos) : wSharedObject(), msh(_msh)
-{
- // Sanity check
- if (nos.size() < 2)
- {
- std::stringstream err;
- err << "Groups should be built with at least 2 physical groups but " << nos.size() << " were given!";
- throw std::runtime_error(err.str());
- }
- // Fill Groups
- for (auto no : nos)
- {
- Group *g = new Group(msh, no);
- groups.push_back(g);
- }
-}
-Groups::Groups(std::shared_ptr<MshData> _msh, std::vector<std::string> const &names)
- : wSharedObject(), msh(_msh)
-{
- // Sanity check
- if (names.size() < 2)
- {
- std::stringstream err;
- err << "Groups should be built with at least 2 physical groups but " << names.size() << " were given!";
- throw std::runtime_error(err.str());
- }
- // Fill Groups
- for (auto name : names)
- {
- Group *g = new Group(msh, name);
- groups.push_back(g);
- }
-}
-Groups::~Groups()
-{
- for (auto g : groups)
- delete g;
-}
\ No newline at end of file
diff --git a/tbox/src/wGroups.h b/tbox/src/wGroups.h
deleted file mode 100644
index 895fabc4..00000000
--- a/tbox/src/wGroups.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WGROUPS_H
-#define WGROUPS_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <string>
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Handle group of several physical regions (tag)
- * @authors Adrien Crovato
- */
-class TBOX_API Groups : public fwk::wSharedObject
-{
-public:
-#ifndef SWIG
- std::shared_ptr<MshData> msh;
-#endif
- std::vector<Group *> groups;
-
- Groups(std::shared_ptr<MshData> _msh, std::vector<int> const &nos);
- Groups(std::shared_ptr<MshData> _msh, std::vector<std::string> const &names);
- ~Groups();
-};
-
-} // namespace tbox
-
-#endif //WGROUPS_H
diff --git a/tbox/src/wHex8.cpp b/tbox/src/wHex8.cpp
deleted file mode 100644
index 606ce106..00000000
--- a/tbox/src/wHex8.cpp
+++ /dev/null
@@ -1,132 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wHex8.h"
-#include "wSfHex8.h"
-#include "wGaussHex8.h"
-#include "wCacheHex8.h"
-#include "wNode.h"
-
-using namespace tbox;
-
-Hex8::Hex8(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-/**
- * @brief Return cache handling shape functions and Gauss points for all Hex8 elements
- */
-Cache &Hex8::getVCache() const
-{
- return getCache(order);
-}
-
-/**
- * @brief Initialize precomputed values
- */
-void Hex8::initValues(bool isvol, int ordr)
-{
- // Set flags
- isVol = isvol;
- order = ordr;
- hasVals = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- Js.resize(ngp);
- iJs.resize(ngp);
- detJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Initialize precomputed gradients
- */
-void Hex8::initGradients()
-{
- // Set flags
- hasGrads = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- gradJs.resize(ngp);
- gradDetJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Update Hex8 precomputed values and gradients
- */
-void Hex8::update()
-{
- // Update values
- if (hasVals)
- {
- // Jacobian
- if (!isVol)
- throw std::runtime_error("Hex8::update(): the problem must always have the same dimension as Hex8!\n");
- // Hex8 is always of same dimension as Problem (volume element)
- this->buildJ();
- // Volume and CG
- this->computeV();
- this->computeCg();
- }
- // Update gradients
- if (hasGrads)
- {
- // Jacobian
- if (!isVol)
- throw std::runtime_error("Hex8::updateGradients(): the problem must always have the same dimension as Hex8!\n");
- // Hex8 is always of same dimension as Problem (volume element)
- this->buildGradientJ();
- // Volume
- this->buildGradientV(3);
- }
-}
-
-/**
- * @brief Compute Jacobian matrix, inverse and determinant
- *
- * J_ij(3,3) = diN_n * xj_n (n is the node)
- */
-void Hex8::buildJ()
-{
- CacheHex8 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dff = cache.getDsf(k);
-
- Eigen::Matrix3d JJ = Eigen::Matrix3d::Zero(); // temporary fixed-size matrix to efficiently compute the inverse
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- JJ += dff.col(i) * (*it)->pos.transpose();
- Js[k] = JJ;
- iJs[k] = JJ.inverse();
- detJs[k] = JJ.determinant();
- this->checkJac(k);
- }
-}
-
-/**
- * @brief Compute the element volume
- */
-void Hex8::computeV()
-{
- CacheHex8 &cache = getCache(order);
- GaussHex8 &gauss = cache.gauss;
-
- // Gauss integration
- vol = 0.0;
- for (size_t k = 0; k < gauss.getN(); ++k)
- vol += gauss.getW(k) * this->getDetJ(k);
-}
diff --git a/tbox/src/wHex8.h b/tbox/src/wHex8.h
deleted file mode 100644
index 391b73dc..00000000
--- a/tbox/src/wHex8.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WHEX8_H
-#define WHEX8_H
-
-#include "tbox.h"
-#include "wLazy.h"
-#include "wElement.h"
-#include "wCacheHex8.h"
-
-namespace tbox
-{
-
-/**
- * @brief Linear hexaedron finite element
- * @authors Kim Liegeois, Romain Boman, Adrien Crovato
- */
-class TBOX_API Hex8 : public Element
-{
-#ifndef SWIG
-private:
- inline static CacheHex8 &getCache(int n);
-
-protected:
- virtual void buildJ() override;
- virtual void computeV() override;
-#endif
-
-public:
- Hex8(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Hex8() {}
- virtual ELTYPE type() const override { return ELTYPE::HEX8; }
-
-#ifndef SWIG
- virtual void initValues(bool isvol, int ordr = 2) override;
- virtual void initGradients() override;
- virtual void update() override;
- virtual Cache &getVCache() const override;
-#endif
-};
-
-#include "wHex8.inl"
-
-} // namespace tbox
-
-#endif //WHEX8_H
diff --git a/tbox/src/wHex8.inl b/tbox/src/wHex8.inl
deleted file mode 100644
index a2c43adf..00000000
--- a/tbox/src/wHex8.inl
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return cache for Hex8 private methods
- */
-inline CacheHex8 &Hex8::getCache(int n)
-{
- static Lazy<CacheHex8> cache(n);
- return cache.get();
-}
diff --git a/tbox/src/wLazy.h b/tbox/src/wLazy.h
deleted file mode 100644
index 3d8e7970..00000000
--- a/tbox/src/wLazy.h
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WLAZY_H
-#define WLAZY_H
-
-#include "tbox.h"
-
-#include <mutex>
-#include <atomic>
-
-namespace tbox
-{
-
-/**
- * @brief TBB implementation of a "lazy initialization"
- * (thread safe allocation of a shared pointer)
- */
-
-template <typename T>
-class Lazy
-{
- std::atomic<T *> value;
- std::mutex mut;
- int np;
-
-public:
- Lazy(int _np) : value(), np(_np) {}
- ~Lazy()
- {
- delete value;
- //std::cout << "lazy pointer deleted\n";
- }
- T &get()
- {
- if (!value)
- {
- std::unique_lock<std::mutex> lock(mut);
- if (!value)
- value = new T(np);
- }
- return *value;
- }
-};
-
-} // namespace tbox
-
-#endif //WLAZY_H
diff --git a/tbox/src/wLine2.cpp b/tbox/src/wLine2.cpp
deleted file mode 100644
index b28d1316..00000000
--- a/tbox/src/wLine2.cpp
+++ /dev/null
@@ -1,223 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wLine2.h"
-#include "wSfLine2.h"
-#include "wGaussLine2.h"
-#include "wCacheLine2.h"
-#include "wNode.h"
-
-using namespace tbox;
-
-Line2::Line2(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-/**
- * @brief Return cache holding shape functions and Gauss points for all Line2 elements
- */
-Cache &Line2::getVCache() const
-{
- return getCache(order);
-}
-
-/**
- * @brief Initialize precomputed values
- */
-void Line2::initValues(bool isvol, int ordr)
-{
- // Set flags
- isVol = isvol;
- order = ordr;
- hasVals = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- Js.resize(ngp);
- iJs.resize(ngp);
- detJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Initialize precomputed gradients
- */
-void Line2::initGradients()
-{
- // Set flags
- hasGrads = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- gradJs.resize(ngp);
- gradDetJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Update precomputed values and gradients
- */
-void Line2::update()
-{
- // Update values
- if (hasVals)
- {
- // Jacobian
- if (isVol)
- throw std::runtime_error("Line2::update(): the problem must always have a dimension less than Line2!\n");
- // Line2 is never of same dimension as Problem (surface element)
- this->buildSurfaceJ();
- // Length and CG
- this->computeV();
- this->computeCg();
- // Normal
- this->computeNormal();
- }
- // Update gradients
- if (hasGrads)
- {
- // Jacobian
- if (isVol)
- throw std::runtime_error("Line2::updateGradient(): the problem must always have a dimension less than Line2!\n");
- // Line2 is never of same dimension as Problem (surface element)
- this->buildGradientSurfaceJ();
- // Length
- this->buildGradientV(2);
- // Normal
- this->computeGradientNormal();
- }
-}
-
-/**
- * @brief Compute Jacobian determinant
- *
- * detJ = norm(x_i * dN_i)
- */
-void Line2::buildSurfaceJ()
-{
- for (size_t k = 0; k < getCache(order).getVGauss().getN(); ++k)
- detJs[k] = this->buildTangents(k)[0].norm();
-}
-
-/**
- * @brief Compute Jacobian determinant gradient with respect to each node coordinate
- *
- * dDetJ[l = i * 2 + j] = detJ_l * dt0_l;
- */
-void Line2::buildGradientSurfaceJ()
-{
- CacheLine2 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- // Shape functions, tangent vectors and determinant
- Eigen::MatrixXd const &dsf = getCache(order).getDsf(k);
- Eigen::Vector3d detJ = this->buildTangents(k)[0].normalized();
-
- // Jacobian gradient
- gradDetJs[k].resize(2 * 2); // 2 nodes and 2 dimensions (x, y)
- for (size_t i = 0; i < 2; ++i)
- {
- for (size_t j = 0; j < 2; ++j)
- {
- Eigen::Vector3d dt0 = Eigen::Vector3d::Zero();
- dt0(j) = dsf(0, i); // retain sf gradients associated to ith node for dimension j
- gradDetJs[k][i * 2 + j] = detJ.dot(dt0);
- }
- }
- }
-}
-
-/**
- * @brief Compute the element length
- */
-void Line2::computeV()
-{
- CacheLine2 &cache = getCache(order);
- GaussLine2 &gauss = cache.gauss;
-
- // Gauss integration
- vol = 0.0;
- for (size_t k = 0; k < gauss.getN(); ++k)
- vol += gauss.getW(k) * this->getDetJ(k);
-}
-/**
- * @brief Compute length gradient with respect to each node coordinate
- *
- * dV[i] = w_k * dDetJ[i]_k
- */
-void Line2::buildGradientV(int dim)
-{
- GaussLine2 &gauss = getCache(order).gauss;
-
- // Gradient of volume
- gradVol.resize(2 * dim, 0.); // 2 nodes
- for (size_t k = 0; k < gauss.getN(); ++k)
- {
- double w = gauss.getW(k); // GP weight
- std::vector<double> dDetJ = this->getGradDetJ(k); // gradient of Jacobian determinant
- for (size_t i = 0; i < dDetJ.size(); ++i)
- gradVol[i] += w * dDetJ[i];
- }
-}
-
-/**
- * @brief Compute element tangent vectors
- */
-std::vector<Eigen::Vector3d> Line2::computeTangents() const
-{
- return std::vector<Eigen::Vector3d>{nodes[1]->pos - nodes[0]->pos};
-}
-
-/**
- * @brief Build element tangent vectors using shape functions at Gauss point k
- */
-std::vector<Eigen::Vector3d> Line2::buildTangents(size_t k) const
-{
- Eigen::MatrixXd const &dff = getCache(order).getDsf(k);
-
- std::vector<Eigen::Vector3d> t(1, Eigen::Vector3d::Zero());
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- {
- t[0] += (*it)->pos * dff(0, i);
- }
- return t;
-}
-
-/**
- * @brief Compute element unit normal vector
- */
-void Line2::computeNormal()
-{
- Eigen::Vector3d t = this->computeTangents()[0].normalized();
- normal = Eigen::Vector3d(-t(1), t(0), 0.);
-}
-
-/**
- * @brief Compute gradient of element unit normal vector with respect to each node coordinate
- */
-void Line2::computeGradientNormal()
-{
- // Compute normal and norm
- Eigen::Vector3d t = this->computeTangents()[0];
- Eigen::Vector3d n = Eigen::Vector3d(-t(1), t(0), 0.);
- double nn = n.norm();
-
- // Compute gradients
- Eigen::Matrix3d inn = (Eigen::Matrix3d::Identity() - n * n.transpose() / (nn * nn)) / nn; // gradient of n/|n|
- gradNormal.resize(2 * 2); // 2 nodes and 2 dimensions
- gradNormal[0] = inn * Eigen::Vector3d(0, -1, 0);
- gradNormal[1] = inn * Eigen::Vector3d(1, 0, 0);
- gradNormal[2] = inn * Eigen::Vector3d(0, 1, 0);
- gradNormal[3] = inn * Eigen::Vector3d(-1, 0, 0); // outer gradient times gradient of t (pos) wtr x
-}
diff --git a/tbox/src/wLine2.h b/tbox/src/wLine2.h
deleted file mode 100644
index 6b076608..00000000
--- a/tbox/src/wLine2.h
+++ /dev/null
@@ -1,66 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WLINE2_H
-#define WLINE2_H
-
-#include "tbox.h"
-#include "wLazy.h"
-#include "wElement.h"
-#include "wCacheLine2.h"
-
-namespace tbox
-{
-
-/**
- * @brief Linear line finite element
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API Line2 : public Element
-{
-#ifndef SWIG
-private:
- inline static CacheLine2 &getCache(int n);
-
-protected:
- virtual void buildSurfaceJ() override;
- virtual void buildGradientSurfaceJ() override;
- virtual void computeV() override;
- virtual void buildGradientV(int dim) override;
- virtual void computeNormal() override;
- virtual void computeGradientNormal() override;
- virtual std::vector<Eigen::Vector3d> computeTangents() const override;
- virtual std::vector<Eigen::Vector3d> buildTangents(size_t k) const override;
-#endif
-
-public:
- Line2(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Line2() {}
- virtual ELTYPE type() const override { return ELTYPE::LINE2; }
-
-#ifndef SWIG
- virtual void initValues(bool isvol, int ordr = 2) override;
- virtual void initGradients() override;
- virtual void update() override;
- virtual Cache &getVCache() const override;
-#endif
-};
-
-#include "wLine2.inl"
-
-} // namespace tbox
-
-#endif //WLINE2_H
diff --git a/tbox/src/wLine2.inl b/tbox/src/wLine2.inl
deleted file mode 100644
index 5dc09184..00000000
--- a/tbox/src/wLine2.inl
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return cache for Line2 private methods
- */
-inline CacheLine2 &Line2::getCache(int n)
-{
- static Lazy<CacheLine2> cache(n);
- return cache.get();
-}
diff --git a/tbox/src/wLinearSolver.cpp b/tbox/src/wLinearSolver.cpp
deleted file mode 100644
index c483c62b..00000000
--- a/tbox/src/wLinearSolver.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wLinearSolver.h"
-using namespace tbox;
-
-/**
- * @brief Analyze the matrix pattern
- */
-void LinearSolver::analyze(Eigen::SparseMatrix<double> const &A)
-{
- throw std::runtime_error("tbox::LinearSolver::analyze not implemented!\n");
-}
-/**
- * @brief Farctorize the matrix
- */
-void LinearSolver::factorize(Eigen::SparseMatrix<double> const &A)
-{
- throw std::runtime_error("tbox::LinearSolver::factorize not implemented!\n");
-}
-/**
- * @brief Solve the set of equations
- */
-void LinearSolver::solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- throw std::runtime_error("tbox::LinearSolver::solve not implemented!\n");
-}
-/**
- * @brief Analyze the matrix pattern, factorize it, and solve the set of equations
- */
-void LinearSolver::compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- throw std::runtime_error("tbox::LinearSolver::compute not implemented!\n");
-}
-/**
- * @brief Get the error norm(Ax - b)
- */
-double LinearSolver::getError()
-{
- throw std::runtime_error("tbox::LinearSolver::getError not implemented!\n");
-}
-/**
- * @brief Get the number of iterations required for solving the set of equations
- */
-int LinearSolver::getIterations()
-{
- throw std::runtime_error("tbox::LinearSolver::getIterations not implemented!\n");
-}
\ No newline at end of file
diff --git a/tbox/src/wLinearSolver.h b/tbox/src/wLinearSolver.h
deleted file mode 100644
index 3e93813a..00000000
--- a/tbox/src/wLinearSolver.h
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WLINEARSOLVER_H
-#define WLINEARSOLVER_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <Eigen/Sparse>
-
-namespace tbox
-{
-
-/**
- * @brief Base interface class for linear solvers
- * @authors Adrien Crovato
- */
-class TBOX_API LinearSolver : public fwk::wSharedObject
-{
-public:
- LinearSolver() {}
- virtual ~LinearSolver() {}
-
-#ifndef SWIG
- virtual void analyze(Eigen::SparseMatrix<double> const &A);
- virtual void factorize(Eigen::SparseMatrix<double> const &A);
- virtual void solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x);
- virtual void compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x);
-
- virtual double getError();
- virtual int getIterations();
-#endif
-};
-
-} // namespace tbox
-
-#endif // WLINEARSOLVER_H
\ No newline at end of file
diff --git a/tbox/src/wLinesearch.cpp b/tbox/src/wLinesearch.cpp
deleted file mode 100644
index 3bf8e330..00000000
--- a/tbox/src/wLinesearch.cpp
+++ /dev/null
@@ -1,397 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wLinesearch.h"
-#include <sstream>
-#include <iomanip>
-#include <cmath>
-#include <stdexcept>
-
-using namespace tbox;
-
-LSFunction::LSFunction() : wObject()
-{
-}
-
-double LSFunction::eval(double alpha)
-{
- return 0.0;
-}
-
-RevFunction::RevFunction(LSFunction &_f) : LSFunction(), f(_f)
-{
-}
-
-double RevFunction::eval(double alpha)
-{
- return f.eval(-alpha);
-}
-
-// ---
-
-Linesearch::Linesearch(LSFunction &_fct) : fct(_fct)
-{
- verbose = 0;
- maxLsIt = 1000;
- tol = 1e-10;
- fevalIt = 0;
-}
-
-/**
- * @brief Set control parameters
- */
-void Linesearch::set(int _maxLSIt, double _lSTol, bool _verbose)
-{
- verbose = _verbose;
- maxLsIt = _maxLSIt;
- tol = _lSTol;
-}
-
-double Linesearch::run()
-{
- throw std::runtime_error("Linesearch::run() not implemented!\n");
-}
-
-// ---
-
-BacktrackLS::BacktrackLS(LSFunction &_fct) : Linesearch(_fct)
-{
-}
-
-/**
- * @brief Backtracking linesearch
- */
-double BacktrackLS::run()
-{
- double a = 1;
- double phi0 = fct.eval(0.);
- fevalIt = 1;
- do
- {
- double phi = fct.eval(a);
- fevalIt++;
- if (phi > phi0)
- a /= 2;
- else
- break;
- } while (fevalIt < maxLsIt);
- return a;
-}
-
-// ---
-
-FleuryLS::FleuryLS(LSFunction &_fct, double _h0, double _hL, bool _revAllowed) : Linesearch(_fct), h0(_h0), hL(_hL), revAllowed(_revAllowed)
-{
- hU = 10.0;
- hS = h0 / 10.0;
- brckIt = 0;
- lsIt = 0;
-}
-
-/**
- * @brief Execute 3-points quadratic linesearch
- */
-double FleuryLS::run()
-{
- double h = h0;
- double phi1 = fct.eval(0);
- double phit = fct.eval(h);
- fevalIt = 2;
-
- if (verbose > 2)
- {
- std::cout << "Starting Backeting \n";
- std::cout << "\t" << std::setprecision(16) << "phi1(" << 0 << ") = " << phi1 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phit(" << h << ") = " << phit << '\n';
- }
-
- // Following is valid if Hessian matrix is positive definite
- // -> derivative is negative at 0.
- double phi2 = 0.0, phi3;
- size_t nB;
- if (phit < phi1)
- {
- for (nB = 0;; ++nB)
- {
- if (h > hU)
- {
- if (verbose > 2)
- {
- std::cout << "Positive slope detected (in ascending bracketing #1)!\n";
- }
-
- if (revAllowed)
- {
- if (verbose > 2)
- {
- std::cout << "Reverse Direction of Line Search (in ascending bracketing #1)!"
- << "\n";
- }
- RevFunction revfct(fct);
- FleuryLS revsearch(revfct, h0, hL, false);
- return revsearch.run();
- }
- else
- {
- if (verbose > 2)
- {
- std::cout << "Error in ascending bracketing #1:\n"
- << std::setprecision(16) << "a1=" << 0 << " a2=" << h << " a3 =" << 2.0 * h << '\n'
- << std::setprecision(16) << "phi1=" << phi1 << " phi2=" << phi2 << " phit=" << phit << '\n'
- << "Using default step:\n"
- << std::setprecision(16) << "a=" << hS << "\n";
- }
- fct.eval(hS);
- fevalIt++;
- brckIt = nB + 1;
- return hS;
- }
- }
- phi2 = phit;
- phit = fct.eval(2 * h);
- fevalIt++;
-
- if (verbose > 2)
- {
- std::cout << "Ascending bracketing iteration # " << nB << ": \n";
- std::cout << "\t"
- << "a1=" << 0 << " a2=" << h << " a3 =" << 2.0 * h << '\n';
- std::cout << "\t"
- << "phi1=" << phi1 << " phi2=" << phi2 << " phit=" << phit << '\n';
- }
-
- if (phit > phi2)
- break;
- h = 2 * h;
- }
- phi3 = phit;
- }
- else
- {
- for (nB = 0;; ++nB)
- {
- if (h < hL)
- {
- if (verbose > 2)
- {
- std::cout << "Positive slope detected (in descending bracketing #2)!\n";
- }
-
- if (revAllowed)
- {
- if (verbose > 2)
- {
- std::cout << "Reverse Direction of Line Search (in descending bracketing #2) !"
- << "\n";
- }
- RevFunction revfct(fct);
- FleuryLS revsearch(revfct, h0, hL, false);
- return revsearch.run();
- }
- else
- {
- if (verbose > 2)
- {
- std::cout << "Error in descending bracketing #2:\n"
- << std::setprecision(16) << "a1=" << 0 << " a2=" << h << " a3 =" << 2.0 * h << '\n'
- << std::setprecision(16) << "phi1=" << phi1 << " phi2=" << phi2 << " phit=" << phit << '\n'
- << "Using default step:\n"
- << std::setprecision(16) << "a=" << hS << "\n";
- }
- fct.eval(hS);
- fevalIt++;
- brckIt = nB + 1;
- return hS;
- }
- }
- phi3 = phit;
- phit = fct.eval(h / 2);
- fevalIt++;
- if (verbose > 2)
- {
- std::cout << "Descending bracketing iteration # " << nB << ": \n";
- std::cout << "\t"
- << "a1=" << 0 << " a3=" << h << " a2 =" << h / 2.0 << '\n';
- std::cout << "\t"
- << "phi1=" << phi1 << " phi3=" << phi3 << " phit=" << phit << '\n';
- }
- if (phit < phi1)
- break;
- h = h / 2;
- }
- phi2 = phit;
- h = h / 2;
- }
-
- double a1 = 0;
- double a2 = h;
- double a3 = 2 * h;
- double a4 = h * (4 * phi2 - 3 * phi1 - phi3) / (4 * phi2 - 2 * phi1 - 2 * phi3);
-
- if (verbose > 2)
- {
- std::cout << "Backeting succeeds in " << nB << " iterations : \n";
- std::cout << "\t" << std::setprecision(16) << "phi1(" << a1 << ") = " << phi1 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi2(" << a2 << ") = " << phi2 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi3(" << a3 << ") = " << phi3 << '\n';
- }
-
- double phi4;
- double aa = 0.0;
- size_t nLS = 0;
- double A = 0.;
- double errorPhi;
- double errorAlpha;
-
- for (nLS = 0;; ++nLS)
- {
- phi4 = fct.eval(a4);
- fevalIt++;
-
- errorAlpha = fabs(a4 - a2);
- errorPhi = fabs(phi4 - phi2);
-
- if (nLS == maxLsIt)
- {
- brckIt = nB + 1;
- lsIt = nLS;
- std::stringstream msg;
- msg << "Line-search doesn't converge within prescribed tolerance :\n";
- msg << "a1=" << std::setprecision(16) << a1 << " a2=" << a2 << " a3=" << a3 << " a4=" << a4 << '\n';
- msg << "phi1=" << std::setprecision(16) << phi1 << " phi2=" << phi2 << " phi3=" << phi3 << " phi4=" << phi4 << '\n';
- msg << "|A| = " << std::setprecision(16) << fabs(A) << ", |phi2-phi4| = " << errorPhi << " and |a2-a4| = " << errorAlpha << '\n';
- throw std::runtime_error(msg.str());
- }
-
- if (verbose > 2)
- {
- std::cout << "Line search iteration # " << nLS << ": \n";
- std::cout << "\t" << std::setprecision(16) << "phi1(" << a1 << ") = " << phi1 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi2(" << a2 << ") = " << phi2 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi3(" << a3 << ") = " << phi3 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi4(" << a4 << ") = " << phi4 << '\n';
- std::cout << "\t" << std::setprecision(16) << "|phi2-phi4| = " << errorPhi << " and |a2-a4| = " << errorAlpha << '\n';
- }
-
- if (a1 <= a4 && a4 <= a2)
- {
- if (phi1 >= phi4 && phi4 <= phi2)
- {
- a3 = a2;
- phi3 = phi2;
- a2 = a4;
- phi2 = phi4;
- }
- else
- {
- a1 = a4;
- phi1 = phi4;
- }
- }
- else
- {
- if (phi2 >= phi4 && phi4 <= phi3)
- {
- a1 = a2;
- phi1 = phi2;
- a2 = a4;
- phi2 = phi4;
- }
- else
- {
- a3 = a4;
- phi3 = phi4;
- }
- }
-
- A = (a2 - a3) * phi1 + (a3 - a1) * phi2 + (a1 - a2) * phi3;
-
- if (verbose > 2)
- {
- std::cout << "\t" << std::setprecision(16) << "|A| = " << fabs(A) << "><" << tol << '\n';
- }
- // phi2 ~ phi4 and a2 ~ a4 -> algorithm converges
- if (fabs(A) <= tol)
- {
- if (phi4 < phi2)
- aa = a4;
- else
- aa = a2;
- break;
- }
-
- a4 = 0.5 * (((a2 * a2) - (a3 * a3)) * phi1 + ((a3 * a3) - (a1 * a1)) * phi2 + ((a1 * a1) - (a2 * a2)) * phi3) /
- (A);
- }
-
- if (verbose > 2)
- {
- std::cout << "Line search succeeds in " << nLS << " iterations : \n";
- std::cout << "\t" << std::setprecision(16) << "|A| = " << fabs(A) << '\n';
- std::cout << "\t" << std::setprecision(16) << "|phi4-phi2| = " << errorPhi << '\n';
- std::cout << "\t" << std::setprecision(16) << "|a4-a2| = " << errorAlpha << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi1(" << a1 << ") = " << phi1 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi2(" << a2 << ") = " << phi2 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi3(" << a3 << ") = " << phi3 << '\n';
- std::cout << "\t" << std::setprecision(16) << "phi4(" << a4 << ") = " << phi4 << '\n';
- }
- brckIt = nB + 1;
- lsIt = nLS;
- return aa;
-}
-
-// ---
-
-BankRoseLS::BankRoseLS(LSFunction &_fct) : Linesearch(_fct)
-{
- K = 0.;
-}
-
-/**
- * @brief Execute Bank & Rose linesearch
- */
-double BankRoseLS::run()
-{
- double phi0 = fct.eval(0);
- fevalIt = 1;
- while (1)
- {
- double t = 1 / (1 + K * phi0);
- double phi = fct.eval(t);
- fevalIt++;
- if (1 / t * (1 - phi / phi0) > tol)
- {
- K /= 10;
- return t;
- }
- else if (fevalIt == maxLsIt)
- {
- std::stringstream msg;
- msg << "Line-search doesn't converge within prescribed tolerance:\n";
- msg << "iter = " << std::setprecision(16) << fevalIt << '\n';
- msg << "K = " << std::setprecision(16) << K << ", t = " << t << '\n';
- msg << "phi/phi0 = " << std::setprecision(16) << phi / phi0 << std::endl;
- throw std::runtime_error(msg.str());
- }
- else
- {
- if (K == 0.)
- K = 1;
- else
- K *= 10;
- }
- }
-}
\ No newline at end of file
diff --git a/tbox/src/wLinesearch.h b/tbox/src/wLinesearch.h
deleted file mode 100644
index 729fc26f..00000000
--- a/tbox/src/wLinesearch.h
+++ /dev/null
@@ -1,127 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WLINESEARCH_H
-#define WLINESEARCH_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <iostream>
-
-#ifndef SWIG
-
-namespace tbox
-{
-
-/**
- * @brief Linesearch function
- * @authors Romain Boman
- */
-class TBOX_API LSFunction : public fwk::wObject
-{
-public:
- LSFunction();
- virtual double eval(double alpha);
-};
-
-class TBOX_API RevFunction : public LSFunction
-{
- LSFunction &f;
-
-public:
- RevFunction(LSFunction &_f);
- virtual double eval(double alpha) override;
-};
-
-/**
- * @brief Linesearch base class
- * @authors Adrien Crovato
- */
-class TBOX_API Linesearch
-{
-protected:
- LSFunction &fct; ///< function
- size_t maxLsIt; ///< max. number of iterations for linesearch
- double tol; ///< tolerance for linesearch
- int verbose; ///< display more info
-
-public:
- size_t fevalIt; ///< function evaluation count
-
- Linesearch(LSFunction &_fct);
-
- virtual void set(int _maxLSIt, double _lSTol, bool _verbose);
- virtual double run();
-};
-
-/**
- * @brief Simple backtrack linesearch
- * @authors Adrien Crovato
- */
-class TBOX_API BacktrackLS : public Linesearch
-{
-public:
- BacktrackLS(LSFunction &_fct);
-
- virtual double run() override;
-};
-
-/**
- * @brief 3-points quadratic linesearch
- *
- * Implemented following Prof. Fleury notes, University of Liege
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API FleuryLS : public Linesearch
-{
-private:
- double hU; ///< upper bound value for bracketing
- double hS; ///< current value for bracketing
- double h0; ///< initial value for bracketing
- double hL; ///< lower bound value for bracketing
- bool revAllowed; ///< allow bracketing in reverse direction
-
-public:
- size_t brckIt; ///< bracketing iteration count
- size_t lsIt; ///< linesearch iteration count
-
- FleuryLS(LSFunction &_fct, double _h0 = 1, double _hL = 1e-10, bool _revAllowed = true);
-
- virtual double run() override;
-};
-
-/**
- * @brief Bank and Rose linesearch
- *
- * Implemented following Bank and Rose, Global Approximate Newton Methods, Numerische Mathematik
- * www.math.hcmuns.edu.vn/~tangoc//bbmot.pdf
- * @authors Adrien Crovato
- */
-class TBOX_API BankRoseLS : public Linesearch
-{
-private:
- double K; ///> damping control
-
-public:
- BankRoseLS(LSFunction &_fct);
- virtual double run() override;
-};
-
-} // namespace tbox
-
-#endif
-
-#endif //WLINESEARCH_H
diff --git a/tbox/src/wMshConvert.cpp b/tbox/src/wMshConvert.cpp
deleted file mode 100644
index 013fff0c..00000000
--- a/tbox/src/wMshConvert.cpp
+++ /dev/null
@@ -1,346 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshConvert.h"
-#include "std_extra.h"
-#include <string>
-#include <cstring>
-#include <sstream>
-#include <fstream>
-#include <set>
-#include <algorithm>
-
-using namespace tbox;
-
-MshConvert::MshConvert(std::shared_ptr<MshData> _msh) : wSharedObject(), msh(_msh)
-{
-}
-
-/**
- * @brief Search for a line in a code
- */
-int MshConvert::searchCode(char const *code, char const *line) const
-{
- return strncmp(code, line, strlen(code));
-}
-
-/**
- * @brief Cnovert a mesh from ANSYS to gmsh format
- */
-void MshConvert::ansys_gmsh(std::string const &fname1, std::string const &fname2)
-{
- // Fonction a generaliser afin de: -prendre en compte les hexaedres et quadrangle.
- // -prendre en compte la presence de differents materiaux.
- // -prendre en compte les elements de contacts.
- // -prendre en compte les elements non lineaires.
-
- std::cout << "converting file " << fname1 << " and save results in " << fname2 << "\n";
-
- FILE *read_file = fopen(fname1.c_str(), "r");
- if (!read_file)
- throw std::runtime_error("Error opening file 1 (load)");
-
- //FILE *written_file = fopen(fname2.c_str(),"w");
- //if (!written_file)
- // throw std::runtime_error("Error opening file 2 (load)");
-
- std::ofstream written_file;
- written_file.open(fname2);
-
- std::cout << "the files are loaded\n";
-
- // first reading
- //
- // goals: count the number of nodes
- // count the number of volume elements
- // set the BC sets of nodes
- bool node_line = false;
- bool element_line = false;
- bool component_line = false;
- bool volume_line = false;
- int number_of_node = 0;
- int number_of_element = -4;
- int number_of_element_2 = 0;
- int set_index = -1;
-
- std::vector<std::string> sets_name;
- std::vector<std::set<int>> sets_nodes;
- std::vector<std::vector<std::string>> sets_elems;
-
- while (1)
- {
- // read next line
- char line[128];
- if (fgets(line, sizeof line, read_file) == NULL)
- break;
- if (searchCode("! NODES", line) == 0)
- node_line = true;
- else if (line[0] != '!' && node_line == true)
- {
- std::istringstream input(line);
- input >> number_of_node;
- }
- else if (searchCode("! ELEMENTS", line) == 0)
- {
- node_line = false;
- element_line = true;
- }
- else if (line[0] != '!' && element_line == true)
- ++number_of_element;
- else if (line[0] == '!' && element_line == true && number_of_element != -4)
- element_line = false;
- else if (searchCode("! COMPONENTS", line) == 0)
- {
- component_line = true;
- }
- else if (line[0] == 'C' && component_line == true)
- {
- std::string tmp_string(line);
- std::string tmp_string2 = tmp_string.substr(8, 10);
- std::string::iterator end_pos = std::remove(tmp_string2.begin(), tmp_string2.end(), ' ');
- tmp_string2.erase(end_pos, tmp_string2.end());
-
- if (tmp_string2 == "Volume")
- {
- volume_line = true;
- continue;
- }
- volume_line = false;
-
- ++set_index;
- sets_name.push_back(tmp_string2);
- std::set<int> tmp;
- sets_nodes.push_back(tmp);
- std::vector<std::string> tmp2;
- sets_elems.push_back(tmp2);
- }
- else if (line[0] != '!' && line[0] != '/' && line[0] != '(' && component_line == true && volume_line == false)
- {
- std::istringstream input(line);
- for (;;)
- {
- int n;
- input >> n;
-
- if (input.eof() || input.bad())
- break;
- else if (input.fail())
- {
- input.clear(); // unset failbit
- input.ignore(std::numeric_limits<std::streamsize>::max(), '\n'); // skip bad input
- }
- else
- sets_nodes[set_index].insert(n);
- }
- }
- }
- fclose(read_file);
-
- for (auto sn : sets_name)
- std::cout << sn;
- std::cout << std::endl;
- for (int i = 0; i <= 0; ++i)
- {
- std::cout << sets_nodes[i].size() << "\n";
-
- std::set<int>::iterator iter;
- for (iter = sets_nodes[i].begin(); iter != sets_nodes[i].end(); ++iter)
- std::cout << *iter << " ";
- std::cout << "\n";
- }
-
- FILE *read_file2 = fopen(fname1.c_str(), "r");
- if (!read_file2)
- throw std::runtime_error("Error opening file 1 (load)");
-
- while (1)
- {
- // read next line
- char line[128];
- if (fgets(line, sizeof line, read_file2) == NULL)
- break;
- else if (searchCode("! ELEMENTS", line) == 0)
- element_line = true;
- else if (line[0] != '!' && element_line == true)
- {
- std::istringstream input(line);
-
- int i = 0;
-
- int n1 = 0, n2 = 0, n3 = 0, n4 = 0;
- for (;;)
- {
- long double n;
- input >> n;
-
- if (input.eof() || input.bad() || n == -1)
- break;
- else if (input.fail())
- {
- input.clear(); // unset failbit
- input.ignore(std::numeric_limits<std::streamsize>::max(), '\n'); // skip bad input
- }
- else if (i == 11)
- n1 = static_cast<int>(n);
- else if (i == 12)
- n2 = static_cast<int>(n);
- else if (i == 13)
- n3 = static_cast<int>(n);
- else if (i == 14)
- n4 = static_cast<int>(n);
-
- ++i;
- }
-
- for (int ii = 0; ii <= set_index; ++ii)
- {
- std::ostringstream output;
- if (sets_nodes[ii].find(n1) != sets_nodes[ii].end() && sets_nodes[ii].find(n2) != sets_nodes[ii].end() && sets_nodes[ii].find(n3) != sets_nodes[ii].end())
- output << n1 << " " << n2 << " " << n3;
- else if (sets_nodes[ii].find(n1) != sets_nodes[ii].end() && sets_nodes[ii].find(n2) != sets_nodes[ii].end() && sets_nodes[ii].find(n4) != sets_nodes[ii].end())
- output << n1 << " " << n2 << " " << n4;
- else if (sets_nodes[ii].find(n1) != sets_nodes[ii].end() && sets_nodes[ii].find(n3) != sets_nodes[ii].end() && sets_nodes[ii].find(n4) != sets_nodes[ii].end())
- output << n1 << " " << n3 << " " << n4;
- else if (sets_nodes[ii].find(n2) != sets_nodes[ii].end() && sets_nodes[ii].find(n3) != sets_nodes[ii].end() && sets_nodes[ii].find(n4) != sets_nodes[ii].end())
- output << n2 << " " << n3 << " " << n4;
- else
- continue;
-
- sets_elems[ii].push_back(output.str());
- //break;
- }
- }
- }
-
- fclose(read_file2);
-
- std::cout << "------------\n";
- // update the number of elements 2
- for (int i = 0; i <= set_index; ++i)
- {
- number_of_element_2 += static_cast<int>(sets_elems[i].size());
- std::cout << sets_elems[i].size() << "\n";
- }
-
- std::cout << number_of_element << "\n";
- std::cout << number_of_element_2 << "\n";
-
- FILE *read_file3 = fopen(fname1.c_str(), "r");
- if (!read_file3)
- throw std::runtime_error("Error opening file 1 (load)");
-
- element_line = false;
- node_line = false;
- bool comment_element_line = false;
-
- written_file << "$MeshFormat\n2.2 0 8\n$EndMeshFormat\n$PhysicalNames\n";
- written_file << set_index + 2 << "\n3 270 \"Volume\"\n";
- for (int i = 0; i <= set_index; ++i)
- {
- written_file << "2 " << 271 + i << " \"" << sets_name[i] << "\"\n";
- }
- written_file << "$EndPhysicalNames\n";
- while (1)
- {
- // read next line
- char line[128];
- if (fgets(line, sizeof line, read_file3) == NULL)
- break;
- if (searchCode("! NODES", line) == 0)
- {
- written_file << "$Nodes \n"
- << number_of_node << "\n";
- node_line = true;
- }
- else if (line[0] != '!' && node_line == true)
- {
- std::istringstream input(line);
- std::ostringstream output;
- for (;;)
- {
- double n;
- input >> n;
-
- if (input.eof() || input.bad())
- break;
- else if (input.fail())
- {
- input.clear(); // unset failbit
- input.ignore(std::numeric_limits<std::streamsize>::max(), '\n'); // skip bad input
- }
- else
- output << n << ' ';
- }
- if (output.str().size() != 0)
- written_file << output.str() << '\n';
- }
- else if (searchCode("! ELEMENTS", line) == 0)
- {
- written_file << "$EndNodes \n$Elements \n"
- << number_of_element + number_of_element_2 << "\n";
- node_line = false;
- element_line = true;
- comment_element_line = true;
-
- int ii = 0;
- for (int i = 0; i <= set_index; ++i)
- for (size_t j = 0; j < sets_elems[i].size(); ++j)
- written_file << ++ii << " 2 2 " << 271 + i << " " << 41 + i << " " << sets_elems[i][j] << "\n";
- }
- else if (line[0] == '!' && comment_element_line == true)
- comment_element_line = false;
- else if (line[0] != '!' && element_line == true)
- {
- std::istringstream input(line);
- std::ostringstream output;
-
- int i = 0;
- for (;;)
- {
- long double n;
- input >> n;
-
- if (input.eof() || input.bad() || n == -1)
- break;
- else if (input.fail())
- {
- input.clear(); // unset failbit
- input.ignore(std::numeric_limits<std::streamsize>::max(), '\n'); // skip bad input
- }
- else if (i == 10)
- {
- written_file << number_of_element_2 + n << " 4 2 270 1 ";
- ++i;
- }
- else if (i > 10)
- {
- written_file << n << ' ';
- ++i;
- }
- else
- ++i;
- }
- if (i != 0)
- written_file << '\n';
- }
- else if (line[0] == '!' && comment_element_line == false && element_line == true)
- {
- written_file << "$EndElements \n";
- element_line = false;
- }
- }
- fclose(read_file3);
-}
\ No newline at end of file
diff --git a/tbox/src/wMshConvert.h b/tbox/src/wMshConvert.h
deleted file mode 100644
index 193e4a8c..00000000
--- a/tbox/src/wMshConvert.h
+++ /dev/null
@@ -1,48 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHCONVERT_H
-#define WMSHCONVERT_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include "wMshData.h"
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Mesh converter
- * @authors Adrien Crovato, Kim Liegeois
- * @todo might need cleaning
- */
-class TBOX_API MshConvert : public fwk::wSharedObject
-{
- int searchCode(char const *code, char const *line) const;
-
-public:
- std::shared_ptr<MshData> msh;
-
- MshConvert(std::shared_ptr<MshData> _msh);
- virtual ~MshConvert() {}
-
- void ansys_gmsh(std::string const &fname1, std::string const &fname2);
-};
-
-} // namespace tbox
-
-#endif //WMSHCONVERT_H
\ No newline at end of file
diff --git a/tbox/src/wMshCrack.cpp b/tbox/src/wMshCrack.cpp
deleted file mode 100644
index 9e11b8a8..00000000
--- a/tbox/src/wMshCrack.cpp
+++ /dev/null
@@ -1,295 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshCrack.h"
-#include "wMshData.h"
-#include "wGroup.h"
-#include "wGroups.h"
-#include "wTag.h"
-#include "wNode.h"
-#include "wElement.h"
-#include "wLine2.h"
-#include "wTri3.h"
-
-using namespace tbox;
-
-MshCrack::MshCrack(std::shared_ptr<MshData> _msh, int _nDim) : wSharedObject(), msh(_msh), nDim(_nDim)
-{
- hasCrack = true; // so that we prevent automatic data structure creation if addCrack() is not called
- crckGrp = nullptr;
- exclGrp = nullptr;
-}
-MshCrack::~MshCrack()
-{
- // Delete temporary groups
- delete crckGrp;
- delete exclGrp;
- for (size_t i = 0; i < bndGrps.size(); ++i)
- delete bndGrps[i];
- for (size_t i = 0; i < bndGrp.size(); ++i)
- delete bndGrp[i];
- std::cout << "~MshCrack()\n";
-}
-
-/**
- * @brief Create temporary group for crack
- */
-void MshCrack::setCrack(std::string const &crckName)
-{
- // Check if a crack needs to be made
- auto it = msh->ntags.find(crckName + '_');
- if (it != msh->ntags.end())
- std::cout << "Groups " << crckName << " and " << crckName << "_ are already existing. MshCrack will not be run!\n";
- else
- {
- hasCrack = false;
- crckGrp = new Group(msh, crckName);
- }
-}
-
-/**
- * @brief Create temporary group for excluded nodes on crack
- */
-void MshCrack::setExcluded(std::string const &exclName)
-{
- if (!hasCrack)
- exclGrp = new Group(msh, exclName);
-}
-
-/**
- * @brief Create temporary groups for crack boundaries
- */
-void MshCrack::addBoundaries(std::vector<std::string> const &bndName)
-{
- if (!hasCrack)
- {
- for (auto name : bndName)
- {
- // Check if the boundaries are explicitely separated...
- try
- {
- Groups *gs = new Groups(msh, std::vector<std::string>{name, name + '_'});
- bndGrps.push_back(gs);
- }
- // ... if not, an algorithm will later try to to separate the elements according to the side of the crack they are touching
- catch (const std::out_of_range &)
- {
- Group *g = new Group(msh, name);
- bndGrp.push_back(g);
- }
- }
- }
-}
-
-/**
- * @brief Create the crack and save the mesh
- */
-void MshCrack::run()
-{
- if (hasCrack)
- std::cout << "MshCrack not run!\n";
- else
- {
- // Check that crack is bounded
- if (bndGrps.empty() && bndGrp.empty())
- throw std::runtime_error("MshCrack::run crack has no boundary (use MshCrack::addBoundary()!\n");
- // Open the crack and modify data structure
- openCrack();
- modifyBoundaries_();
- modifyBoundaries();
- std::cout << "Crack added on " << *(crckGrp->tag) << "(" << crckGrp->tag->name << "_ created)" << std::endl;
- }
-}
-
-/**
- * @brief Duplicate the nodes and elements on the crack and modify the mesh accordingly
- */
-void MshCrack::openCrack()
-{
- // Collect the nodes to be duplicated
- std::vector<Node *> nodes;
- for (auto e : crckGrp->tag->elems)
- for (auto n : e->nodes)
- nodes.push_back(n);
- std::sort(nodes.begin(), nodes.end());
- auto it = std::unique(nodes.begin(), nodes.end());
- nodes.resize(std::distance(nodes.begin(), it));
- // Remove the nodes to be excluded
- if (exclGrp != nullptr)
- {
- // Get junction nodes
- std::vector<Node *> excl;
- for (auto e : exclGrp->tag->elems)
- for (auto n : e->nodes)
- excl.push_back(n);
- std::sort(excl.begin(), excl.end());
- it = std::unique(excl.begin(), excl.end());
- excl.resize(std::distance(excl.begin(), it));
- // Find the intersection and remove
- std::vector<Node *>::iterator endRange;
- endRange = std::set_difference(nodes.begin(), nodes.end(),
- excl.begin(), excl.end(),
- nodes.begin());
- nodes.erase(endRange, nodes.end());
- }
- // Duplicate the nodes, modify the mesh and make a map
- size_t i = msh->nodes.size();
- for (auto n : nodes)
- {
- Node *newNodep = new Node(static_cast<int>(i + 1), n->pos, static_cast<int>(i));
- msh->nodes.push_back(newNodep);
- nodMap[n] = newNodep;
- i++;
- }
-
- // Create new tag and modify the mesh
- Tag *tagp = new Tag(static_cast<int>(msh->ptags.rbegin()->first + 1), crckGrp->tag->name + "_", nDim - 1);
- Tag *tage = new Tag(static_cast<int>(msh->etags.rbegin()->first + 1), crckGrp->tag->name + "_", nDim - 1);
- msh->ntags[crckGrp->tag->name + "_"] = tagp;
- msh->ptags[static_cast<int>(msh->ptags.rbegin()->first + 1)] = tagp;
- msh->etags[static_cast<int>(msh->etags.rbegin()->first + 1)] = tage;
- // Duplicate elements and modify the mesh/tag
- i = msh->elems.size() + 1;
- for (auto e : crckGrp->tag->elems)
- {
- std::vector<Node *> nods(e->nodes.size());
- for (size_t j = 0; j < nods.size(); ++j)
- {
- try
- {
- nods[j] = nodMap.at(e->nodes[e->nodes.size() - j - 1]);
- }
- catch (const std::out_of_range &)
- {
- nods[j] = e->nodes[e->nodes.size() - j - 1];
- }
- }
- if (e->type() == ELTYPE::LINE2 && nDim == 2)
- msh->elems.push_back(new Line2(static_cast<int>(i), tagp, tage, e->parts, nods));
- else if (e->type() == ELTYPE::TRI3 && nDim == 3)
- msh->elems.push_back(new Tri3(static_cast<int>(i), tagp, tage, e->parts, nods));
- else
- {
- std::stringstream err;
- err << "Msh::Crack: could not create element of type " << e->type() << " for dimension " << nDim << "!\n";
- throw std::runtime_error(err.str());
- }
- i++;
- }
-}
-
-/**
- * @brief Swap the elements nodes on one side of the crack and merge physical tags
- */
-void MshCrack::modifyBoundaries_()
-{
- for (auto gs : bndGrps)
- {
- // Modify element nodes touching the crack
- for (auto e : gs->groups[1]->tag->elems)
- swapNodes(e);
- // Merge tags
- Tag *refTag = gs->groups[0]->tag;
- Tag *oldTag = gs->groups[1]->tag;
- // Modify element tags
- for (auto e : gs->groups[1]->tag->elems)
- e->ptag = refTag;
- // Append elements to new tag
- refTag->elems.insert(refTag->elems.end(), oldTag->elems.begin(), oldTag->elems.end());
- // Delete old tag and remove from mesh maps
- msh->ptags.erase(oldTag->no);
- msh->ntags.erase(oldTag->name);
- delete oldTag;
- }
-}
-
-/**
- * @brief Detect the elements on one side of the crack and swap their nodes
- */
-void MshCrack::modifyBoundaries()
-{
- // compute crack CGs and normals
- std::vector<Eigen::Vector3d> crkCG(crckGrp->tag->elems.size()), crkN(crckGrp->tag->elems.size());
- for (size_t i = 0; i < crckGrp->tag->elems.size(); ++i)
- {
- crckGrp->tag->elems[i]->computeCg();
- crkCG[i] = crckGrp->tag->elems[i]->cg;
- crckGrp->tag->elems[i]->computeNormal();
- crkN[i] = crckGrp->tag->elems[i]->normal;
- }
- // find elements on the opposite side of the crack and swap their nodes
- for (auto g : bndGrp)
- {
- // find elements that have at least one node on the crack and compute their CG
- std::map<Element *, Eigen::Vector3d> onCrk;
- for (auto e : g->tag->elems)
- {
- for (auto n : e->nodes)
- {
- if (nodMap.find(n) != nodMap.end())
- {
- //Eigen::Vector3d cg(0, 0, 0);
- //for (auto n_ : e->nodes)
- // cg += n_->pos;
- //cg /= e->nodes.size();
- //onCrk[e] = cg;
- e->computeCg();
- onCrk[e] = e->cg;
- break;
- }
- }
- }
- // find closest element, check side and swap nodes
- for (auto p : onCrk)
- {
- // find mininal distance bewteen CGs
- size_t idx = 0;
- std::vector<Eigen::Vector3d> deltaCG(crkCG.size());
- for (size_t i = 0; i < crkCG.size(); ++i)
- {
- deltaCG[i] = p.second - crkCG[i];
- if (deltaCG[i].norm() < deltaCG[idx].norm())
- idx = i;
- }
- // check sign of dot product
- if (deltaCG[idx].dot(crkN[idx]) < 0)
- swapNodes(p.first);
- }
- }
-}
-
-/**
- * @brief Replace nodes of elements on opposite side of crack by opposite nodes
- */
-void MshCrack::swapNodes(Element *e)
-{
- for (size_t i = 0; i < e->nodes.size(); ++i)
- {
- try
- {
- e->nodes[i] = nodMap.at(e->nodes[i]);
- }
- catch (const std::out_of_range &)
- {
- //std::cout << e->nodes[i]->no << "not found in map!\n";
- }
- }
-}
-
-void MshCrack::write(std::ostream &out) const
-{
- out << "MshCrack on " << msh << std::endl;
-}
\ No newline at end of file
diff --git a/tbox/src/wMshCrack.h b/tbox/src/wMshCrack.h
deleted file mode 100644
index fe45c9d1..00000000
--- a/tbox/src/wMshCrack.h
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHCRACK_H
-#define WMSHCRACK_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include "wMshExport.h"
-#include <vector>
-#include <map>
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Duplicate nodes and elements in a physical group and make mesh consistent
- *
- * Similar to plugin "crack" from gmsh but allows more control. Currently coded
- * only for Line2 and Tri3.
- * @authors Adrien Crovato
- */
-class TBOX_API MshCrack : public fwk::wSharedObject
-{
-private:
- bool hasCrack; ///< flag telling if mesh already has crack
- std::map<Node *, Node *> nodMap; ///< map between nodes on both side of crack
- Group *crckGrp; ///< physical group of crack
- Group *exclGrp; ///< physical group of nodes not to be duplicated
- std::vector<Groups *> bndGrps; ///< list of pair of physical groups touching crack
- std::vector<Group *> bndGrp; ///< list of physical groups touching crack
-
- void openCrack();
- void modifyBoundaries_();
- void modifyBoundaries();
- void swapNodes(Element *e);
-
-public:
- std::shared_ptr<MshData> msh;
- int nDim;
-
- MshCrack(std::shared_ptr<MshData> _msh, int _nDim);
- virtual ~MshCrack();
-
- void setCrack(std::string const &crckName);
- void addBoundaries(std::vector<std::string> const &bndName);
- void setExcluded(std::string const &exclName);
- void run();
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WMSHCRACK_H
\ No newline at end of file
diff --git a/tbox/src/wMshData.cpp b/tbox/src/wMshData.cpp
deleted file mode 100644
index ff0c6456..00000000
--- a/tbox/src/wMshData.cpp
+++ /dev/null
@@ -1,68 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshData.h"
-#include "wNode.h"
-#include "wElement.h"
-#include "wTag.h"
-
-using namespace tbox;
-
-MshData::MshData() : wSharedObject(), verb(false), name("unnamed")
-{
-}
-
-void MshData::write(std::ostream &out) const
-{
- out << "MshData ['" << name << "']= \n";
- out << "\t" << nodes.size() << " nodes\n";
- out << "\t" << elems.size() << " elements\n";
- out << "\t" << ptags.size() << " physical tags\n";
- out << "\t" << etags.size() << " elementary tags\n";
- out << "\t" << parts.size() << " partitions\n";
-}
-
-MshData::~MshData()
-{
- std::cout << "~MshData()\n";
- clear();
-}
-
-/**
- * @brief Clear the memory
- */
-void MshData::clear()
-{
- for (auto n : nodes)
- delete n;
- nodes.clear();
-
- for (auto e : elems)
- delete e;
- elems.clear();
-
- for (auto &p : ptags)
- delete p.second;
- ptags.clear();
-
- for (auto &p : etags)
- delete p.second;
- etags.clear();
-
- for (auto &p : parts)
- delete p.second;
- parts.clear();
-}
diff --git a/tbox/src/wMshData.h b/tbox/src/wMshData.h
deleted file mode 100644
index d3d99f6f..00000000
--- a/tbox/src/wMshData.h
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHDATA_H
-#define WMSHDATA_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <string>
-#include <vector>
-#include <map>
-
-namespace tbox
-{
-
-/**
- * @brief Mesh data structure
- * @authors Romain Boman, Adrien Crovato, Kim Liegeois
- */
-class TBOX_API MshData : public fwk::wSharedObject
-{
- bool verb;
-
-public:
- std::vector<Node *> nodes; ///< nodes
- std::vector<Element *> elems; ///< elements
- std::string name; ///< name
-
- std::map<int, Tag *> ptags; ///< physical tags
- std::map<int, Tag *> etags; ///< elementary tags
- std::map<int, Tag *> parts; ///< partition tags
- std::map<std::string, Tag *> ntags; ///< named tags
-
- MshData();
- virtual ~MshData();
-
- void clear();
- void debug(bool v = true) { verb = v; }
- virtual void write(std::ostream &out) const override;
-};
-
-} // namespace tbox
-
-#endif //WMSHDATA_H
diff --git a/tbox/src/wMshDeform.cpp b/tbox/src/wMshDeform.cpp
deleted file mode 100644
index 22463cc4..00000000
--- a/tbox/src/wMshDeform.cpp
+++ /dev/null
@@ -1,511 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshDeform.h"
-#include "wMshData.h"
-#include "wGroup.h"
-#include "wGroups.h"
-#include "wTag.h"
-#include "wNode.h"
-#include "wElement.h"
-#include "wCache.h"
-#include "wGauss.h"
-#include "wGmres.h"
-
-#include <tbb/global_control.h>
-#include <tbb/parallel_for_each.h>
-#include <tbb/spin_mutex.h>
-#include <deque>
-
-using namespace tbox;
-
-MshDeform::MshDeform(std::shared_ptr<MshData> _msh, int _nDim) : wSharedObject(), nDim(_nDim), field(false), fixed(false), moving(false), msh(_msh)
-{
- // Check problem dimension
- if (nDim != 2 && nDim != 3)
- throw std::runtime_error("tbox::MshDeform: nDim should be 2 or 3!\n");
- // Default
- fldGrp = nullptr;
- symBndGrp = nullptr;
-
- // Initialize multithreading
- nthreads = 1;
- // Get mesh size
- mshSize = msh->nodes.size();
-}
-
-/**
- * @brief Set internal field
- */
-void MshDeform::setField(std::string const &fldName)
-{
- // Create temporary field group
- fldGrp = new Group(msh, fldName);
- field = true;
-}
-
-/**
- * @brief Add fixed boundaries
- */
-void MshDeform::addFixed(std::vector<std::string> const &fxdBndName)
-{
- // Create temporary boundary groups
- for (size_t i = 0; i < fxdBndName.size(); ++i)
- {
- Group *g = new Group(msh, fxdBndName[i]);
- fxdBndGrp.push_back(g);
- }
- fixed = true;
-}
-
-/**
- * @brief Add moving boundaries
- */
-void MshDeform::addMoving(std::vector<std::string> const &movBndName)
-{
- // Create temporary boundary groups
- for (size_t i = 0; i < movBndName.size(); ++i)
- {
- Group *g = new Group(msh, movBndName[i]);
- movBndGrp.push_back(g);
- }
- moving = true;
-}
-
-/**
- * @brief Set symmetry boundary
- */
-void MshDeform::setSymmetry(std::string const &symBndName, size_t _blck)
-{
- // Get blocked direction
- blck = _blck;
- if (blck != 0 && blck != 1 && blck != 2)
- throw std::runtime_error("tbox::MshDeform::setSymmetry: blck should be 0, 1 or 2 (for x, y and z direction resp.)!\n");
- // Create temporary boundary groups
- symBndGrp = new Group(msh, symBndName);
-}
-
-/**
- * @brief Add internal boundaries
- */
-void MshDeform::addInternal(std::vector<std::string> const &intBndName)
-{
- // Create temporary internal link
- if (intBndName.size() != 2)
- throw std::runtime_error("MshDeform: input intBndName must be a pair of internal boundaries!\n");
- Groups *gs = new Groups(msh, intBndName);
- intBndGrps.push_back(gs);
-}
-
-/**
- * @brief Initialize data structure
- */
-void MshDeform::initialize()
-{
- // Sanity checks
- if (!field)
- throw std::runtime_error("MshDeform: field has not been found! Use setField() to add a field.\n");
- else if (!fixed)
- throw std::runtime_error("MshDeform: fixed boundaries have not been found! Use addFixed() to add at least one boundary.\n");
- else if (!moving)
- throw std::runtime_error("MshDeform: moving boundaries have not been found! Use addMoving() to add at least one boundary.\n");
-
- // Store the field elements
- for (auto e : fldGrp->tag->elems)
- fldElems.push_back(e);
-
- // Create vector of fixed boundaries nodes
- for (auto bnd : fxdBndGrp)
- for (auto e : bnd->tag->elems)
- for (auto n : e->nodes)
- fxdBndNodes.push_back(n);
- uniqueSort(fxdBndNodes);
-
- // Create vector of moving boundaries nodes
- for (auto bnd : movBndGrp)
- {
- for (auto e : bnd->tag->elems)
- {
- movBndElems.push_back(e);
- for (auto n : e->nodes)
- movBndNodes.push_back(n);
- }
- }
- uniqueSort(movBndNodes);
-
- // Create vector of symmetry boundary nodes
- if (symBndGrp)
- {
- for (auto e : symBndGrp->tag->elems)
- {
- symBndElems.push_back(e);
- for (auto n : e->nodes)
- symBndNodes.push_back(n);
- }
- uniqueSort(symBndNodes);
- }
-
- // Create the nodes pair for internal boundaries
- for (auto bnds : intBndGrps)
- {
- // Temporary container for internal nodes
- std::vector<Node *> nodes0, nodes1;
- for (auto e : bnds->groups[0]->tag->elems)
- {
- intBndElems.push_back(e);
- for (auto n : e->nodes)
- nodes0.push_back(n);
- }
- for (auto e : bnds->groups[1]->tag->elems)
- {
- intBndElems.push_back(e);
- for (auto n : e->nodes)
- nodes1.push_back(n);
- }
- uniqueSort(nodes0);
- uniqueSort(nodes1);
- // Create the nodes pair
- if (nodes0.size() != nodes1.size())
- throw std::runtime_error("MshDeform: internal boudnaries must have the same number of nodes!");
- for (auto n0 : nodes0)
- {
- for (auto n1 : nodes1)
- {
- if ((n0->pos - n1->pos).norm() <= 1e-14 && n0 != n1)
- {
- intBndPair.push_back(std::pair<Node *, Node *>(n0, n1));
- break;
- }
- }
- }
- }
-
- // List of rows to build stiffness matrix
- rows.resize(nDim * mshSize);
- for (size_t i = 0; i < mshSize; ++i)
- for (size_t m = 0; m < nDim; ++m)
- rows[nDim * i + m] = static_cast<int>(nDim * msh->nodes[i]->row + m);
- // Periodic boundary condition step 1
- // -> for each node pair(a, b): node a contributions will be added to node b rows
- for (auto p : intBndPair)
- for (size_t m = 0; m < nDim; ++m)
- rows[nDim * (p.first->row) + m] = static_cast<int>(nDim * (p.second->row) + m);
-
- // Delete temporary
- delete fldGrp;
- for (size_t i = 0; i < fxdBndGrp.size(); ++i)
- delete fxdBndGrp[i];
- for (size_t i = 0; i < movBndGrp.size(); ++i)
- delete movBndGrp[i];
- delete symBndGrp;
- for (size_t i = 0; i < intBndGrps.size(); ++i)
- delete intBndGrps[i];
-}
-
-/**
- * @brief Store moving nodes position before deformation
- */
-void MshDeform::savePos()
-{
- initPos.resize(nDim * movBndNodes.size());
- for (size_t i = 0; i < movBndNodes.size(); ++i)
- for (int m = 0; m < nDim; ++m)
- initPos[nDim * i + m] = movBndNodes[i]->pos(m);
-}
-
-/**
- * @brief Compute mechanical stiffness matrix for one element
- *
- * K_ij(6,6) = int eps_k H_ijkl eps_l dV = B(6,3)H(3,3)B(3,6)
- * K_ij(12,12) = int eps_k H_ijkl eps_l dV = B(12,6)H(6,6)B(6,12)
- * @todo should be in a dedicated static class
- */
-Eigen::MatrixXd MshDeform::buildK(tbox::Element const &e, Eigen::MatrixXd const &H)
-{
- // Get precomputed values
- Cache &cache = e.getVCache();
- Gauss &gauss = cache.getVGauss();
- size_t ns = e.nodes.size(); // number of nodes
-
- // Elementary stiffness matrix
- Eigen::MatrixXd K = Eigen::MatrixXd::Zero(nDim * ns, nDim * ns);
- for (size_t k = 0; k < gauss.getN(); ++k)
- {
- // Jacobian inverse
- Eigen::MatrixXd const &iJ = e.getJinv(k);
- // Fill B matrix (shape functions)
- Eigen::MatrixXd const &dff = cache.getDsf(k);
- Eigen::MatrixXd B;
- if (nDim == 2)
- {
- B = Eigen::MatrixXd::Zero(3, 2 * ns);
- for (size_t i = 0; i < ns; ++i)
- {
- // Compute [Ni,x Ni,y]
- Eigen::VectorXd dN = iJ * dff.col(i);
- B(0, 2 * i) = dN(0);
- B(1, 2 * i + 1) = dN(1);
- B(2, 2 * i + 1) = dN(0);
- B(2, 2 * i) = dN(1);
- }
- }
- else
- {
- B = Eigen::MatrixXd::Zero(6, 3 * ns);
- for (size_t i = 0; i < ns; ++i)
- {
- // Compute [Ni,x Ni,y Ni,z]
- Eigen::VectorXd dN = iJ * dff.col(i);
- B(0, 3 * i) = dN(0);
- B(1, 3 * i + 1) = dN(1);
- B(2, 3 * i + 2) = dN(2);
- B(3, 3 * i + 1) = dN(2);
- B(3, 3 * i + 2) = dN(1);
- B(4, 3 * i) = dN(2);
- B(4, 3 * i + 2) = dN(0);
- B(5, 3 * i) = dN(1);
- B(5, 3 * i + 1) = dN(0);
- }
- }
-
- // Compute stiffness matrix
- K += B.transpose() * H * B * gauss.getW(k) * e.getDetJ(k);
- }
- return K;
-}
-
-/**
- * @brief Build the mesh deformation matrix using linear elasticity law
- *
- * Dwight RP, Robust Mesh Deformation using the Linear Elasticity Equations.
- * Journal of Computational Fluid Dynamics 12: 401-406, 2009
- */
-void MshDeform::build(Eigen::SparseMatrix<double, Eigen::RowMajor> &K)
-{
- // Multithread
- tbb::spin_mutex mutex;
-
- // List of triplets to build stifness matrix
- std::deque<Eigen::Triplet<double>> T;
-
- // Build stiffness matrix
- tbb::parallel_for_each(fldElems.begin(), fldElems.end(), [&](Element *e) {
- // Hooke tensor
- Eigen::MatrixXd H;
- if (nDim == 2)
- {
- H = Eigen::Matrix3d::Zero();
- double nu = 0.; // Poisson ratio [-1, 0.5]
- double E = 1 / e->getVol(); // Young modulus
- H(0, 0) = 1 - nu;
- H(1, 1) = 1 - nu;
- H(2, 2) = (1 - 2 * nu) / 2;
- H(0, 1) = nu;
- H(1, 0) = H(0, 1);
- H *= E / ((1 + nu) * (1 - 2 * nu));
- }
- else
- {
- H = Eigen::MatrixXd::Zero(6, 6);
- double nu = 0.; // Poisson ratio [-1, 0.5]
- double E = 1 / e->getVol(); // Young modulus
- H(0, 0) = 1 - nu;
- H(1, 1) = 1 - nu;
- H(2, 2) = 1 - nu;
- H(3, 3) = (1 - 2 * nu) / 2;
- H(4, 4) = (1 - 2 * nu) / 2;
- H(5, 5) = (1 - 2 * nu) / 2;
- H(0, 1) = nu;
- H(1, 0) = H(0, 1);
- H(0, 2) = nu;
- H(2, 0) = H(0, 2);
- H(1, 2) = nu;
- H(2, 1) = H(1, 2);
- H *= E / ((1 + nu) * (1 - 2 * nu));
- }
- // Elementary stiffness matrix
- Eigen::MatrixXd Ke = this->buildK(*e, H);
- // Assembly
- tbb::spin_mutex::scoped_lock lock(mutex);
- for (size_t i = 0; i < e->nodes.size(); ++i)
- {
- for (int m = 0; m < nDim; ++m)
- {
- size_t rowi = nDim * (e->nodes[i]->row) + m;
- for (size_t j = 0; j < e->nodes.size(); ++j)
- {
- for (int n = 0; n < nDim; ++n)
- {
- int rowj = nDim * (e->nodes[j]->row) + n;
- T.push_back(Eigen::Triplet<double>(rows[rowi], rowj, Ke(nDim * i + m, nDim * j + n)));
- }
- }
- }
- }
- });
- // Periodic boundary condition step 2
- // -> for each node pair(a, b): write "pos_a - pos_b" = 0 on row a
- for (auto p : intBndPair)
- for (int m = 0; m < nDim; ++m)
- {
- T.push_back(Eigen::Triplet<double>(nDim * (p.first->row) + m, nDim * (p.first->row) + m, 1.));
- T.push_back(Eigen::Triplet<double>(nDim * (p.first->row) + m, nDim * (p.second->row) + m, -1.));
- }
- // Build matrix without BCs
- K.setFromTriplets(T.begin(), T.end());
- // Apply Dirichlet condition on fixed boundaries
- for (size_t i = 0; i < fxdBndNodes.size(); i++)
- {
- for (int m = 0; m < nDim; ++m)
- {
- size_t rowi = nDim * (fxdBndNodes[i]->row) + m;
- for (Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it(K, rowi); it; ++it)
- {
- if (it.row() == it.col())
- it.valueRef() = 1.;
- else
- it.valueRef() = 0.;
- }
- }
- }
- // Apply Dirichlet condition on symmetry boundaries
- for (size_t i = 0; i < symBndNodes.size(); i++)
- {
- size_t rowi = nDim * (symBndNodes[i]->row) + blck;
- for (Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it(K, rowi); it; ++it)
- {
- if (it.row() == it.col())
- it.valueRef() = 1.;
- else
- it.valueRef() = 0.;
- }
- }
- // Apply Dirichlet condition on moving boundaries
- for (size_t i = 0; i < movBndNodes.size(); i++)
- {
- for (int m = 0; m < nDim; ++m)
- {
- size_t rowi = nDim * (movBndNodes[i]->row) + m;
- for (Eigen::SparseMatrix<double, Eigen::RowMajor>::InnerIterator it(K, rowi); it; ++it)
- {
- if (it.row() == it.col())
- it.valueRef() = 1.;
- else
- it.valueRef() = 0.;
- }
- }
- }
- // Clean matrix and turn to compressed row format
- K.prune(0.);
- K.makeCompressed();
-}
-
-/**
- * @brief Build the mesh deformation force vector (B.C.) using linear elasticity law
- *
- * Dwight RP, Robust Mesh Deformation using the Linear Elasticity Equations.
- * Journal of Computational Fluid Dynamics 12: 401-406, 2009
- */
-void MshDeform::build(Eigen::VectorXd &f)
-{
- // Apply Dirichlet condition on moving boundaries
- for (size_t i = 0; i < movBndNodes.size(); i++)
- {
- for (int m = 0; m < nDim; ++m)
- {
- size_t rowi = nDim * (movBndNodes[i]->row) + m;
- f(rowi) = movBndNodes[i]->pos(m) - initPos[nDim * i + m];
- }
- }
-}
-
-/**
- * @brief Deform the mesh following linear elasticity law
- *
- * Dwight RP, Robust Mesh Deformation using the Linear Elasticity Equations.
- * Journal of Computational Fluid Dynamics 12: 401-406, 2009
- */
-void MshDeform::deform()
-{
- // Multithread
- tbb::global_control control(tbb::global_control::max_allowed_parallelism, nthreads);
-
- // Stiffness matrix
- Eigen::SparseMatrix<double, Eigen::RowMajor> K(nDim * mshSize, nDim * mshSize);
- // force (RHS) and displacement (UKN) vectors
- Eigen::VectorXd f = Eigen::VectorXd::Zero(nDim * mshSize), q = Eigen::VectorXd::Zero(nDim * mshSize);
-
- // Build stiffness matrix and RHS
- std::cout << "--- Deforming mesh using linear elasticiy equations ---\n"
- << "Number of threads: " << nthreads << "\n"
- << "Assembling matrices... " << std::flush;
- this->build(K);
- this->build(f);
- std::cout << "done" << std::endl;
- // Solve the SoE
- std ::cout << "Solving equations... " << std::flush;
- Gmres gmres;
- // set the preconditioner
- gmres.setFillFactor(2);
- gmres.setDropTol(1e-6);
- // set the gmres
- gmres.setTolerance(1e-8);
- gmres.setRestart(50);
- gmres.setMaxIterations(500);
- // solve
- Eigen::Map<Eigen::VectorXd> f_(f.data(), f.size()), q_(q.data(), q.size());
- gmres.compute(K, f_, q_);
- std::cout << "done (#it: " << gmres.getIterations() << ", error: " << std::scientific << gmres.getError() << std::fixed << ")" << std::endl;
-
- // Update position
- std ::cout << "Updating mesh... " << std::flush;
- for (auto n : msh->nodes)
- {
- for (int m = 0; m < nDim; m++)
- n->pos(m) += q(nDim * (n->row) + m);
- }
- // Reset moving boundary position
- for (auto n : movBndNodes)
- {
- for (int m = 0; m < nDim; m++)
- n->pos(m) -= q(nDim * (n->row) + m);
- }
- // Update element memory
- for (auto e : fldElems)
- e->update();
- for (auto e : movBndElems)
- e->update();
- for (auto e : symBndElems)
- e->update();
- for (auto e : intBndElems)
- e->update();
- std::cout << "done" << std::endl;
-}
-
-/**
- * @brief Sort a vector and remove duplicates
- */
-void MshDeform::uniqueSort(std::vector<Node *> &nodes)
-{
- std::sort(nodes.begin(), nodes.end());
- auto it = std::unique(nodes.begin(), nodes.end());
- nodes.resize(std::distance(nodes.begin(), it));
-}
-
-void MshDeform::write(std::ostream &out) const
-{
- out << "MshDeform on " << msh << std::endl;
-}
diff --git a/tbox/src/wMshDeform.h b/tbox/src/wMshDeform.h
deleted file mode 100644
index 90b661ad..00000000
--- a/tbox/src/wMshDeform.h
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHDEFORM_H
-#define WMSHDEFORM_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <map>
-#include <memory>
-#include <Eigen/Sparse>
-
-namespace tbox
-{
-
-/**
- * @brief Handle mesh deformation
- * @authors Adrien Crovato
- */
-class TBOX_API MshDeform : public fwk::wSharedObject
-{
-private:
- size_t mshSize; ///< number of nodes in the mesh
- int nDim; ///< dimension of the problem (2 or 3)
- std::vector<int> rows; ///< unknown local index
- bool field; ///< flag to check if field has been added
- bool fixed; ///< flag to check if at least one fixed boundary has been added
- bool moving; ///< flag to check if at least one moving boundary has been added
- Group *fldGrp; ///< temporary group for field
- std::vector<Group *> fxdBndGrp; ///< temporary group for fixed boundaries
- std::vector<Group *> movBndGrp; ///< temporary group for moving boundaries
- Group *symBndGrp; ///< temporary group for symmetry boundary
- std::vector<Groups *> intBndGrps; ///< temporary group for internal boundaries
- std::vector<Element *> fldElems; ///< field elements
- std::vector<Element *> movBndElems; ///< moving boundaries elements
- std::vector<Element *> symBndElems; ///< symmetry boundary elements
- std::vector<Element *> intBndElems; ///< internal boundaries elements
- std::vector<Node *> fxdBndNodes; ///< fixed boundaries nodes
- std::vector<Node *> movBndNodes; ///< moving boundaries nodes
- std::vector<Node *> symBndNodes; ///< symmetry boundary nodes
- size_t blck; ///< blocked dimension for symmetry B.C.
- std::vector<std::pair<Node *, Node *>> intBndPair; ///< internal boundaries node pairs
- std::vector<double> initPos; ///< initial positions of nodes before mesh deformation
-
- void uniqueSort(std::vector<Node *> &nodes);
- Eigen::MatrixXd buildK(tbox::Element const &e, Eigen::MatrixXd const &H);
-
-public:
- std::shared_ptr<MshData> msh;
- int nthreads;
-
- MshDeform(std::shared_ptr<MshData> _msh, int _nDim);
- virtual ~MshDeform() { std::cout << "~MshDeform()\n"; }
-
- void setField(std::string const &fldName);
- void addMoving(std::vector<std::string> const &fxdBndName);
- void addFixed(std::vector<std::string> const &movBndName);
- void setSymmetry(std::string const &symBndName, size_t _blck);
- void addInternal(std::vector<std::string> const &intBndName);
- void initialize();
-
- void savePos();
- void build(Eigen::SparseMatrix<double, Eigen::RowMajor> &K);
- void build(Eigen::VectorXd &f);
- void deform();
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WMSHDEFORM_H
\ No newline at end of file
diff --git a/tbox/src/wMshExport.cpp b/tbox/src/wMshExport.cpp
deleted file mode 100644
index 3eca1043..00000000
--- a/tbox/src/wMshExport.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshExport.h"
-
-using namespace tbox;
-
-MshExport::MshExport(std::shared_ptr<MshData> _msh) : wSharedObject(),
- msh(_msh), binary(true),
- verb(false)
-{
-}
-
-void MshExport::save(std::string const &fname) const
-{
- throw std::runtime_error("tbox::MshExport::save not implemented!\n");
-}
-void MshExport::save(std::string const &fname, Results const &r) const
-{
- throw std::runtime_error("tbox::MshExport::save not implemented!\n");
-}
diff --git a/tbox/src/wMshExport.h b/tbox/src/wMshExport.h
deleted file mode 100644
index 50627aa1..00000000
--- a/tbox/src/wMshExport.h
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHEXPORT_H
-#define WMSHEXPORT_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include "wMshData.h"
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Base class to write mesh
- * @authors Adrien Crovato, Romain Boman
- */
-class TBOX_API MshExport : public fwk::wSharedObject
-{
-public:
- std::shared_ptr<MshData> msh;
- bool binary;
- bool verb;
-
- MshExport(std::shared_ptr<MshData> _msh);
- virtual ~MshExport() {}
-
- virtual void save(std::string const &fname) const;
-#ifndef SWIG
- virtual void save(std::string const &fname, Results const &r) const;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WMSHEXPORT_H
diff --git a/tbox/src/wMshImport.cpp b/tbox/src/wMshImport.cpp
deleted file mode 100644
index 50eec162..00000000
--- a/tbox/src/wMshImport.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMshImport.h"
-
-using namespace tbox;
-
-MshImport::MshImport(std::shared_ptr<MshData> _msh) : wSharedObject(),
- msh(_msh), verb(false)
-{
-}
-
-void MshImport::load(std::string const &fname, int myrank)
-{
- throw std::runtime_error("tbox::MshImport::load not implemented!\n");
-}
-
-void MshImport::load(std::string const &fname, Results &r, int n)
-{
- throw std::runtime_error("tbox::MshImport::load not implemented!\n");
-}
diff --git a/tbox/src/wMshImport.h b/tbox/src/wMshImport.h
deleted file mode 100644
index 07ebcf52..00000000
--- a/tbox/src/wMshImport.h
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMSHIMPORT_H
-#define WMSHIMPORT_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include "wMshData.h"
-#include <memory>
-
-namespace tbox
-{
-
-/**
- * @brief Base class to read and load mesh
- * @authors Adrien Crovato, Romain Boman
- */
-class TBOX_API MshImport : public fwk::wSharedObject
-{
-public:
- std::shared_ptr<MshData> msh;
- bool verb;
-
- MshImport(std::shared_ptr<MshData> _msh);
- virtual ~MshImport() {}
-
- virtual void load(std::string const &fname, int myrank);
- virtual void load(std::string const &fname, Results &r, int n = 0);
-};
-
-} // namespace tbox
-
-#endif //WMSHIMPORT_H
diff --git a/tbox/src/wMumps.cpp b/tbox/src/wMumps.cpp
deleted file mode 100644
index 4fe89818..00000000
--- a/tbox/src/wMumps.cpp
+++ /dev/null
@@ -1,171 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wMumps.h"
-#ifdef WAVES_USE_MUMPS
-
-#include <sstream>
-using namespace tbox;
-
-// macros so that indices match documentation
-#define ICNTL(I) icntl[(I)-1]
-#define INFO(I) info[(I)-1]
-
-Mumps::Mumps() : LinearSolver()
-{
- id.comm_fortran = -987654; // USE_COMM_WORLD;
- id.par = 1; // host involved in factorization phase
- id.sym = 0; // 0=unsymmetric, 1=symdef+, 2=symmetric
- id.job = -1; // initialization phase
- dmumps_c(&id);
-
- // Set default options (must set after id.job = -1)
- // Verbosity level
- id.ICNTL(1) = -1; // stream for error messages [def=6]
- id.ICNTL(2) = -1; // stream for diag printing, statistics, warnings [def=0]
- id.ICNTL(3) = -1; // stream for global information [def=6]
- id.ICNTL(4) = 0; // level of printing [def=2]
- // Matrix re-ordering
- //0 : amd, 2 : amf, 3 : scotch, 4 : pord, 5 : metis, 6 :qamd, 7 : auto [def=7]
- id.ICNTL(7) = 3; // defaults to scotch because mumps comes witch scotch if installed using apt
- // Error analysis
- id.ICNTL(11) = 0; // disabled
- // Increase memory
- id.ICNTL(14) = 40;
- // Determinant
- id.ICNTL(33) = 0; // disabled
-}
-Mumps::~Mumps()
-{
- id.job = -2;
- dmumps_c(&id);
-}
-
-/**
- * @brief Setup the matrix A
- */
-void Mumps::configure(Eigen::SparseMatrix<double> const &A)
-{
- // Check that matrix A is square
- if (A.rows() != A.cols())
- throw std::runtime_error("tbox::Mumps::configure Matrix A is not square!\n");
- // Build data structure
- // the matrix size, structure and number of nonzero entries can change at each iteration!
- size_t nz = A.nonZeros();
- rows.clear();
- cols.clear();
- matx.clear();
- rows.reserve(nz);
- cols.reserve(nz);
- matx.reserve(nz);
- // Get the nonzero indices and values
- for (size_t k = 0; k < A.outerSize(); ++k)
- for (Eigen::SparseMatrix<double>::InnerIterator it(A, k); it; ++it)
- {
- rows.push_back(static_cast<MUMPS_INT>(it.row() + 1));
- cols.push_back(static_cast<MUMPS_INT>(it.col() + 1));
- matx.push_back(it.value());
- }
- // Set sizes
- id.n = int(A.rows());
- id.nz = int(nz);
- // Set matrix
- id.a = &matx[0];
- // Set id
- id.irn = &rows[0];
- id.jcn = &cols[0];
-}
-
-void Mumps::analyze(Eigen::SparseMatrix<double> const &A)
-{
- this->configure(A);
- id.job = 1;
- dmumps_c(&id);
-}
-void Mumps::factorize(Eigen::SparseMatrix<double> const &A)
-{
- this->configure(A);
- id.job = 2;
- dmumps_c(&id);
-}
-void Mumps::solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- Eigen::VectorXd vect = b;
- id.rhs = vect.data();
- id.job = 3;
- dmumps_c(&id);
- check();
- x = vect;
-}
-void Mumps::compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- this->configure(A);
- Eigen::VectorXd vect = b;
- id.rhs = vect.data();
- id.job = 6;
- dmumps_c(&id);
- check();
- x = vect;
-}
-
-/**
- * @brief Check if an error occured during solve
- */
-void Mumps::check()
-{
- if (id.INFO(1) < 0)
- {
- std::stringstream err;
- err << "tbox::Mumps: MUMPS failed with error " << id.INFO(1);
- switch (id.INFO(1))
- {
- case -2:
- err << ": NZ = " << id.INFO(2) << " is out of range!\n";
- throw std::runtime_error(err.str());
- case -6:
- case -10:
- err << ": matrix is singular!\n";
- throw std::runtime_error(err.str());
- case -9:
- err << ": increase ICNTL(14)!\n";
- throw std::runtime_error(err.str());
- case -13:
- err << ": not enough memory!\n";
- throw std::runtime_error(err.str());
- default:
- err << "!\n";
- throw std::runtime_error(err.str());
- }
- }
-}
-
-/**
- * @brief Set option for MUMPS
- */
-void Mumps::setOption(int k, int v)
-{
- if (k > 0)
- id.ICNTL(k) = v;
- else
- throw std::runtime_error("tbox::Mumps::setOption: option id 'k' must be strictly positive!\n");
-}
-
-void Mumps::write(std::ostream &out) const
-{
- out << "MUMPS" << std::endl;
-}
-
-#endif // WAVES_USE_MUMPS
diff --git a/tbox/src/wMumps.h b/tbox/src/wMumps.h
deleted file mode 100644
index 7eee1ca8..00000000
--- a/tbox/src/wMumps.h
+++ /dev/null
@@ -1,75 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WMUMPS_H
-#define WMUMPS_H
-
-#include "tbox.h"
-#ifdef WAVES_USE_MUMPS
-
-#include "wLinearSolver.h"
-#include <dmumps_c.h>
-#include <Eigen/Sparse>
-#include <limits>
-
-namespace tbox
-{
-
-/**
- * @todo also output error in analyze and factorize, if any
- */
-
-/**
- * @brief MUMPS interface
- *
- * Reference: https://github.com/rboman/math0471/blob/master/mumps/main.cpp
- * Reference gmm_MUMPS_interface.h (old)
- * @authors Adrien Crovato
- */
-class TBOX_API Mumps : public LinearSolver
-{
-private:
- DMUMPS_STRUC_C id; ///< mumps structure
- std::vector<MUMPS_INT> rows; ///< rows id
- std::vector<MUMPS_INT> cols; ///< columns id
- std::vector<double> matx; ///< matrix nonzero entries
-
- void configure(Eigen::SparseMatrix<double> const &A);
- void check();
-
-public:
- Mumps();
- ~Mumps();
-
-#ifndef SWIG
- virtual void analyze(Eigen::SparseMatrix<double> const &A) override;
- virtual void factorize(Eigen::SparseMatrix<double> const &A) override;
- virtual void solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
- virtual void compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
-
- virtual double getError() override { return std::numeric_limits<double>::epsilon(); }
- virtual int getIterations() override { return 1; }
-
- virtual void write(std::ostream &out) const override;
-#endif
- void setOption(int k, int v);
-};
-
-} // namespace tbox
-
-#endif // WAVES_USE_MUMPS
-
-#endif // WMUMPS_H
diff --git a/tbox/src/wNode.cpp b/tbox/src/wNode.cpp
deleted file mode 100644
index 6c931d58..00000000
--- a/tbox/src/wNode.cpp
+++ /dev/null
@@ -1,35 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wNode.h"
-
-using namespace tbox;
-
-void Node::write(std::ostream &out) const
-{
- out << "node #" << no << " = " << pos.transpose() << " row=" << row;
-}
-
-Node::Node(int n, Eigen::Vector3d const &p, int r) : wObject(), no(n), pos(p), row(r)
-{
-}
-
-Node::Node()
-{
- no = 0;
- pos = Eigen::Vector3d(0., 0., 0.);
- row = -1;
-}
diff --git a/tbox/src/wNode.h b/tbox/src/wNode.h
deleted file mode 100644
index afcfd7e6..00000000
--- a/tbox/src/wNode.h
+++ /dev/null
@@ -1,49 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WNODE_H
-#define WNODE_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <vector>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Node data structure
- * @authors Romain Boman
- */
-class TBOX_API Node : public fwk::wObject
-{
-public:
- int no; ///< node number
- Eigen::Vector3d pos; ///< spatial position
- int row; ///< row number in data vectors
-
- Node(int n, Eigen::Vector3d const &p, int r);
- Node();
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WNODE_H
diff --git a/tbox/src/wPardiso.cpp b/tbox/src/wPardiso.cpp
deleted file mode 100644
index fbefb7f1..00000000
--- a/tbox/src/wPardiso.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wPardiso.h"
-#ifdef WAVES_USE_MKL
-
-using namespace tbox;
-
-void Pardiso::analyze(Eigen::SparseMatrix<double> const &A)
-{
- solver.analyzePattern(A);
-}
-void Pardiso::factorize(Eigen::SparseMatrix<double> const &A)
-{
- solver.factorize(A);
-}
-void Pardiso::solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- x = solver.solve(b);
-}
-void Pardiso::compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- solver.compute(A);
- x = solver.solve(b);
-}
-
-/**
- * @brief Set option for Pardiso
- */
-void Pardiso::setOption(int k, int v)
-{
- if (k >= 0)
- solver.pardisoParameterArray()[k] = v;
- else
- throw std::runtime_error("tbox::Pardiso::setOption: option id 'k' must be positive!\n");
-}
-
-void Pardiso::write(std::ostream &out) const
-{
- out << "Pardiso (MKL/Eigen)" << std::endl;
-}
-
-#endif // WAVES_USE_MKL
diff --git a/tbox/src/wPardiso.h b/tbox/src/wPardiso.h
deleted file mode 100644
index a723c660..00000000
--- a/tbox/src/wPardiso.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WPARDISO_H
-#define WPARDISO_H
-
-#include "tbox.h"
-#ifdef WAVES_USE_MKL
-
-#include "wLinearSolver.h"
-#include <Eigen/PardisoSupport>
-#include <limits>
-
-namespace tbox
-{
-
-/**
- * @brief Intel Pardiso interface
- * @authors Adrien Crovato
- */
-class TBOX_API Pardiso : public LinearSolver
-{
- Eigen::PardisoLU<Eigen::SparseMatrix<double>> solver;
-
-public:
- Pardiso() : LinearSolver() {}
- virtual ~Pardiso() {}
-
-#ifndef SWIG
- virtual void analyze(Eigen::SparseMatrix<double> const &A) override;
- virtual void factorize(Eigen::SparseMatrix<double> const &A) override;
- virtual void solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
- virtual void compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
-
- virtual double getError() override { return std::numeric_limits<double>::epsilon(); }
- virtual int getIterations() override { return 1; }
-
- virtual void write(std::ostream &out) const override;
-#endif
- void setOption(int k, int v);
-};
-
-} // namespace tbox
-
-#endif // WAVES_USE_MKL
-
-#endif // WPARDISO_H
diff --git a/tbox/src/wPoint1.cpp b/tbox/src/wPoint1.cpp
deleted file mode 100644
index e4cb27af..00000000
--- a/tbox/src/wPoint1.cpp
+++ /dev/null
@@ -1,37 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wPoint1.h"
-#include "wCachePoint1.h"
-#include "wLazy.h"
-
-using namespace tbox;
-
-Point1::Point1(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-CachePoint1 &Point1::getCache(int n)
-{
- static Lazy<CachePoint1> cache(n);
- return cache.get();
-}
-
-Cache &Point1::getVCache() const
-{
- return getCache(order);
-}
diff --git a/tbox/src/wPoint1.h b/tbox/src/wPoint1.h
deleted file mode 100644
index fc78eb37..00000000
--- a/tbox/src/wPoint1.h
+++ /dev/null
@@ -1,43 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WPOINT1_H
-#define WPOINT1_H
-
-#include "tbox.h"
-#include "wElement.h"
-
-namespace tbox
-{
-
-/**
- * @brief Point element (0D)
- * @authors Romain Boman
- */
-class TBOX_API Point1 : public Element
-{
-public:
- Point1(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ELTYPE type() const override { return ELTYPE::POINT1; }
-
-private:
- static CachePoint1 &getCache(int n);
- virtual Cache &getVCache() const override;
-};
-
-} // namespace tbox
-
-#endif //WPOINT1_H
diff --git a/tbox/src/wQuad4.cpp b/tbox/src/wQuad4.cpp
deleted file mode 100644
index c2ee84f6..00000000
--- a/tbox/src/wQuad4.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wQuad4.h"
-#include "wSfQuad4.h"
-#include "wGaussQuad4.h"
-#include "wCacheQuad4.h"
-#include "wNode.h"
-
-using namespace tbox;
-
-Quad4::Quad4(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-/**
- * @brief Return cache holding shape functions and Gauss points for all Quad4 elements
- */
-Cache &Quad4::getVCache() const
-{
- return getCache(order);
-}
-
-/**
- * @brief Initialize precomputed values
- */
-void Quad4::initValues(bool isvol, int ordr)
-{
- // Set flags
- isVol = isvol;
- order = ordr;
- hasVals = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- Js.resize(ngp);
- iJs.resize(ngp);
- detJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Initialize precomputed gradients
- */
-void Quad4::initGradients()
-{
- // Set flags
- hasGrads = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- gradJs.resize(ngp);
- gradDetJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Update precomputed values and gradients
- */
-void Quad4::update()
-{
- // Update values
- if (hasVals)
- {
- // Jacobian and normal
- // Quad4 is not of same dimension as Problem (surface element)
- if (!isVol)
- {
- this->buildSurfaceJ();
- this->computeNormal();
- }
- // Quad4 is of same dimension as Problem (volume element)
- else
- this->buildJ();
- // Volume and CG
- this->computeV();
- this->computeCg();
- }
- // Update gradients
- if (hasGrads)
- {
- // Jacobian, volume and normal
- // Quad4 is not of same dimension as Problem (surface element)
- if (!isVol)
- {
- this->buildGradientSurfaceJ();
- this->buildGradientV(3); // gradient of surface
- this->computeGradientNormal();
- }
- // Quad4 is of same dimension as Problem (volume element)
- else
- {
- this->buildGradientJ();
- this->buildGradientV(2); // gradient of volume
- }
- }
-}
-
-/**
- * @brief Compute Jacobian determinant
- *
- * detJ = norm(x_i dN_i,xi X x_i dN_i,eta)
- */
-void Quad4::buildSurfaceJ()
-{
- for (size_t k = 0; k < getCache(order).getVGauss().getN(); ++k)
- {
- std::vector<Eigen::Vector3d> ts = this->buildTangents(k);
- detJs[k] = ts[0].cross(ts[1]).norm();
- }
-}
-/**
- * @brief Compute Jacobian matrix, inverse and determinant at Gauss point k
- *
- * J_ij(2,2) = diN_n * xj_n (n is the node)
- */
-void Quad4::buildJ()
-{
- CacheQuad4 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dff = cache.getDsf(k);
-
- Eigen::Matrix2d JJ = Eigen::Matrix2d::Zero(); // temporary fixed-size matrix to efficiently compute the inverse
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- JJ += dff.col(i) * (*it)->pos.transpose().block<1, 2>(0, 0);
- Js[k] = JJ;
- iJs[k] = JJ.inverse();
- detJs[k] = JJ.determinant();
- this->checkJac(k);
- }
-}
-
-/**
- * @brief Return the element surface
- */
-void Quad4::computeV()
-{
- CacheQuad4 &cache = getCache(order);
- GaussQuad4 &gauss = cache.gauss;
-
- // Gauss integration
- vol = 0.0;
- for (size_t k = 0; k < gauss.getN(); ++k)
- vol += gauss.getW(k) * this->getDetJ(k);
-}
-
-/**
- * @brief Compute element tangent vectors
- */
-std::vector<Eigen::Vector3d> Quad4::computeTangents() const
-{
- Eigen::Vector3d x1 = nodes[0]->pos;
- Eigen::Vector3d x3 = nodes[2]->pos;
- Eigen::Vector3d x4 = nodes[3]->pos;
-
- return std::vector<Eigen::Vector3d>{(x3 - x1), (x4 - x1)};
-}
-
-/**
- * @brief Build element tangent vectors using shape functions at Gauss point k
- */
-std::vector<Eigen::Vector3d> Quad4::buildTangents(size_t k) const
-{
- Eigen::MatrixXd const &dff = getCache(order).getDsf(k);
-
- std::vector<Eigen::Vector3d> t(2, Eigen::Vector3d::Zero());
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- {
- t[0] += (*it)->pos * dff(0, i);
- t[1] += (*it)->pos * dff(1, i);
- }
- return t;
-}
-
-/**
- * @brief Compute element unit normal vector
- */
-void Quad4::computeNormal()
-{
- std::vector<Eigen::Vector3d> ts = this->computeTangents();
- normal = ts[0].cross(ts[1]).normalized();
-}
diff --git a/tbox/src/wQuad4.h b/tbox/src/wQuad4.h
deleted file mode 100644
index 75cde412..00000000
--- a/tbox/src/wQuad4.h
+++ /dev/null
@@ -1,64 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WQUAD4_H
-#define WQUAD4_H
-
-#include "tbox.h"
-#include "wLazy.h"
-#include "wElement.h"
-#include "wCacheQuad4.h"
-
-namespace tbox
-{
-
-/**
- * @brief Linear quadrangle finite element
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API Quad4 : public Element
-{
-#ifndef SWIG
-private:
- inline static CacheQuad4 &getCache(int n);
-
-protected:
- virtual void buildJ() override;
- virtual void buildSurfaceJ() override;
- virtual void computeV() override;
- virtual std::vector<Eigen::Vector3d> computeTangents() const override;
- virtual std::vector<Eigen::Vector3d> buildTangents(size_t k) const override;
- virtual void computeNormal() override;
-#endif
-
-public:
- Quad4(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Quad4() {}
- virtual ELTYPE type() const override { return ELTYPE::QUAD4; }
-
-#ifndef SWIG
- virtual void initValues(bool isvol, int ordr = 2) override;
- virtual void initGradients() override;
- virtual void update() override;
- virtual Cache &getVCache() const override;
-#endif
-};
-
-#include "wQuad4.inl"
-
-} // namespace tbox
-
-#endif //WQUAD4_H
diff --git a/tbox/src/wQuad4.inl b/tbox/src/wQuad4.inl
deleted file mode 100644
index e77859ff..00000000
--- a/tbox/src/wQuad4.inl
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return cache for Quad4 private methods
- */
-inline CacheQuad4 &Quad4::getCache(int n)
-{
- static Lazy<CacheQuad4> cache(n);
- return cache.get();
-}
diff --git a/tbox/src/wResults.cpp b/tbox/src/wResults.cpp
deleted file mode 100644
index 3cde9f46..00000000
--- a/tbox/src/wResults.cpp
+++ /dev/null
@@ -1,79 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wResults.h"
-
-using namespace tbox;
-
-Results::Results()
-{
- nt = 0;
- time = 0.0;
-}
-
-void Results::write(std::ostream &out) const
-{
- out << "Results (nt=" << nt << ", time=" << time << ")\n";
-
- if (!scalars_at_nodes.empty())
- {
- out << scalars_at_nodes.size() << " scalars at nodes: ";
- for (auto &p : scalars_at_nodes)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
- if (!scalars_at_elems.empty())
- {
- out << scalars_at_elems.size() << " scalars at elems: ";
- for (auto &p : scalars_at_elems)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
- if (!vectors_at_nodes.empty())
- {
- out << vectors_at_nodes.size() << " vectors at nodes: ";
- for (auto &p : vectors_at_nodes)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
- if (!vectors_at_elems.empty())
- {
- out << vectors_at_elems.size() << " vectors at elems: ";
- for (auto &p : vectors_at_elems)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
- if (!tensors_at_nodes.empty())
- {
- out << tensors_at_nodes.size() << " tensors at nodes: ";
- for (auto &p : tensors_at_nodes)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
- if (!tensors_at_elems.empty())
- {
- out << tensors_at_elems.size() << " tensors at elems: ";
- for (auto &p : tensors_at_elems)
- {
- out << "\t'" << p.first << "' (size=" << p.second->size() << ")\n";
- }
- }
-}
diff --git a/tbox/src/wResults.h b/tbox/src/wResults.h
deleted file mode 100644
index 7ffa42f0..00000000
--- a/tbox/src/wResults.h
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WRESULTS_H
-#define WRESULTS_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <string>
-#include <vector>
-#include <map>
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Results data structure
- * @authors Romain Boman
- */
-class TBOX_API Results : public fwk::wObject
-{
-public:
-#ifndef SWIG
- int nt;
- double time;
- std::map<std::string, std::vector<double> *> scalars_at_nodes;
- std::map<std::string, std::vector<double> *> scalars_at_slave_nodes;
- std::map<std::string, std::vector<double> *> scalars_at_elems;
- std::map<std::string, std::vector<Eigen::Vector3d> *> vectors_at_nodes;
- std::map<std::string, std::vector<Eigen::Vector3d> *> vectors_at_elems;
- std::map<std::string, std::vector<Eigen::MatrixXd> *> tensors_at_nodes;
- std::map<std::string, std::vector<Eigen::MatrixXd> *> tensors_at_elems;
-#endif
-
- Results();
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WRESULTS_H
diff --git a/tbox/src/wSfHex8.cpp b/tbox/src/wSfHex8.cpp
deleted file mode 100644
index efda54be..00000000
--- a/tbox/src/wSfHex8.cpp
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSfHex8.h"
-
-using namespace tbox;
-
-void SfHex8::eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const
-{
- ff.resize(8);
- double x = ksi(0);
- double y = ksi(1);
- double z = ksi(2);
-
- ff(0) = 0.125 * (1.0 + x) * (1.0 + y) * (1.0 - z);
- ff(1) = 0.125 * (1.0 - x) * (1.0 + y) * (1.0 - z);
- ff(2) = 0.125 * (1.0 - x) * (1.0 - y) * (1.0 - z);
- ff(3) = 0.125 * (1.0 + x) * (1.0 - y) * (1.0 - z);
- ff(4) = 0.125 * (1.0 + x) * (1.0 + y) * (1.0 + z);
- ff(5) = 0.125 * (1.0 - x) * (1.0 + y) * (1.0 + z);
- ff(6) = 0.125 * (1.0 - x) * (1.0 - y) * (1.0 + z);
- ff(7) = 0.125 * (1.0 + x) * (1.0 - y) * (1.0 + z);
-}
-
-void SfHex8::evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const
-{
- dff.resize(3, 8);
- double x = ksi(0);
- double y = ksi(1);
- double z = ksi(2);
-
- dff(0, 0) = 0.125 * (1.0 + y) * (1.0 - z);
- dff(1, 0) = 0.125 * (1.0 + x) * (1.0 - z);
- dff(2, 0) = -0.125 * (1.0 + x) * (1.0 + y);
- dff(0, 1) = -0.125 * (1.0 + y) * (1.0 - z);
- dff(1, 1) = 0.125 * (1.0 - x) * (1.0 - z);
- dff(2, 1) = -0.125 * (1.0 - x) * (1.0 + y);
- dff(0, 2) = -0.125 * (1.0 - y) * (1.0 - z);
- dff(1, 2) = -0.125 * (1.0 - x) * (1.0 - z);
- dff(2, 2) = -0.125 * (1.0 - x) * (1.0 - y);
- dff(0, 3) = 0.125 * (1.0 - y) * (1.0 - z);
- dff(1, 3) = -0.125 * (1.0 + x) * (1.0 - z);
- dff(2, 3) = -0.125 * (1.0 + x) * (1.0 - y);
- dff(0, 4) = 0.125 * (1.0 + y) * (1.0 + z);
- dff(1, 4) = 0.125 * (1.0 + x) * (1.0 + z);
- dff(2, 4) = 0.125 * (1.0 + x) * (1.0 + y);
- dff(0, 5) = -0.125 * (1.0 + y) * (1.0 + z);
- dff(1, 5) = 0.125 * (1.0 - x) * (1.0 + z);
- dff(2, 5) = 0.125 * (1.0 - x) * (1.0 + y);
- dff(0, 6) = -0.125 * (1.0 - y) * (1.0 + z);
- dff(1, 6) = -0.125 * (1.0 - x) * (1.0 + z);
- dff(2, 6) = 0.125 * (1.0 - x) * (1.0 - y);
- dff(0, 7) = 0.125 * (1.0 - y) * (1.0 + z);
- dff(1, 7) = -0.125 * (1.0 + x) * (1.0 + z);
- dff(2, 7) = 0.125 * (1.0 + x) * (1.0 - y);
-}
diff --git a/tbox/src/wSfHex8.h b/tbox/src/wSfHex8.h
deleted file mode 100644
index 0e599115..00000000
--- a/tbox/src/wSfHex8.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSFHEX8_H
-#define WSFHEX8_H
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Hex8 shape functions
- * @authors Romain Boman
- */
-class TBOX_API SfHex8
-{
-public:
- SfHex8() {}
- void eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const;
- void evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const;
-};
-
-} // namespace tbox
-
-#endif //WSFHEX8_H
diff --git a/tbox/src/wSfLine2.cpp b/tbox/src/wSfLine2.cpp
deleted file mode 100644
index 7f99efd6..00000000
--- a/tbox/src/wSfLine2.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSfLine2.h"
-
-using namespace tbox;
-
-void SfLine2::eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const
-{
- ff.resize(2);
- double x = ksi(0);
-
- ff(0) = 0.5 * (1.0 + x);
- ff(1) = 0.5 * (1.0 - x);
-}
-
-void SfLine2::evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const
-{
- dff.resize(1, 2);
-
- dff(0, 0) = 0.5;
- dff(0, 1) = -0.5;
-}
diff --git a/tbox/src/wSfLine2.h b/tbox/src/wSfLine2.h
deleted file mode 100644
index d29ad34f..00000000
--- a/tbox/src/wSfLine2.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSFLINE2_H
-#define WSFLINE2_H
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Line2 shape functions
- * @authors Romain Boman
- */
-class TBOX_API SfLine2
-{
-public:
- SfLine2() {}
- void eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const;
- void evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const;
-};
-
-} // namespace tbox
-
-#endif //WSFLINE2_H
diff --git a/tbox/src/wSfQuad4.cpp b/tbox/src/wSfQuad4.cpp
deleted file mode 100644
index da595381..00000000
--- a/tbox/src/wSfQuad4.cpp
+++ /dev/null
@@ -1,47 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSfQuad4.h"
-
-using namespace tbox;
-
-void SfQuad4::eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const
-{
- ff.resize(4);
- double x = ksi(0);
- double y = ksi(1);
-
- ff(0) = 0.250 * (1.0 + x) * (1.0 + y);
- ff(1) = 0.250 * (1.0 - x) * (1.0 + y);
- ff(2) = 0.250 * (1.0 - x) * (1.0 - y);
- ff(3) = 0.250 * (1.0 + x) * (1.0 - y);
-}
-
-void SfQuad4::evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const
-{
- dff.resize(2, 4);
- double x = ksi(0);
- double y = ksi(1);
-
- dff(0, 0) = 0.250 * (1.0 + y);
- dff(1, 0) = 0.250 * (1.0 + x);
- dff(0, 1) = -0.250 * (1.0 + y);
- dff(1, 1) = 0.250 * (1.0 - x);
- dff(0, 2) = -0.250 * (1.0 - y);
- dff(1, 2) = -0.250 * (1.0 - x);
- dff(0, 3) = 0.250 * (1.0 - y);
- dff(1, 3) = -0.250 * (1.0 + x);
-}
diff --git a/tbox/src/wSfQuad4.h b/tbox/src/wSfQuad4.h
deleted file mode 100644
index 93ef0dab..00000000
--- a/tbox/src/wSfQuad4.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSFQUAD4_H
-#define WSFQUAD4_H
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Quad4 shape functions
- * @authors Romain Boman
- */
-class TBOX_API SfQuad4
-{
-public:
- SfQuad4() {}
- void eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const;
- void evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const;
-};
-
-} // namespace tbox
-
-#endif //WSFQUAD4_H
diff --git a/tbox/src/wSfTetra4.cpp b/tbox/src/wSfTetra4.cpp
deleted file mode 100644
index 322e5ccd..00000000
--- a/tbox/src/wSfTetra4.cpp
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSfTetra4.h"
-
-using namespace tbox;
-
-void SfTetra4::eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const
-{
- ff.resize(4);
- double x = ksi(0);
- double y = ksi(1);
- double z = ksi(2);
-
- ff(0) = 1.0 - x - y - z;
- ff(1) = x;
- ff(2) = y;
- ff(3) = z;
-}
-
-void SfTetra4::evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const
-{
- dff.resize(3, 4);
-
- dff(0, 0) = -1.0;
- dff(1, 0) = -1.0;
- dff(2, 0) = -1.0;
- dff(0, 1) = 1.0;
- dff(1, 1) = 0.0;
- dff(2, 1) = 0.0;
- dff(0, 2) = 0.0;
- dff(1, 2) = 1.0;
- dff(2, 2) = 0.0;
- dff(0, 3) = 0.0;
- dff(1, 3) = 0.0;
- dff(2, 3) = 1.0;
-}
diff --git a/tbox/src/wSfTetra4.h b/tbox/src/wSfTetra4.h
deleted file mode 100644
index f40e8323..00000000
--- a/tbox/src/wSfTetra4.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSFTETRA4_H
-#define WSFTETRA4_H
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Tetra4 shape functions
- * @authors Romain Boman
- */
-class TBOX_API SfTetra4
-{
-public:
- SfTetra4() {}
- void eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const;
- void evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const;
-};
-
-} // namespace tbox
-
-#endif //WSFTETRA4_H
diff --git a/tbox/src/wSfTri3.cpp b/tbox/src/wSfTri3.cpp
deleted file mode 100644
index ff79cda4..00000000
--- a/tbox/src/wSfTri3.cpp
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSfTri3.h"
-
-using namespace tbox;
-
-void SfTri3::eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const
-{
- ff.resize(3);
- double x = ksi(0);
- double y = ksi(1);
-
- ff(0) = 1.0 - x - y;
- ff(1) = x;
- ff(2) = y;
-}
-
-void SfTri3::evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const
-{
- dff.resize(2, 3);
-
- dff(0, 0) = -1.0;
- dff(1, 0) = -1.0;
- dff(0, 1) = 1.0;
- dff(1, 1) = 0.0;
- dff(0, 2) = 0.0;
- dff(1, 2) = 1.0;
-}
diff --git a/tbox/src/wSfTri3.h b/tbox/src/wSfTri3.h
deleted file mode 100644
index 5e8f2286..00000000
--- a/tbox/src/wSfTri3.h
+++ /dev/null
@@ -1,40 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSFTRI3_H
-#define WSFTRI3_H
-
-#include "tbox.h"
-#include <Eigen/Dense>
-
-namespace tbox
-{
-
-/**
- * @brief Tri3 shape functions
- * @authors Romain Boman
- */
-class TBOX_API SfTri3
-{
-public:
- SfTri3() {}
- void eval(Eigen::Vector3d const &ksi, Eigen::VectorXd &ff) const;
- void evalD(Eigen::Vector3d const &ksi, Eigen::MatrixXd &dff) const;
-};
-
-} // namespace tbox
-
-#endif //WSFTRI3_H
diff --git a/tbox/src/wSparseLu.cpp b/tbox/src/wSparseLu.cpp
deleted file mode 100644
index e22a5271..00000000
--- a/tbox/src/wSparseLu.cpp
+++ /dev/null
@@ -1,41 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wSparseLu.h"
-using namespace tbox;
-
-void SparseLu::analyze(Eigen::SparseMatrix<double> const &A)
-{
- solver.analyzePattern(A);
-}
-void SparseLu::factorize(Eigen::SparseMatrix<double> const &A)
-{
- solver.factorize(A);
-}
-void SparseLu::solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- x = solver.solve(b);
-}
-void SparseLu::compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x)
-{
- solver.compute(A);
- x = solver.solve(b);
-}
-
-void SparseLu::write(std::ostream &out) const
-{
- out << "SparseLU (Eigen)" << std::endl;
-}
diff --git a/tbox/src/wSparseLu.h b/tbox/src/wSparseLu.h
deleted file mode 100644
index 323a5d62..00000000
--- a/tbox/src/wSparseLu.h
+++ /dev/null
@@ -1,57 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WSPARSELU_H
-#define WSPARSELU_H
-
-#include "tbox.h"
-#include "wLinearSolver.h"
-#include <Eigen/Sparse>
-#include <limits>
-
-namespace tbox
-{
-
-/**
- * @brief SparseLU interface
- *
- * Note that SparseLU should be used with ColMajor matrices
- * @authors Adrien Crovato
- */
-class TBOX_API SparseLu : public LinearSolver
-{
- Eigen::SparseLU<Eigen::SparseMatrix<double>> solver;
-
-public:
- SparseLu() : LinearSolver() {}
- virtual ~SparseLu() {}
-
-#ifndef SWIG
- virtual void analyze(Eigen::SparseMatrix<double> const &A) override;
- virtual void factorize(Eigen::SparseMatrix<double> const &A) override;
- virtual void solve(Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
- virtual void compute(Eigen::SparseMatrix<double> const &A, Eigen::Map<Eigen::VectorXd> const &b, Eigen::Map<Eigen::VectorXd> &x) override;
-
- virtual double getError() override { return std::numeric_limits<double>::epsilon(); }
- virtual int getIterations() override { return 1; }
-
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif // WSPARSELU_H
diff --git a/tbox/src/wTag.cpp b/tbox/src/wTag.cpp
deleted file mode 100644
index e0089e79..00000000
--- a/tbox/src/wTag.cpp
+++ /dev/null
@@ -1,36 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTag.h"
-#include "wElement.h"
-#include <map>
-
-using namespace tbox;
-
-void Tag::write(std::ostream &out) const
-{
- out << "Tag #" << no << " (" << dim;
- out << "D) named \"" << name << "\" (" << elems.size() << " elements) ";
-
- // count each type
- std::map<ELTYPE, int> types;
- for (auto e : elems)
- types[e->type()] += 1;
-
- // display
- for (auto &p : types)
- out << p.first << ":" << p.second << " ";
-}
diff --git a/tbox/src/wTag.h b/tbox/src/wTag.h
deleted file mode 100644
index 0c264e62..00000000
--- a/tbox/src/wTag.h
+++ /dev/null
@@ -1,60 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTAG_H
-#define WTAG_H
-
-#include "tbox.h"
-#include "wObject.h"
-#include <string>
-#include <vector>
-
-namespace tbox
-{
-
-/**
- * @brief a Tag is a named group of 1D, 2D or 3D elements
- *
- * The label related to:
- * - the underlying geometrical entity of the elements
- * - a (named) "physical entity"
- * - a mesh partition
- * @authors Romain Boman
- */
-
-class TBOX_API Tag : public fwk::wObject
-{
-public:
- int no; ///< label
- int dim; ///< dimension (1, 2 or 3 for 1D, 2D or 3D - see .msh)
- std::string name; ///< name given in gmsh
- std::vector<Element *> elems; ///< list of elements with this tag
-
- Tag(int _no, std::string const &_name = Tag::defaultName(), int _dim = 0) : wObject(), no(_no), dim(_dim), name(_name) {}
- static const std::string &defaultName()
- {
- static const std::string name("---");
- return name;
- }
-
-#ifndef SWIG
- virtual void write(std::ostream &out) const override;
-#endif
-};
-
-} // namespace tbox
-
-#endif //WTAG_H
diff --git a/tbox/src/wTetra4.cpp b/tbox/src/wTetra4.cpp
deleted file mode 100644
index 8c1b42ab..00000000
--- a/tbox/src/wTetra4.cpp
+++ /dev/null
@@ -1,195 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTetra4.h"
-#include "wSfTetra4.h"
-#include "wGaussTetra4.h"
-#include "wCacheTetra4.h"
-#include "wNode.h"
-
-using namespace tbox;
-
-Tetra4::Tetra4(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-/**
- * @brief Return cache handling shape functions and Gauss points for all Tetra4 elements
- */
-Cache &Tetra4::getVCache() const
-{
- return getCache(order);
-}
-
-/**
- * @brief Initialize precomputed values
- */
-void Tetra4::initValues(bool isvol, int ordr)
-{
- // Set flags
- isVol = isvol;
- order = ordr;
- hasVals = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- Js.resize(ngp);
- iJs.resize(ngp);
- detJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Initialize precomputed gradients
- */
-void Tetra4::initGradients()
-{
- // Set flags
- hasGrads = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- gradJs.resize(ngp);
- gradDetJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Update precomputed values and gradients
- */
-void Tetra4::update()
-{
- // Update gradients
- if (hasVals)
- {
- // Jacobian
- if (!isVol)
- throw std::runtime_error("Tetra4::update(): the problem must always have the same dimension as Tetra4!\n");
- // Tetra4 is always of same dimension as Problem (volume element)
- this->buildJ();
- // Volume and CG
- this->computeV();
- this->computeCg();
- }
- // Update gradients
- if (hasGrads)
- {
- // Jacobian
- if (!isVol)
- throw std::runtime_error("Tetra4::updateGradients(): the problem must always have the same dimension as Tetra4!\n");
- // Tetra4 is always of same dimension as Problem (volume element)
- this->buildGradientJ();
- // Volume
- this->buildGradientV(3);
- }
-}
-
-/**
- * @brief Compute Jacobian matrix, inverse and determinant
- *
- * J_ij(3,3) = diN_n * xj_n (n is the node)
- */
-void Tetra4::buildJ()
-{
- CacheTetra4 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dff = cache.getDsf(k);
-
- Eigen::Matrix3d JJ = Eigen::Matrix3d::Zero(); // temporary fixed-size matrix to efficiently compute the inverse
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- JJ += dff.col(i) * ((*it)->pos).transpose();
- Js[k] = JJ;
- iJs[k] = JJ.inverse();
- detJs[k] = JJ.determinant();
- this->checkJac(k);
- }
-}
-
-/**
- * @brief Compute Jacobian matrix and determinant gradient with respect to each node coordinate
- *
- * dJ[l = i * 3 + j](3,3) = dN_i(3,1) * dxy_i(1,3)/dx_l (for node i and dimension j)
- */
-void Tetra4::buildGradientJ()
-{
- CacheTetra4 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dsf = getCache(order).getDsf(k);
-
- // Jacobian
- gradJs[k].resize(4 * 3); // 4 nodes and 3 dimensions (x, y, z)
- for (size_t i = 0; i < 4; ++i)
- {
- for (size_t j = 0; j < 3; ++j)
- {
- gradJs[k][i * 3 + j] = Eigen::Matrix3d::Zero();
- gradJs[k][i * 3 + j].col(j) = dsf.col(i); // retain sf gradients associated to ith node for dimension j
- }
- }
- // Determinant
- double detJ = this->getDetJ(k);
- Eigen::MatrixXd const &iJ = this->getJinv(k);
- gradDetJs[k].resize(4 * 3);
- for (size_t i = 0; i < 4 * 3; ++i)
- gradDetJs[k][i] = detJ * (iJ * gradJs[k][i]).trace();
- }
-}
-
-/**
- * @brief Return the element volume
- */
-void Tetra4::computeV()
-{
- CacheTetra4 &cache = getCache(order);
- GaussTetra4 &gauss = cache.gauss;
-
- // Gauss integration
- vol = 0.0;
- for (size_t k = 0; k < gauss.getN(); ++k)
- vol += gauss.getW(k) * this->getDetJ(k);
-}
-/**
- * @brief Compute volume gradient with respect to each node coordinate
- *
- * dV[i] = w_k * dDetJ[i]_k
- */
-void Tetra4::buildGradientV(int dim)
-{
- GaussTetra4 &gauss = getCache(order).gauss;
-
- // Gradient of volume
- gradVol.resize(4 * dim, 0.); // 4 nodes
- for (size_t k = 0; k < gauss.getN(); ++k)
- {
- double w = gauss.getW(k); // GP weight
- std::vector<double> dDetJ = this->getGradDetJ(k); // gradient of Jacobian determinant
- for (size_t i = 0; i < dDetJ.size(); ++i)
- gradVol[i] += w * dDetJ[i];
- }
-}
-
-/**
- * @brief Compute gradient of a scalar field at Gauss point k
- */
-Eigen::VectorXd Tetra4::computeGradient(std::vector<double> const &u, size_t k) const
-{
- // Solution vector
- Eigen::Vector4d ue;
- for (size_t i = 0; i < nodes.size(); ++i)
- ue(i) = u[nodes[i]->row];
- // gradient in global axis: inv(J)_ij * d_jN_i * ue_i
- return this->getJinv(k) * getCache(order).getDsf(k) * ue;
-}
diff --git a/tbox/src/wTetra4.h b/tbox/src/wTetra4.h
deleted file mode 100644
index 371dcba8..00000000
--- a/tbox/src/wTetra4.h
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTETRA4_H
-#define WTETRA4_H
-
-#include "tbox.h"
-#include "wLazy.h"
-#include "wElement.h"
-#include "wCacheTetra4.h"
-
-namespace tbox
-{
-
-/**
- * @brief Linear tetrahedron finite element
- * @authors Kim Liegeois, Romain Boman, Adrien Crovato
- */
-class TBOX_API Tetra4 : public Element
-{
-#ifndef SWIG
-private:
- inline static CacheTetra4 &getCache(int n);
-
-protected:
- virtual void buildJ() override;
- virtual void buildGradientJ() override;
- virtual void computeV() override;
- virtual void buildGradientV(int dim) override;
-#endif
-
-public:
- Tetra4(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Tetra4() {}
- virtual ELTYPE type() const override { return ELTYPE::TETRA4; }
-
-#ifndef SWIG
- virtual void initValues(bool isvol, int ordr = 2) override;
- virtual void initGradients() override;
- virtual void update() override;
- virtual Cache &getVCache() const override;
- virtual Eigen::VectorXd computeGradient(std::vector<double> const &u, size_t k) const override;
-#endif
-};
-
-#include "wTetra4.inl"
-
-} // namespace tbox
-
-#endif //WTETRA4_H
diff --git a/tbox/src/wTetra4.inl b/tbox/src/wTetra4.inl
deleted file mode 100644
index 64d5d52a..00000000
--- a/tbox/src/wTetra4.inl
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return cache for Tetra4 private methods
- */
-inline CacheTetra4 &Tetra4::getCache(int n)
-{
- static Lazy<CacheTetra4> cache(n);
- return cache.get();
-}
diff --git a/tbox/src/wTri3.cpp b/tbox/src/wTri3.cpp
deleted file mode 100644
index ea16dd09..00000000
--- a/tbox/src/wTri3.cpp
+++ /dev/null
@@ -1,311 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wTri3.h"
-#include "wSfTri3.h"
-#include "wGaussTri3.h"
-#include "wCacheTri3.h"
-#include "wNode.h"
-
-using namespace tbox;
-
-Tri3::Tri3(int n, Tag *_ptag, Tag *_etag,
- std::vector<Tag *> &_parts, std::vector<Node *> &nods) : Element(n, _ptag, _etag, _parts, nods)
-{
-}
-
-/**
- * @brief Return cache holding shape functions and Gauss points for all Tri3 elements
- */
-Cache &Tri3::getVCache() const
-{
- return getCache(order);
-}
-
-/**
- * @brief Initialize precomputed values
- */
-void Tri3::initValues(bool isvol, int ordr)
-{
- // Set flags
- isVol = isvol;
- order = ordr;
- hasVals = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- Js.resize(ngp);
- iJs.resize(ngp);
- detJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Initialize precomputed gradients
- */
-void Tri3::initGradients()
-{
- // Set flags
- hasGrads = true;
- // Update values
- size_t ngp = getCache(order).getVGauss().getN();
- gradJs.resize(ngp);
- gradDetJs.resize(ngp);
- this->update();
-}
-/**
- * @brief Update precomputed values and gradients
- */
-void Tri3::update()
-{
- // Update values
- if (hasVals)
- {
- // Jacobian and normal
- // Tri3 is not of same dimension as Problem (surface element)
- if (!isVol)
- {
- this->buildSurfaceJ();
- this->computeNormal();
- }
- // Tri3 is of same dimension as Problem (volume element)
- else
- this->buildJ();
- // Volume and CG
- this->computeV();
- this->computeCg();
- }
- // Update gradients
- if (hasGrads)
- {
- // Jacobian, volume and normal
- // Tri3 is not of same dimension as Problem (surface element)
- if (!isVol)
- {
- this->buildGradientSurfaceJ();
- this->buildGradientV(3);
- this->computeGradientNormal();
- }
- // Tri3 is of same dimension as Problem (volume element)
- else
- {
- this->buildGradientJ();
- this->buildGradientV(2);
- }
- }
-}
-
-/**
- * @brief Compute Jacobian determinant
- *
- * detJ = norm(x_i dN_i,xi X x_i dN_i,eta)
- */
-void Tri3::buildSurfaceJ()
-{
- for (size_t k = 0; k < getCache(order).getVGauss().getN(); ++k)
- {
- std::vector<Eigen::Vector3d> ts = this->buildTangents(k);
- detJs[k] = ts[0].cross(ts[1]).norm();
- }
-}
-/**
- * @brief Compute Jacobian matrix, inverse and determinant
- *
- * J_ij(2,2) = diN_n * xj_n (n is the node)
- */
-void Tri3::buildJ()
-{
- CacheTri3 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dff = getCache(order).getDsf(k);
-
- Eigen::Matrix2d JJ = Eigen::Matrix2d::Zero(); // temporary fixed-size matrix to efficiently compute the inverse
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- JJ += dff.col(i) * (*it)->pos.transpose().block<1, 2>(0, 0);
- Js[k] = JJ;
- iJs[k] = JJ.inverse();
- detJs[k] = JJ.determinant();
- this->checkJac(k);
- }
-}
-
-/**
- * @brief Compute Jacobian determinant gradient with respect to each node coordinate
- *
- * dDetJ[l = i * 3 + j] = detJ_l * (dt0 \cross t1 + t0 \cross dt1)_l;
- */
-void Tri3::buildGradientSurfaceJ()
-{
- CacheTri3 &cache = getCache(order);
- for (size_t k = 0; k < getCache(order).getVGauss().getN(); ++k)
- {
- // Shape functions, tangent vectors and determinant
- Eigen::MatrixXd const &dsf = cache.getDsf(k);
- std::vector<Eigen::Vector3d> ts = this->buildTangents(k);
- Eigen::Vector3d detJ = ts[0].cross(ts[1]).normalized();
-
- // Jacobian gradient
- gradDetJs[k].resize(3 * 3); // 3 nodes and 3 dimensions (x, y, z)
- for (size_t i = 0; i < 3; ++i)
- {
- for (size_t j = 0; j < 3; ++j)
- {
- Eigen::Vector3d dt0 = Eigen::Vector3d::Zero(), dt1 = Eigen::Vector3d::Zero();
- dt0(j) = dsf(0, i);
- dt1(j) = dsf(1, i); // retain sf gradients associated to ith node for dimension j
- gradDetJs[k][i * 3 + j] = detJ.dot(dt0.cross(ts[1]) + ts[0].cross(dt1));
- }
- }
- }
-}
-/**
- * @brief Compute Jacobian matrix gradient with respect to each node coordinate
- *
- * dJ[l = i * 2 + j](2,2) = dN_i(2,1) * dxy_i(1,2)/dx_l (for node i and dimension j)
- */
-void Tri3::buildGradientJ()
-{
- CacheTri3 &cache = getCache(order);
- for (size_t k = 0; k < cache.getVGauss().getN(); ++k)
- {
- Eigen::MatrixXd const &dsf = cache.getDsf(k);
-
- // Jacobian
- gradJs[k].resize(3 * 2); // 3 nodes and 2 dimensions (x, y)
- for (size_t i = 0; i < 3; ++i)
- {
- for (size_t j = 0; j < 2; ++j)
- {
- gradJs[k][i * 2 + j] = Eigen::Matrix2d::Zero();
- gradJs[k][i * 2 + j].col(j) = dsf.col(i); // retain sf gradients associated to ith node for dimension j
- }
- }
- // Determinant
- double detJ = this->getDetJ(k);
- Eigen::MatrixXd const &iJ = this->getJinv(k);
- gradDetJs[k].resize(3 * 2);
- for (size_t i = 0; i < 3 * 2; ++i)
- gradDetJs[k][i] = detJ * (iJ * gradJs[k][i]).trace();
- }
-}
-
-/**
- * @brief Return the element surface
- */
-void Tri3::computeV()
-{
- CacheTri3 &cache = getCache(order);
- GaussTri3 &gauss = cache.gauss;
-
- // Gauss integration
- vol = 0.0;
- for (size_t k = 0; k < gauss.getN(); ++k)
- vol += gauss.getW(k) * this->getDetJ(k);
-}
-/**
- * @brief Compute volume gradient with respect to each node coordinate
- *
- * dV[i] = w_k * dDetJ[i]_k
- */
-void Tri3::buildGradientV(int dim)
-{
- GaussTri3 &gauss = getCache(order).gauss;
-
- // Gradient of volume
- gradVol.resize(3 * dim, 0.); // 3 nodes
- for (size_t k = 0; k < gauss.getN(); ++k)
- {
- double w = gauss.getW(k); // GP weight
- std::vector<double> dDetJ = this->getGradDetJ(k); // gradient of Jacobian determinant
- for (size_t i = 0; i < dDetJ.size(); ++i)
- gradVol[i] += w * dDetJ[i];
- }
-}
-
-/**
- * @brief Compute element tangent vectors
- */
-std::vector<Eigen::Vector3d> Tri3::computeTangents() const
-{
- Eigen::Vector3d x1 = nodes[0]->pos;
- Eigen::Vector3d x2 = nodes[1]->pos;
- Eigen::Vector3d x3 = nodes[2]->pos;
-
- return std::vector<Eigen::Vector3d>{(x2 - x1), (x3 - x1)};
-}
-
-/**
- * @brief Build element tangent vectors using shape functions at Gauss point k
- */
-std::vector<Eigen::Vector3d> Tri3::buildTangents(size_t k) const
-{
- Eigen::MatrixXd const &dff = getCache(order).getDsf(k);
-
- std::vector<Eigen::Vector3d> t(2, Eigen::Vector3d::Zero());
- size_t i = 0;
- for (auto it = nodes.begin(); it != nodes.end(); ++it, ++i)
- {
- t[0] += (*it)->pos * dff(0, i);
- t[1] += (*it)->pos * dff(1, i);
- }
- return t;
-}
-
-/**
- * @brief Compute element unit normal vector
- */
-void Tri3::computeNormal()
-{
- std::vector<Eigen::Vector3d> ts = this->computeTangents();
- normal = ts[0].cross(ts[1]).normalized();
-}
-
-/**
- * @brief Compute gradient of element unit normal vector with respect to each node coordinate
- */
-void Tri3::computeGradientNormal()
-{
- // Compute normal and norm
- std::vector<Eigen::Vector3d> ts = this->computeTangents();
- Eigen::Vector3d n = ts[0].cross(ts[1]);
- double nn = n.norm();
-
- // Compute gradients
- Eigen::Matrix3d inn = (Eigen::Matrix3d::Identity() - n * n.transpose() / (nn * nn)) / nn; // gradient of n/|n|
- gradNormal.resize(3 * 3); // 3 nodes and 3 dimensions
- for (size_t i = 0; i < 3; ++i)
- {
- for (size_t j = 0; j < 3; ++j)
- {
- Eigen::Matrix3d dx = Eigen::Matrix3d::Zero();
- dx(j, i) = 1; // dpos_i / dx_j
- gradNormal[i * 3 + j] = inn * ((dx.col(1) - dx.col(0)).cross(ts[1]) + (ts[0]).cross(dx.col(2) - dx.col(0))); // outer gradient times gradient of cross product
- }
- }
-}
-
-/**
- * @brief Compute gradient of a scalar field at Gauss point k
- */
-Eigen::VectorXd Tri3::computeGradient(std::vector<double> const &u, size_t k) const
-{
- // Solution vector
- Eigen::Vector3d ue;
- for (size_t i = 0; i < nodes.size(); ++i)
- ue(i) = u[nodes[i]->row];
- // Gradient in global axis: inv(J)_ij * d_jN_i * ue_i
- return this->getJinv(k) * getCache(order).getDsf(k) * ue;
-}
diff --git a/tbox/src/wTri3.h b/tbox/src/wTri3.h
deleted file mode 100644
index c042c4c5..00000000
--- a/tbox/src/wTri3.h
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WTRI3_H
-#define WTRI3_H
-
-#include "tbox.h"
-#include "wLazy.h"
-#include "wElement.h"
-#include "wCacheTri3.h"
-
-namespace tbox
-{
-
-/**
- * @brief Linear triangle finite element
- * @authors Romain Boman, Adrien Crovato
- */
-class TBOX_API Tri3 : public Element
-{
-#ifndef SWIG
-private:
- inline static CacheTri3 &getCache(int order);
-
-protected:
- virtual void buildJ() override;
- virtual void buildSurfaceJ() override;
- virtual void buildGradientJ() override;
- virtual void buildGradientSurfaceJ() override;
- virtual void computeV() override;
- virtual void buildGradientV(int dim) override;
- virtual void computeNormal() override;
- virtual void computeGradientNormal() override;
- virtual std::vector<Eigen::Vector3d> computeTangents() const override;
- virtual std::vector<Eigen::Vector3d> buildTangents(size_t k) const override;
-#endif
-
-public:
- Tri3(int n, Tag *_ptag, Tag *_etag, std::vector<Tag *> &_parts, std::vector<Node *> &nods);
- virtual ~Tri3() {}
- virtual ELTYPE type() const override { return ELTYPE::TRI3; }
-
-#ifndef SWIG
- virtual void initValues(bool isvol, int ordr = 2) override;
- virtual void initGradients() override;
- virtual void update() override;
- virtual Cache &getVCache() const override;
- virtual Eigen::VectorXd computeGradient(std::vector<double> const &u, size_t k) const override;
-#endif
-};
-
-#include "wTri3.inl"
-
-} // namespace tbox
-
-#endif //WTRI3_H
diff --git a/tbox/src/wTri3.inl b/tbox/src/wTri3.inl
deleted file mode 100644
index 57f12736..00000000
--- a/tbox/src/wTri3.inl
+++ /dev/null
@@ -1,24 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-/**
- * @brief Return cache for Tri3 private methods
- */
-inline CacheTri3 &Tri3::getCache(int n)
-{
- static Lazy<CacheTri3> cache(n);
- return cache.get();
-}
diff --git a/tbox/src/wUnitTest.cpp b/tbox/src/wUnitTest.cpp
deleted file mode 100644
index 7b886c29..00000000
--- a/tbox/src/wUnitTest.cpp
+++ /dev/null
@@ -1,98 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wUnitTest.h"
-#include "wMshData.h"
-#include "wNode.h"
-#include "wElement.h"
-#include "wGmshImport.h"
-#include "wGmshExport.h"
-#include "wResults.h"
-#include "wMshDeform.h"
-#include <Eigen/Dense>
-
-using namespace tbox;
-
-/**
- * @brief Write and read results to/from disk
- */
-void UnitTest::gmshIO(GmshExport *writer, GmshImport *reader)
-{
- // Mesh
- auto mesh = writer->msh; // should be the same than in reader->msh
-
- // Variables to be written then read
- std::vector<double> x(mesh->nodes.size(), 0), type(mesh->elems.size(), 0); // x-position, element type
- std::vector<Eigen::Vector3d> xyz(mesh->nodes.size(), Eigen::Vector3d::Zero()); // x,y,z-position
-
- // Temporary results container
- Results res;
- res.scalars_at_nodes["x"] = &x;
- res.vectors_at_nodes["xyz"] = &xyz;
- res.scalars_at_elems["type"] = &type;
-
- // Fill the variables and write them to disk
- for (size_t i = 0; i < mesh->nodes.size(); ++i)
- {
- x[i] = mesh->nodes[i]->pos(0);
- xyz[i] = mesh->nodes[i]->pos;
- }
- for (size_t i = 0; i < mesh->elems.size(); ++i)
- type[i] = static_cast<double>(mesh->elems[i]->type());
- writer->binary = false; // because we cannot read files in bin format yet...
- writer->save(mesh->name, res);
-
- // Clear the variables and read them from disk
- std::fill(x.begin(), x.end(), 0);
- std::fill(xyz.begin(), xyz.end(), Eigen::Vector3d::Zero());
- std::fill(type.begin(), type.end(), 0);
- reader->load(mesh->name + ".pos", res, 0);
-
- // Test that the variables have the required value
- for (size_t i = 0; i < x.size(); ++i)
- if (x[i] != mesh->nodes[i]->pos(0))
- this->error("gmshIO", std::to_string(x[i]), std::to_string(mesh->nodes[i]->pos(0)));
- for (size_t i = 0; i < xyz.size(); ++i)
- if (xyz[i] != mesh->nodes[i]->pos)
- this->error("gmshIO",
- "(" + std::to_string(xyz[i](0)) + "," + std::to_string(xyz[i](1)) + "," + std::to_string(xyz[i](2)) + ")",
- "(" + std::to_string(mesh->nodes[i]->pos(0)) + "," + std::to_string(mesh->nodes[i]->pos(1)) + "," + std::to_string(mesh->nodes[i]->pos(2)) + ")");
- for (size_t i = 0; i < type.size(); ++i)
- if (type[i] != static_cast<double>(mesh->elems[i]->type()))
- this->error("gmshIO", std::to_string(type[i]), std::to_string(static_cast<double>(mesh->elems[i]->type())));
-}
-
-/**
- * @brief Deform a mesh of dimension d
- */
-void UnitTest::mshDeform(MshDeform *mshDef, int d)
-{
- // Initialize memory (volume element only)
- for (auto e : mshDef->msh->elems)
- if ((d == 2 && e->type() == ELTYPE::TRI3) || (d == 3 && e->type() == ELTYPE::TETRA4))
- e->initValues(true);
- // Call deform
- mshDef->deform();
-}
-
-/**
- * @brief Print error on failure
- */
-void UnitTest::error(std::string const &name, std::string const &computed, std::string const &expected)
-{
- std::string message = "tbox::UnitTest::" + name + " failed! Computed: " + computed + " but expected: " + expected + ".\n";
- throw std::runtime_error(message);
-}
diff --git a/tbox/src/wUnitTest.h b/tbox/src/wUnitTest.h
deleted file mode 100644
index 4a515676..00000000
--- a/tbox/src/wUnitTest.h
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WUNITTEST_H
-#define WUNITTEST_H
-
-#include "tbox.h"
-#include "wObject.h"
-
-namespace tbox
-{
-
-/**
- * @brief Tests for tbox
- * @authors Adrien Crovato
- */
-class TBOX_API UnitTest : public fwk::wObject
-{
- void error(std::string const &name, std::string const &computed, std::string const &expected);
-
-public:
- UnitTest() : wObject() {}
- virtual ~UnitTest() {}
-
- void gmshIO(GmshExport *writer, GmshImport *reader);
- void mshDeform(MshDeform *mshDef, int d);
-};
-
-} // namespace tbox
-
-#endif //WUNITTEST_H
diff --git a/tbox/tests/basicops.py b/tbox/tests/basicops.py
deleted file mode 100644
index 0d1fb9c9..00000000
--- a/tbox/tests/basicops.py
+++ /dev/null
@@ -1,35 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import tbox
-
-def main():
-
- print("creating a Point")
- p1 = tbox.Vector3d(0., 0., 0.)
- print(p1)
- print("creating a Node")
- n1 = tbox.Node(1, p1, 0)
- print(n1)
- print("accessing Node position")
- pos = n1.pos
- print(pos)
-
-if __name__ == "__main__":
- main()
-
diff --git a/tbox/tests/fem/elem1s.py b/tbox/tests/fem/elem1s.py
deleted file mode 100644
index a14f11b9..00000000
--- a/tbox/tests/fem/elem1s.py
+++ /dev/null
@@ -1,34 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-# basic tests on single finite elements
-
-import tbox
-import tbox.gmsh as gmsh
-
-def main(**d):
-
- # 1 triangle
- print('='*80+'\nTesting Tri\n'+'='*80)
- msh = gmsh.MeshLoader('tri1.geo',__file__).execute()
-
- el = msh.ntags['S1'].elems[0]
- print(el)
-
- # 1 hex
- print('='*80+'\nTesting Hex\n'+'='*80)
- msh = gmsh.MeshLoader('hex1.geo',__file__).execute()
-
- el = msh.ntags['Volume'].elems[0]
- print(el)
-
- # 1 quad
- print('='*80+'\nTesting Quad\n'+'='*80)
-
- msh = gmsh.MeshLoader('quad1.geo',__file__).execute()
-
- el = msh.ntags['S1'].elems[0]
- print(el)
-
-
-if __name__ == "__main__":
- main()
diff --git a/tbox/tests/fem/hex1.geo b/tbox/tests/fem/hex1.geo
deleted file mode 100644
index 6926b5ed..00000000
--- a/tbox/tests/fem/hex1.geo
+++ /dev/null
@@ -1,49 +0,0 @@
-// a cube meshed with hex
-
-DefineConstant[ Lx = { 1, Min 5, Max 20, Step 1, Name "Lengths/Lx" } ];
-DefineConstant[ Ly = { 1, Min 5, Max 20, Step 1, Name "Lengths/Ly" } ];
-DefineConstant[ Lz = { 1, Min 1, Max 2, Step 1, Name "Lengths/Lz" } ];
-
-DefineConstant[ Nx = { 1, Min 1, Max 200, Step 10, Name "Mesh/Nx" } ];
-DefineConstant[ Ny = { 1, Min 1, Max 200, Step 10, Name "Mesh/Ny" } ];
-DefineConstant[ Nz = { 1, Min 1, Max 200, Step 10, Name "Mesh/Nz" } ];
-
-lc = 1; // useless
-Point(1) = { 0, 0, 0, lc};
-Point(2) = { Lx, 0, 0, lc};
-Point(3) = { Lx, Ly, 0, lc};
-Point(4) = { 0, Ly, 0, lc};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-
-Line Loop(5) = {1, 2, 3, 4};
-
-Plane Surface(6) = {5};
-
-Transfinite Line {1, 3} = Nx+1 Using Progression 1;
-Transfinite Line {4, 2} = Ny+1 Using Progression 1;
-
-Transfinite Surface {6};
-Recombine Surface {6};
-Extrude {0, 0, Lz} {
- Surface{6}; Layers{Nz}; Recombine;
-}
-Physical Volume("Volume") = {1};
-
-Physical Surface("FaceZ0") = {6};
-Physical Surface("FaceZ1") = {28};
-Physical Surface("FaceY0") = {15};
-Physical Surface("FaceX1") = {19};
-Physical Surface("FaceY1") = {23};
-Physical Surface("FaceX0") = {27};
-
-Physical Line("Line1") = {13};
-Physical Line("Line2") = {14};
-Physical Line("Line3") = {18};
-Physical Line("Line4") = {22};
-
-
-
diff --git a/tbox/tests/fem/quad1.geo b/tbox/tests/fem/quad1.geo
deleted file mode 100644
index 4aac824c..00000000
--- a/tbox/tests/fem/quad1.geo
+++ /dev/null
@@ -1,36 +0,0 @@
-// a square meshed with quads
-
-DefineConstant[ Lx = { 1, Min 5, Max 20, Step 1, Name "Lengths/Lx" } ];
-DefineConstant[ Ly = { 1, Min 5, Max 20, Step 1, Name "Lengths/Ly" } ];
-
-DefineConstant[ Nx = { 1, Min 1, Max 200, Step 10, Name "Mesh/Nx" } ];
-DefineConstant[ Ny = { 1, Min 1, Max 200, Step 10, Name "Mesh/Ny" } ];
-
-lc = 1; // useless
-Point(1) = { 0, 0, 0, lc};
-Point(2) = { Lx, 0, 0, lc};
-Point(3) = { Lx, Ly, 0, lc};
-Point(4) = { 0, Ly, 0, lc};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-
-Line Loop(1) = {1, 2, 3, 4};
-Plane Surface(1) = {1};
-
-Transfinite Line {1, 3} = Nx+1 Using Progression 1;
-Transfinite Line {2, 4} = Ny+1 Using Progression 1;
-Recombine Surface {1};
-
-Physical Point("P1") = {1};
-Physical Point("P2") = {2};
-Physical Point("P3") = {3};
-Physical Point("P4") = {4};
-Physical Line("Bottom") = {1};
-Physical Line("Right") = {2};
-Physical Line("Top") = {3};
-Physical Line("Left") = {4};
-Physical Surface("S1") = {1};
-
diff --git a/tbox/tests/fem/tri1.geo b/tbox/tests/fem/tri1.geo
deleted file mode 100644
index eef7a140..00000000
--- a/tbox/tests/fem/tri1.geo
+++ /dev/null
@@ -1,21 +0,0 @@
-// a triangle
-
-Point(1) = { 0, 0, 0, 2};
-Point(2) = { 1, 0, 0, 2};
-Point(3) = { 0, 1, 0, 2};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 1};
-
-Line Loop(1) = {1, 2, 3};
-Plane Surface(1) = {1};
-
-Physical Point("P1") = {1};
-Physical Point("P2") = {2};
-Physical Point("P3") = {3};
-Physical Line("L1") = {1};
-Physical Line("L2") = {2};
-Physical Line("L3") = {3};
-Physical Surface("S1") = {1};
-
diff --git a/tbox/tests/gmshio.py b/tbox/tests/gmshio.py
deleted file mode 100755
index 6e876a86..00000000
--- a/tbox/tests/gmshio.py
+++ /dev/null
@@ -1,51 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import tbox
-import tbox.gmsh as gmsh
-
-def main():
- # test read/write mesh
- msh = gmsh.MeshLoader("models/model.geo",__file__).execute()
- printtags(msh)
-
- gmshWriter = tbox.GmshExport(msh)
- print(gmshWriter)
- gmshWriter.save(msh.name)
-
- gmshReader = tbox.GmshImport(msh) # could be reused from gmsh.MeshLoader
- print(gmshReader)
-
- # test read/write results
- test = tbox.UnitTest()
- test.gmshIO(gmshWriter, gmshReader)
-
-def printtags(mshdata):
- print("\n-ptags:")
- for t in list(mshdata.ptags.items()):
- print(t[1])
- print("\n-etags:")
- for t in list(mshdata.etags.items()):
- print(t[1])
- print("\n-partitions:")
- for t in list(mshdata.parts.items()):
- print(t[1])
-
-if __name__ == "__main__":
- main()
-
diff --git a/tbox/tests/helloworld.slurm.sh b/tbox/tests/helloworld.slurm.sh
deleted file mode 100755
index fd76eec2..00000000
--- a/tbox/tests/helloworld.slurm.sh
+++ /dev/null
@@ -1,18 +0,0 @@
-#!/bin/bash
-# Submission script for NIC4
-#SBATCH --job-name=helloworld
-#SBATCH --time=00:00:10 # hh:mm:ss
-#
-#SBATCH --ntasks=2
-#SBATCH --mem-per-cpu=200 # megabytes
-#SBATCH --partition=defq
-#
-#SBATCH --mail-user=rboman
-#SBATCH --mail-type=ALL
-#
-#SBATCH --comment=math0471
-
-. ~/.bash_profile master2
-
-module list
-mpirun python-mpi helloworld.py
diff --git a/tbox/tests/meshDeformation.py b/tbox/tests/meshDeformation.py
deleted file mode 100644
index a1870488..00000000
--- a/tbox/tests/meshDeformation.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# Test mesh deformation
-
-import numpy as np
-import tbox
-import tbox.gmsh as gmsh
-import fwk
-from fwk.wutils import parseargs
-
-def main():
-
- # timer
- tms = fwk.Timers()
- tms["total"].start()
-
- # parameters for mesh deformation
- dx = 0.1
- dy = -0.6
-
- # mesh an beam
- pars = {}
- msh = gmsh.MeshLoader("models/beam.geo",__file__).execute(**pars)
- gmshWriter = tbox.GmshExport(msh)
- # create mesh deformation handler
- mshDef = tbox.MshDeform(msh, 2)
- mshDef.setField("internalField")
- mshDef.addFixed(["clamp"])
- mshDef.addMoving(["tip"])
- mshDef.initialize()
- args = parseargs()
- mshDef.nthreads = args.k
-
- # deform the mesh (dummy translation of "tip" nodes)
- mshDef.savePos()
- msh.nodes[1].pos[0] += dx
- msh.nodes[1].pos[1] += dy
- msh.nodes[2].pos[0] += dx
- msh.nodes[2].pos[1] += dy
-
- # deform the mesh
- test = tbox.UnitTest()
- tms["deform"].start()
- test.mshDeform(mshDef, 2)
- tms["deform"].stop()
- gmshWriter.save("beam_def")
-
- # display timers
- tms["total"].stop()
- print("CPU statistics")
- print(tms)
-
- # eof
- print('')
-
-if __name__ == "__main__":
- main()
diff --git a/tbox/tests/meshDeformation3.py b/tbox/tests/meshDeformation3.py
deleted file mode 100644
index 9fe169ee..00000000
--- a/tbox/tests/meshDeformation3.py
+++ /dev/null
@@ -1,72 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# Test mesh deformation
-
-import numpy as np
-import tbox
-import tbox.gmsh as gmsh
-import fwk
-from fwk.wutils import parseargs
-
-def main():
-
- # timer
- tms = fwk.Timers()
- tms["total"].start()
-
- # parameters for mesh deformation
- dz = 1.5
-
- # mesh an beam
- pars = {}
- msh = gmsh.MeshLoader("models/beam3.geo",__file__).execute(**pars)
- gmshWriter = tbox.GmshExport(msh)
- # create mesh deformation handler
- mshDef = tbox.MshDeform(msh, 3)
- mshDef.setField("field")
- mshDef.addFixed(["clamp"])
- mshDef.addMoving(["tip"])
- mshDef.initialize()
- args = parseargs()
- mshDef.nthreads = args.k
-
- # deform the mesh (dummy translation of "tip" nodes)
- mshDef.savePos()
- msh.nodes[4].pos[2] += dz
- msh.nodes[5].pos[2] += dz
- msh.nodes[6].pos[2] += dz
- msh.nodes[7].pos[2] += dz
-
- # deform the mesh
- test = tbox.UnitTest()
- tms["deform"].start()
- test.mshDeform(mshDef, 3)
- tms["deform"].stop()
- gmshWriter.save(msh.name+"_def")
-
- # display timers
- tms["total"].stop()
- print("CPU statistics")
- print(tms)
-
- # eof
- print('')
-
-if __name__ == "__main__":
- main()
diff --git a/tbox/tests/models/beam.geo b/tbox/tests/models/beam.geo
deleted file mode 100644
index c67ef26a..00000000
--- a/tbox/tests/models/beam.geo
+++ /dev/null
@@ -1,21 +0,0 @@
-Point(1) = {0 ,0,0};
-Point(2) = {10,0,0};
-Point(3) = {10,1,0};
-Point(4) = {0 ,1,0};
-
-Line(1) = {1,2};
-Line(2) = {2,3};
-Line(3) = {3,4};
-Line(4) = {4,1};
-
-Line Loop(1) = {1,2,3,4};
-Surface(1) = {1};
-
-Transfinite Line{1, 3} = 10+1;
-Transfinite Line{2, 4} = 1+1;
-
-Transfinite Surface{1} = {1, 2, 3, 4};
-
-Physical Surface("internalField", 10) = {1};
-Physical Line("clamp", 11) = {4};
-Physical Line("tip", 12) = {2};
diff --git a/tbox/tests/models/beam3.geo b/tbox/tests/models/beam3.geo
deleted file mode 100644
index 23d5d9a1..00000000
--- a/tbox/tests/models/beam3.geo
+++ /dev/null
@@ -1,47 +0,0 @@
-Point(1) = {0 ,0,0,1};
-Point(2) = {1 ,0,0,1};
-Point(3) = {1 ,0,2,1};
-Point(4) = {0 ,0,2,1};
-Point(5) = {0 ,10,0,1};
-Point(6) = {1 ,10,0,1};
-Point(7) = {1 ,10,2,1};
-Point(8) = {0 ,10,2,1};
-
-
-Line(1) = {1,2};
-Line(2) = {2,3};
-Line(3) = {3,4};
-Line(4) = {4,1};
-Line(5) = {5,6};
-Line(6) = {6,7};
-Line(7) = {7,8};
-Line(8) = {8,5};
-Line(9) = {1,5};
-Line(10) = {2,6};
-Line(11) = {3,7};
-Line(12) = {4,8};
-
-Line Loop(1) = {1,2,3,4};
-Surface(1) = {-1};
-Line Loop(2) = {5,6,7,8};
-Surface(2) = {2};
-Line Loop(3) = {1,10,-5,-9};
-Surface(3) = {3};
-Line Loop(4) = {2,11,-6,-10};
-Surface(4) = {4};
-Line Loop(5) = {3,12,-7,-11};
-Surface(5) = {5};
-Line Loop(6) = {4,9,-8,-12};
-Surface(6) = {6};
-
-Surface Loop(1) = {1,2,3,4,5,6};
-Volume(1) = (1);
-
-Transfinite Line{1,2,3,4,5,6,7,8} = 1+1;
-Transfinite Line{9,10,11,12} = 10+1;
-Transfinite Surface{1,2,3,4,5,6};
-
-Physical Volume("field") = {1};
-Physical Surface("clamp") = {1};
-Physical Surface("tip") = {2};
-Physical Surface("side") = {3,4,5,6};
diff --git a/tbox/tests/models/model.geo b/tbox/tests/models/model.geo
deleted file mode 100644
index 2543d346..00000000
--- a/tbox/tests/models/model.geo
+++ /dev/null
@@ -1,14 +0,0 @@
-Point(1) = { 0, 0, 0, 0.1};
-Point(2) = { 1, 0, 0, 0.2};
-Point(3) = { 1, 1, 0, 0.3};
-Point(4) = { 0, 1, 0, 0.1};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-
-Line Loop(1) = {1, 2, 3, 4};
-Plane Surface(1) = {1};
-
-
diff --git a/tbox/tests/mpi/helloworld.py b/tbox/tests/mpi/helloworld.py
deleted file mode 100644
index 1a247750..00000000
--- a/tbox/tests/mpi/helloworld.py
+++ /dev/null
@@ -1,32 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-"""
-Parallel Hello World
-"""
-
-from mpi4py import MPI
-import sys
-
-size = MPI.COMM_WORLD.Get_size()
-rank = MPI.COMM_WORLD.Get_rank()
-name = MPI.Get_processor_name()
-
-sys.stdout.write(
- "Hello, World! I am process %d of %d on %s.\n"
- % (rank, size, name))
diff --git a/tbox/utils.py b/tbox/utils.py
deleted file mode 100644
index 7d32f8dc..00000000
--- a/tbox/utils.py
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-"""@package docstring
-Utilities for tbox
-Adrien Crovato
-"""
-
-def myrange(start, stop, step):
- """Extended range with custom step
- Adrien Crovato
- """
- vec = []
- i = start
- while i <= stop:
- vec.append(i)
- i += step
- return vec
-
-def plot(x, y, xlbl, ylbl, title, invert=False):
- """Plot using matplotlib
- Adrien Crovato
- @todo extend to pass unlimited number of arguments
- """
- from fwk.wutils import parseargs
- args = parseargs()
- if not args.nogui:
- import matplotlib.pyplot as plt
- # define font
- font = {'family': 'serif',
- 'color': 'darkred',
- 'weight': 'normal',
- 'size': 16,}
- # plot results
- plt.plot(x, y, 'b-',lw=2)
- plt.xlabel(xlbl, fontdict=font)
- plt.ylabel(ylbl, fontdict=font)
- plt.title(title, fontdict=font)
- if invert:
- plt.gca().invert_yaxis()
- #plt.grid(True)
- plt.show()
-
-def sort(id, data):
- """Sort data array against id (line connectivity list)
- Adrien Crovato
- """
- import numpy as np
- # sort id vector
- id = id[id[:,0].argsort(),:]
- # deep copy of data
- _data = np.zeros((data.shape[0], data.shape[1]))
- _data[:] = data
- # sort data against id
- _max = np.argmax(data[:,0])
- data[0,:] = _data[_max,:]
- nextId = id[np.where(id[:, 0]==_max)[0][0], 0]
- for i in range(1, id.shape[0]):
- data[i,:] = _data[id[nextId,1],:]
- nextId = id[nextId,1]
-
-def read(filename):
- """Read from file and store in data array
- Adrien Croavto
- """
- import io
- import numpy as np
- # read file
- fl = io.open(filename, 'r')
- label = fl.readline().split(',')
- fl.close()
- data = np.loadtxt(filename, delimiter=',', skiprows=1)
- return data
-
-def write(data, name, frmt, dlm, hdr, cmts):
- """Write data array to file
- Adrien Crovato
- """
- import numpy as np
- print('writing data file ' + name + '.')
- np.savetxt(name, data, fmt=frmt, delimiter=dlm, header=hdr, comments=cmts)
diff --git a/tbox/viewer.py b/tbox/viewer.py
deleted file mode 100644
index ddabbc90..00000000
--- a/tbox/viewer.py
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import os, os.path
-
-class GUI:
- """Default GUI for gmsh
- Romain Boman
- """
- def __init__(self):
- pass
- def open(self,prefix):
- mshfile = prefix+".msh"
- if not os.path.isfile(mshfile):
- raise Exception("file not found %s" % mshfile)
- posfile = prefix+".pos"
- if not os.path.isfile(posfile):
- raise Exception("file not found %s" % posfile)
- optfile = prefix+".opt"
- if not os.path.isfile(optfile):
- self.defopt(optfile)
- cmd="gmsh %s %s %s" % (mshfile, posfile, optfile)
- os.system(cmd)
-
- def defopt(self,fname='defaultflowOpt.opt'):
- f = open(fname,'w')
- f.write("General.Orthographic = 0;\n")
- f.close()
-
diff --git a/tboxVtk/CMakeLists.txt b/tboxVtk/CMakeLists.txt
deleted file mode 100644
index 156e07c4..00000000
--- a/tboxVtk/CMakeLists.txt
+++ /dev/null
@@ -1,20 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# Add source dir
-ADD_SUBDIRECTORY( src )
-ADD_SUBDIRECTORY( _src )
-
-# Add test dir
-MACRO_AddTest(${CMAKE_CURRENT_SOURCE_DIR}/tests)
diff --git a/tboxVtk/__init__.py b/tboxVtk/__init__.py
deleted file mode 100644
index d687db1b..00000000
--- a/tboxVtk/__init__.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# -*- coding: utf-8 -*-
-# tboxVtk MODULE initialization file
-
-# Copyright 2018 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import fwk
-from tboxVtkw import *
-
diff --git a/tboxVtk/_src/CMakeLists.txt b/tboxVtk/_src/CMakeLists.txt
deleted file mode 100644
index dbf06c35..00000000
--- a/tboxVtk/_src/CMakeLists.txt
+++ /dev/null
@@ -1,49 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake file for the SWIG interface of tboxVtk.so
-
-INCLUDE(${SWIG_USE_FILE})
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.swg)
-FILE(GLOB ISRCS *.i)
-
-SET(CMAKE_SWIG_FLAGS "")
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
-
-SET(SWINCFLAGS
--I${PROJECT_SOURCE_DIR}/tboxVtk/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
-)
-SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
-
-if (${CMAKE_VERSION} VERSION_LESS "3.8.0")
- SWIG_ADD_MODULE(tboxVtkw python ${ISRCS} ${SRCS})
-else()
- SWIG_ADD_LIBRARY(tboxVtkw LANGUAGE python SOURCES ${ISRCS} ${SRCS})
-endif()
-MACRO_DebugPostfix(_tboxVtkw)
-
-TARGET_INCLUDE_DIRECTORIES(_tboxVtkw PRIVATE ${PROJECT_SOURCE_DIR}/tboxVtk/_src
- ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
- ${PYTHON_INCLUDE_PATH}
-)
-
-SWIG_LINK_LIBRARIES(tboxVtkw
- tboxVtk tbox fwk ${PYTHON_LIBRARIES}
-)
diff --git a/tboxVtk/_src/tboxVtkw.h b/tboxVtk/_src/tboxVtkw.h
deleted file mode 100644
index f1349687..00000000
--- a/tboxVtk/_src/tboxVtkw.h
+++ /dev/null
@@ -1,17 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wVtkExport.h"
diff --git a/tboxVtk/_src/tboxVtkw.i b/tboxVtk/_src/tboxVtkw.i
deleted file mode 100644
index 2a7ec115..00000000
--- a/tboxVtk/_src/tboxVtkw.i
+++ /dev/null
@@ -1,55 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// tboxVtk.i: SWIG input file of the tboxVtk python interface
-
-%feature("autodoc","1");
-
-%module(docstring=
-"'tboxVtkw' module: Vtk for shared tools
-(c) ULg - A&M",
-directors="1",
-threads="1"
-) tboxVtkw
-%{
-
-//#if defined(_WIN32) && defined(__GNUC__)
-#undef _hypot
-#include <cmath>
-//#endif
-
-#include <memory>
-#include <string>
-#include <sstream>
-#include <typeinfo>
-#include "tboxVtk.h"
-
-#include "fwkw.h"
-#include "tboxw.h"
-#include "tboxVtkw.h"
-
-%}
-
-%include "fwkw.swg"
-
-// ----------- MODULES UTILISES ------------
-%import "tboxw.i"
-
-// ----------- TBOXVTK CLASSES ----------------
-%include "tboxVtk.h"
-
-%shared_ptr(tboxVtk::VtkExport)
-%include "wVtkExport.h"
diff --git a/tboxVtk/cutter.py b/tboxVtk/cutter.py
deleted file mode 100644
index f0dc2260..00000000
--- a/tboxVtk/cutter.py
+++ /dev/null
@@ -1,89 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# @brief VTK cut plane post-processing
-# @authors Adrien Crovato, Kim Liegeois
-
-try:
- import vtk
-except:
- raise Exception('VTK not found. Aborting!\n')
-
-class Cutter:
- def __init__(self, _grid):
- self.grid = _grid
-
- def cut(self, tag, cutO, cutN, tag_name="tag"):
- '''
- Cut the physical group ided "tag" with a plane defined by point "cutO" and normal "cutN"
- '''
- import numpy as np
- # create a threshold containing the physical group (tag) to cut
- thresh = vtk.vtkThreshold()
- thresh.ThresholdBetween(tag,tag)
- thresh.SetInputConnection(self.grid)
- thresh.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, tag_name) # "tag" is the default name set in tboxVtk::VtkExport::save
- thresh.Update()
- # create cutting plane
- plane = vtk.vtkPlane()
- plane.SetOrigin(cutO[0], cutO[1], cutO[2])
- plane.SetNormal(cutN[0], cutN[1], cutN[2])
- # cut the threshold and get data
- cutter = vtk.vtkCutter()
- cutter.SetCutFunction(plane)
- cutter.SetInputConnection(thresh.GetOutputPort())
- cutter.Update()
- return cutter.GetOutput()
-
- def extract(self, cutData, tagDim, vname, atPoint = True):
- '''
- Extract points "pts", connectivity list "elems" and data "vals" named "vname" from cutting plane data "cutData".
- The physical group dimension is given by "tagDim" and "atPoint" is True if vname is defined at points.
- '''
- import numpy as np
- # transfer point coordinates
- _pts = cutData.GetPoints()
- pts = np.zeros((_pts.GetNumberOfPoints(), 3))
- for i in range(0, pts.shape[0]):
- for j in range(0, 3):
- pts[i][j] = _pts.GetPoint(i)[j]
- # transfer connectivity
- if tagDim == 3:
- _elems = cutData.GetPolys().GetData()
- nV = 3 # assumes that all Poly(gon)s are triangles
- elif tagDim == 2:
- _elems = cutData.GetLines().GetData()
- nV = 2
- else:
- raise Exception('tagDim can only be 2 or 3 but ' + tagDim + ' was given!\n')
- elems = np.zeros((_elems.GetNumberOfTuples() // (nV+1), nV), dtype=int)
- for i in range(0, elems.shape[0]):
- for j in range(0, nV):
- elems[i][j] = _elems.GetTuple((nV+1)*i+j+1)[0]
- # transfer variables
- vals = {}
- for name in vname:
- if atPoint: # data at points
- _vals = cutData.GetPointData().GetArray(name)
- else: # data at elements
- _vals = cutData.GetCellData().GetArray(name)
- vals[name] = np.zeros((_vals.GetNumberOfTuples(), _vals.GetNumberOfComponents()))
- for i in range(0, vals[name].shape[0]):
- for j in range(0, vals[name].shape[1]):
- vals[name][i][j] = _vals.GetTuple(i)[j]
- return pts, elems, vals
diff --git a/tboxVtk/lineExtractor.py b/tboxVtk/lineExtractor.py
deleted file mode 100644
index df305b5c..00000000
--- a/tboxVtk/lineExtractor.py
+++ /dev/null
@@ -1,153 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# @brief VTK cut plane post-processing
-# @authors Adrien Crovato, Kim Liegeois
-
-try:
- import vtk
-except:
- raise Exception('VTK not found. Aborting!\n')
-
-class LineExtractor:
- def __init__(self, _grid):
- self.grid = _grid
-
- def cut(self, tag, p1, p2, tag_name="tag"):
- '''
- Cut the physical group ided tag_name="tag" with a line defined by point "p1" and normal "p2"
- '''
- import numpy as np
- self.p1 = np.zeros((3,))
- self.p2 = np.zeros((3,))
- for j in range(0, 3):
- self.p1[j] = p1[j]
- self.p2[j] = p2[j]
-
- p12 = self.p2-self.p1
-
- v1 = np.zeros((3,))
- v1[0] = 1
-
- if np.linalg.norm(np.cross(v1,p12)) != 0:
- v1 = np.cross(v1, p12)
- v2 = np.cross(v1, p12)
- else:
- v1[0] = 0
- v1[1] = 1
- v2 = np.zeros((3,))
- v2[2] = 1
-
- # create a threshold containing the physical group (tag) to cut
- thresh = vtk.vtkThreshold()
- thresh.ThresholdBetween(tag,tag)
- thresh.SetInputConnection(self.grid)
- thresh.SetInputArrayToProcess(0, 0, 0, vtk.vtkDataObject.FIELD_ASSOCIATION_CELLS, tag_name) # "tag" is the default name set in tboxVtk::VtkExport::save
- thresh.Update()
- # create the first cutting plane
- plane1 = vtk.vtkPlane()
- plane1.SetOrigin(p1[0], p1[1], p1[2])
- plane1.SetNormal(v1[0], v1[1], v1[2])
- plane2 = vtk.vtkPlane()
- plane2.SetOrigin(p1[0], p1[1], p1[2])
- plane2.SetNormal(v2[0], v2[1], v2[2])
- # cut the threshold and get data
- cutter1 = vtk.vtkFiltersCorePython.vtkCutter()
- cutter1.SetCutFunction(plane1)
- cutter1.SetInputConnection(thresh.GetOutputPort())
- cutter1.Update()
-
- cutter2 = vtk.vtkFiltersCorePython.vtkCutter()
- cutter2.SetCutFunction(plane2)
- cutter2.SetInputConnection(cutter1.GetOutputPort())
- cutter2.Update()
-
- return cutter2.GetOutput()
-
- def extract(self, cutData, vname, atPoint = True):
- '''
- Extract points "pts", connectivity list "elems" and data "vals" named "vname" from cutting plane data "cutData".
- The physical group dimension is given by "tagDim" and "atPoint" is True if vname is defined at points.
- '''
- import numpy as np
- # transfer point coordinates
- norm_p1p2 = np.linalg.norm(self.p2-self.p1)
- _pts = cutData.GetPoints()
- pts = np.zeros((_pts.GetNumberOfPoints(), ))
- for i in range(0, len(pts)):
- tmp = np.zeros((3,))
- for j in range(0, 3):
- tmp[j] = _pts.GetPoint(i)[j]
- pts[i] = np.inner(self.p2-self.p1,tmp-self.p1) / norm_p1p2
- indices_tmp = np.argsort(pts)
- pts = pts
- pts_res = pts[indices_tmp]
- indices_2 = np.argwhere((pts_res >= 0) & (pts_res <= norm_p1p2))
- pts_res = pts_res[indices_2]
- # transfer connectivity
- _elems = cutData.GetLines().GetData()
- nV = 2
- max_nb_elems = _elems.GetNumberOfTuples() // (nV+1)
- current_nb_elems = 0
- indices_elems = np.zeros((max_nb_elems,), dtype=int)
- for i in range(0, max_nb_elems):
- has_to_be_kept = True
- for j in range(0, nV):
- node_id = int(_elems.GetTuple((nV+1)*i+j+1)[0])
- if pts[node_id] < 0 or pts[node_id] > norm_p1p2:
- has_to_be_kept = False
- break
- if has_to_be_kept:
- current_nb_elems = current_nb_elems + 1
- indices_elems[i] = 1
- indices_elems_2 = np.zeros((current_nb_elems,), dtype=int)
- elems = np.zeros((current_nb_elems, nV), dtype=int)
- mean_per_elems = np.zeros((current_nb_elems,))
- current_i = -1
- for i in range(0, max_nb_elems):
- if indices_elems[i]:
- current_i = current_i + 1
- indices_elems_2[current_i] = i
- for j in range(0, nV):
- node_id = int(_elems.GetTuple((nV+1)*i+j+1)[0])
- elems[current_i][j] = np.argwhere(pts[node_id] == pts_res)[0][0]
- mean_per_elems[current_i] = mean_per_elems[current_i] + 0.5*pts[node_id]
- indices_elems_3 = np.argsort(mean_per_elems)
- elems = elems[indices_elems_3][:]
- # transfer variables
- vals = {}
- for name in vname:
- if atPoint: # data at points
- _vals = cutData.GetPointData().GetArray(name)
- else: # data at elements
- _vals = cutData.GetCellData().GetArray(name)
- vals[name] = np.zeros((_vals.GetNumberOfTuples(), _vals.GetNumberOfComponents()))
- for i in range(0, vals[name].shape[0]):
- for j in range(0, vals[name].shape[1]):
- if atPoint:
- vals[name][i][j] = _vals.GetTuple(i)[j]
- else:
- vals[name][i][j] = _vals.GetTuple(i)[j]
- if atPoint:
- tmp = vals[name][indices_tmp][:]
- vals[name] = tmp[indices_2][:]
- else:
- tmp = vals[name][indices_elems_2][:]
- vals[name] = tmp[indices_elems_3][:]
-
- return pts_res, elems, vals
diff --git a/tboxVtk/qt5vtk6/QVTKRenderWindowInteractor.py b/tboxVtk/qt5vtk6/QVTKRenderWindowInteractor.py
deleted file mode 100644
index 09c5e3da..00000000
--- a/tboxVtk/qt5vtk6/QVTKRenderWindowInteractor.py
+++ /dev/null
@@ -1,644 +0,0 @@
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-"""
-A simple VTK widget for PyQt or PySide.
-See http://www.trolltech.com for Qt documentation,
-http://www.riverbankcomputing.co.uk for PyQt, and
-http://pyside.github.io for PySide.
-
-This class is based on the vtkGenericRenderWindowInteractor and is
-therefore fairly powerful. It should also play nicely with the
-vtk3DWidget code.
-
-Created by Prabhu Ramachandran, May 2002
-Based on David Gobbi's QVTKRenderWidget.py
-
-Changes by Gerard Vermeulen Feb. 2003
- Win32 support.
-
-Changes by Gerard Vermeulen, May 2003
- Bug fixes and better integration with the Qt framework.
-
-Changes by Phil Thompson, Nov. 2006
- Ported to PyQt v4.
- Added support for wheel events.
-
-Changes by Phil Thompson, Oct. 2007
- Bug fixes.
-
-Changes by Phil Thompson, Mar. 2008
- Added cursor support.
-
-Changes by Rodrigo Mologni, Sep. 2013 (Credit to Daniele Esposti)
- Bug fix to PySide: Converts PyCObject to void pointer.
-
-Changes by Greg Schussman, Aug. 2014
- The keyPressEvent function now passes keysym instead of None.
-
-Changes by Alex Tsui, Apr. 2015
- Port from PyQt4 to PyQt5.
-
-Changes by Fabian Wenzel, Jan. 2016
- Support for Python3
-"""
-
-
-
-
-import vtk # added by RoBo
-PyQtImpl = None # added by RoBo
-
-# Check whether a specific PyQt implementation was chosen
-try:
- import vtk.qt
- PyQtImpl = vtk.qt.PyQtImpl
-except ImportError:
- pass
-
-# Check whether a specific QVTKRenderWindowInteractor base
-# class was chosen, can be set to "QGLWidget"
-QVTKRWIBase = "QWidget"
-try:
- import vtk.qt
- QVTKRWIBase = vtk.qt.QVTKRWIBase
-except ImportError:
- pass
-
-if PyQtImpl is None:
- # Autodetect the PyQt implementation to use
- try:
- import PyQt5
- PyQtImpl = "PyQt5"
- except ImportError:
- try:
- import PyQt4
- PyQtImpl = "PyQt4"
- except ImportError:
- try:
- import PySide
- PyQtImpl = "PySide"
- except ImportError:
- raise ImportError("Cannot load either PyQt or PySide")
-
-if PyQtImpl == "PyQt5":
- if QVTKRWIBase == "QGLWidget":
- from PyQt5.QtOpenGL import QGLWidget
- from PyQt5.QtWidgets import QWidget
- from PyQt5.QtWidgets import QSizePolicy
- from PyQt5.QtWidgets import QApplication
- from PyQt5.QtCore import Qt
- from PyQt5.QtCore import QTimer
- from PyQt5.QtCore import QObject
- from PyQt5.QtCore import QSize
- from PyQt5.QtCore import QEvent
-elif PyQtImpl == "PyQt4":
- if QVTKRWIBase == "QGLWidget":
- from PyQt4.QtOpenGL import QGLWidget
- from PyQt4.QtGui import QWidget
- from PyQt4.QtGui import QSizePolicy
- from PyQt4.QtGui import QApplication
- from PyQt4.QtCore import Qt
- from PyQt4.QtCore import QTimer
- from PyQt4.QtCore import QObject
- from PyQt4.QtCore import QSize
- from PyQt4.QtCore import QEvent
-elif PyQtImpl == "PySide":
- if QVTKRWIBase == "QGLWidget":
- from PySide.QtOpenGL import QGLWidget
- from PySide.QtGui import QWidget
- from PySide.QtGui import QSizePolicy
- from PySide.QtGui import QApplication
- from PySide.QtCore import Qt
- from PySide.QtCore import QTimer
- from PySide.QtCore import QObject
- from PySide.QtCore import QSize
- from PySide.QtCore import QEvent
-else:
- raise ImportError("Unknown PyQt implementation " + repr(PyQtImpl))
-
-# Define types for base class, based on string
-if QVTKRWIBase == "QWidget":
- QVTKRWIBaseClass = QWidget
-elif QVTKRWIBase == "QGLWidget":
- QVTKRWIBaseClass = QGLWidget
-else:
- raise ImportError("Unknown base class for QVTKRenderWindowInteractor " + QVTKRWIBase)
-
-class QVTKRenderWindowInteractor(QVTKRWIBaseClass):
-
- """ A QVTKRenderWindowInteractor for Python and Qt. Uses a
- vtkGenericRenderWindowInteractor to handle the interactions. Use
- GetRenderWindow() to get the vtkRenderWindow. Create with the
- keyword stereo=1 in order to generate a stereo-capable window.
-
- The user interface is summarized in vtkInteractorStyle.h:
-
- - Keypress j / Keypress t: toggle between joystick (position
- sensitive) and trackball (motion sensitive) styles. In joystick
- style, motion occurs continuously as long as a mouse button is
- pressed. In trackball style, motion occurs when the mouse button
- is pressed and the mouse pointer moves.
-
- - Keypress c / Keypress o: toggle between camera and object
- (actor) modes. In camera mode, mouse events affect the camera
- position and focal point. In object mode, mouse events affect
- the actor that is under the mouse pointer.
-
- - Button 1: rotate the camera around its focal point (if camera
- mode) or rotate the actor around its origin (if actor mode). The
- rotation is in the direction defined from the center of the
- renderer's viewport towards the mouse position. In joystick mode,
- the magnitude of the rotation is determined by the distance the
- mouse is from the center of the render window.
-
- - Button 2: pan the camera (if camera mode) or translate the actor
- (if object mode). In joystick mode, the direction of pan or
- translation is from the center of the viewport towards the mouse
- position. In trackball mode, the direction of motion is the
- direction the mouse moves. (Note: with 2-button mice, pan is
- defined as <Shift>-Button 1.)
-
- - Button 3: zoom the camera (if camera mode) or scale the actor
- (if object mode). Zoom in/increase scale if the mouse position is
- in the top half of the viewport; zoom out/decrease scale if the
- mouse position is in the bottom half. In joystick mode, the amount
- of zoom is controlled by the distance of the mouse pointer from
- the horizontal centerline of the window.
-
- - Keypress 3: toggle the render window into and out of stereo
- mode. By default, red-blue stereo pairs are created. Some systems
- support Crystal Eyes LCD stereo glasses; you have to invoke
- SetStereoTypeToCrystalEyes() on the rendering window. Note: to
- use stereo you also need to pass a stereo=1 keyword argument to
- the constructor.
-
- - Keypress e: exit the application.
-
- - Keypress f: fly to the picked point
-
- - Keypress p: perform a pick operation. The render window interactor
- has an internal instance of vtkCellPicker that it uses to pick.
-
- - Keypress r: reset the camera view along the current view
- direction. Centers the actors and moves the camera so that all actors
- are visible.
-
- - Keypress s: modify the representation of all actors so that they
- are surfaces.
-
- - Keypress u: invoke the user-defined function. Typically, this
- keypress will bring up an interactor that you can type commands in.
-
- - Keypress w: modify the representation of all actors so that they
- are wireframe.
- """
-
- # Map between VTK and Qt cursors.
- _CURSOR_MAP = {
- 0: Qt.ArrowCursor, # VTK_CURSOR_DEFAULT
- 1: Qt.ArrowCursor, # VTK_CURSOR_ARROW
- 2: Qt.SizeBDiagCursor, # VTK_CURSOR_SIZENE
- 3: Qt.SizeFDiagCursor, # VTK_CURSOR_SIZENWSE
- 4: Qt.SizeBDiagCursor, # VTK_CURSOR_SIZESW
- 5: Qt.SizeFDiagCursor, # VTK_CURSOR_SIZESE
- 6: Qt.SizeVerCursor, # VTK_CURSOR_SIZENS
- 7: Qt.SizeHorCursor, # VTK_CURSOR_SIZEWE
- 8: Qt.SizeAllCursor, # VTK_CURSOR_SIZEALL
- 9: Qt.PointingHandCursor, # VTK_CURSOR_HAND
- 10: Qt.CrossCursor, # VTK_CURSOR_CROSSHAIR
- }
-
- def __init__(self, parent=None, **kw):
- # the current button
- self._ActiveButton = Qt.NoButton
-
- # private attributes
- self.__saveX = 0
- self.__saveY = 0
- self.__saveModifiers = Qt.NoModifier
- self.__saveButtons = Qt.NoButton
- self.__wheelDelta = 0
-
- # do special handling of some keywords:
- # stereo, rw
-
- try:
- stereo = bool(kw['stereo'])
- except KeyError:
- stereo = False
-
- try:
- rw = kw['rw']
- except KeyError:
- rw = None
-
- # create base qt-level widget
- if QVTKRWIBase == "QWidget":
- if "wflags" in kw:
- wflags = kw['wflags']
- else:
- wflags = Qt.WindowFlags()
- QWidget.__init__(self, parent, wflags | Qt.MSWindowsOwnDC)
- elif QVTKRWIBase == "QGLWidget":
- QGLWidget.__init__(self, parent)
-
- if rw: # user-supplied render window
- self._RenderWindow = rw
- else:
- self._RenderWindow = vtk.vtkRenderWindow()
-
- WId = self.winId()
-
- # Python2
- if type(WId).__name__ == 'PyCObject':
- from ctypes import pythonapi, c_void_p, py_object
-
- pythonapi.PyCObject_AsVoidPtr.restype = c_void_p
- pythonapi.PyCObject_AsVoidPtr.argtypes = [py_object]
-
- WId = pythonapi.PyCObject_AsVoidPtr(WId)
-
- # Python3
- elif type(WId).__name__ == 'PyCapsule':
- from ctypes import pythonapi, c_void_p, py_object, c_char_p
-
- pythonapi.PyCapsule_GetName.restype = c_char_p
- pythonapi.PyCapsule_GetName.argtypes = [py_object]
-
- name = pythonapi.PyCapsule_GetName(WId)
-
- pythonapi.PyCapsule_GetPointer.restype = c_void_p
- pythonapi.PyCapsule_GetPointer.argtypes = [py_object, c_char_p]
-
- WId = pythonapi.PyCapsule_GetPointer(WId, name)
-
- self._RenderWindow.SetWindowInfo(str(int(WId)))
-
- if stereo: # stereo mode
- self._RenderWindow.StereoCapableWindowOn()
- self._RenderWindow.SetStereoTypeToCrystalEyes()
-
- try:
- self._Iren = kw['iren']
- except KeyError:
- self._Iren = vtk.vtkGenericRenderWindowInteractor()
- self._Iren.SetRenderWindow(self._RenderWindow)
-
- # do all the necessary qt setup
- self.setAttribute(Qt.WA_OpaquePaintEvent)
- self.setAttribute(Qt.WA_PaintOnScreen)
- self.setMouseTracking(True) # get all mouse events
- self.setFocusPolicy(Qt.WheelFocus)
- self.setSizePolicy(QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Expanding))
-
- self._Timer = QTimer(self)
- self._Timer.timeout.connect(self.TimerEvent)
-
- self._Iren.AddObserver('CreateTimerEvent', self.CreateTimer)
- self._Iren.AddObserver('DestroyTimerEvent', self.DestroyTimer)
- self._Iren.GetRenderWindow().AddObserver('CursorChangedEvent',
- self.CursorChangedEvent)
-
- #Create a hidden child widget and connect its destroyed signal to its
- #parent ``Finalize`` slot. The hidden children will be destroyed before
- #its parent thus allowing cleanup of VTK elements.
- self._hidden = QWidget(self)
- self._hidden.hide()
- self._hidden.destroyed.connect(self.Finalize)
-
- def __getattr__(self, attr):
- """Makes the object behave like a vtkGenericRenderWindowInteractor"""
- if attr == '__vtk__':
- return lambda t=self._Iren: t
- elif hasattr(self._Iren, attr):
- return getattr(self._Iren, attr)
- else:
- raise AttributeError(self.__class__.__name__ +
- " has no attribute named " + attr)
-
- def Finalize(self):
- '''
- Call internal cleanup method on VTK objects
- '''
- self._RenderWindow.Finalize()
-
- def CreateTimer(self, obj, evt):
- self._Timer.start(10)
-
- def DestroyTimer(self, obj, evt):
- self._Timer.stop()
- return 1
-
- def TimerEvent(self):
- self._Iren.TimerEvent()
-
- def CursorChangedEvent(self, obj, evt):
- """Called when the CursorChangedEvent fires on the render window."""
- # This indirection is needed since when the event fires, the current
- # cursor is not yet set so we defer this by which time the current
- # cursor should have been set.
- QTimer.singleShot(0, self.ShowCursor)
-
- def HideCursor(self):
- """Hides the cursor."""
- self.setCursor(Qt.BlankCursor)
-
- def ShowCursor(self):
- """Shows the cursor."""
- vtk_cursor = self._Iren.GetRenderWindow().GetCurrentCursor()
- qt_cursor = self._CURSOR_MAP.get(vtk_cursor, Qt.ArrowCursor)
- self.setCursor(qt_cursor)
-
- def closeEvent(self, evt):
- self.Finalize()
-
- def sizeHint(self):
- return QSize(400, 400)
-
- def paintEngine(self):
- return None
-
- def paintEvent(self, ev):
- self._Iren.Render()
-
- def resizeEvent(self, ev):
- w = self.width()
- h = self.height()
- vtk.vtkRenderWindow.SetSize(self._RenderWindow, w, h)
- self._Iren.SetSize(w, h)
- self._Iren.ConfigureEvent()
- self.update()
-
- def _GetCtrlShift(self, ev):
- ctrl = shift = False
-
- if hasattr(ev, 'modifiers'):
- if ev.modifiers() & Qt.ShiftModifier:
- shift = True
- if ev.modifiers() & Qt.ControlModifier:
- ctrl = True
- else:
- if self.__saveModifiers & Qt.ShiftModifier:
- shift = True
- if self.__saveModifiers & Qt.ControlModifier:
- ctrl = True
-
- return ctrl, shift
-
- def enterEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- self._Iren.SetEventInformationFlipY(self.__saveX, self.__saveY,
- ctrl, shift, chr(0), 0, None)
- self._Iren.EnterEvent()
-
- def leaveEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- self._Iren.SetEventInformationFlipY(self.__saveX, self.__saveY,
- ctrl, shift, chr(0), 0, None)
- self._Iren.LeaveEvent()
-
- def mousePressEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- repeat = 0
- if ev.type() == QEvent.MouseButtonDblClick:
- repeat = 1
- self._Iren.SetEventInformationFlipY(ev.x(), ev.y(),
- ctrl, shift, chr(0), repeat, None)
-
- self._ActiveButton = ev.button()
-
- if self._ActiveButton == Qt.LeftButton:
- self._Iren.LeftButtonPressEvent()
- elif self._ActiveButton == Qt.RightButton:
- self._Iren.RightButtonPressEvent()
- elif self._ActiveButton == Qt.MidButton:
- self._Iren.MiddleButtonPressEvent()
-
- def mouseReleaseEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- self._Iren.SetEventInformationFlipY(ev.x(), ev.y(),
- ctrl, shift, chr(0), 0, None)
-
- if self._ActiveButton == Qt.LeftButton:
- self._Iren.LeftButtonReleaseEvent()
- elif self._ActiveButton == Qt.RightButton:
- self._Iren.RightButtonReleaseEvent()
- elif self._ActiveButton == Qt.MidButton:
- self._Iren.MiddleButtonReleaseEvent()
-
- def mouseMoveEvent(self, ev):
- self.__saveModifiers = ev.modifiers()
- self.__saveButtons = ev.buttons()
- self.__saveX = ev.x()
- self.__saveY = ev.y()
-
- ctrl, shift = self._GetCtrlShift(ev)
- self._Iren.SetEventInformationFlipY(ev.x(), ev.y(),
- ctrl, shift, chr(0), 0, None)
- self._Iren.MouseMoveEvent()
-
- def keyPressEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- if ev.key() < 256:
- key = str(ev.text())
- else:
- key = chr(0)
-
- keySym = _qt_key_to_key_sym(ev.key())
- if shift and len(keySym) == 1 and keySym.isalpha():
- keySym = keySym.upper()
-
- self._Iren.SetEventInformationFlipY(self.__saveX, self.__saveY,
- ctrl, shift, key, 0, keySym)
- self._Iren.KeyPressEvent()
- self._Iren.CharEvent()
-
- def keyReleaseEvent(self, ev):
- ctrl, shift = self._GetCtrlShift(ev)
- if ev.key() < 256:
- key = chr(ev.key())
- else:
- key = chr(0)
-
- self._Iren.SetEventInformationFlipY(self.__saveX, self.__saveY,
- ctrl, shift, key, 0, None)
- self._Iren.KeyReleaseEvent()
-
- def wheelEvent(self, ev):
- if hasattr(ev, 'delta'):
- self.__wheelDelta += ev.delta()
- else:
- self.__wheelDelta += ev.angleDelta().y()
-
- if self.__wheelDelta >= 120:
- self._Iren.MouseWheelForwardEvent()
- self.__wheelDelta = 0
- elif self.__wheelDelta <= -120:
- self._Iren.MouseWheelBackwardEvent()
- self.__wheelDelta = 0
-
- def GetRenderWindow(self):
- return self._RenderWindow
-
- def Render(self):
- self.update()
-
-
-def QVTKRenderWidgetConeExample():
- """A simple example that uses the QVTKRenderWindowInteractor class."""
-
- # every QT app needs an app
- app = QApplication(['QVTKRenderWindowInteractor'])
-
- # create the widget
- widget = QVTKRenderWindowInteractor()
- widget.Initialize()
- widget.Start()
- # if you dont want the 'q' key to exit comment this.
- widget.AddObserver("ExitEvent", lambda o, e, a=app: a.quit())
-
- ren = vtk.vtkRenderer()
- widget.GetRenderWindow().AddRenderer(ren)
-
- cone = vtk.vtkConeSource()
- cone.SetResolution(8)
-
- coneMapper = vtk.vtkPolyDataMapper()
- coneMapper.SetInputConnection(cone.GetOutputPort())
-
- coneActor = vtk.vtkActor()
- coneActor.SetMapper(coneMapper)
-
- ren.AddActor(coneActor)
-
- # show the widget
- widget.show()
- # start event processing
- app.exec_()
-
-
-_keysyms = {
- Qt.Key_Backspace: 'BackSpace',
- Qt.Key_Tab: 'Tab',
- Qt.Key_Backtab: 'Tab',
- # Qt.Key_Clear : 'Clear',
- Qt.Key_Return: 'Return',
- Qt.Key_Enter: 'Return',
- Qt.Key_Shift: 'Shift_L',
- Qt.Key_Control: 'Control_L',
- Qt.Key_Alt: 'Alt_L',
- Qt.Key_Pause: 'Pause',
- Qt.Key_CapsLock: 'Caps_Lock',
- Qt.Key_Escape: 'Escape',
- Qt.Key_Space: 'space',
- # Qt.Key_Prior : 'Prior',
- # Qt.Key_Next : 'Next',
- Qt.Key_End: 'End',
- Qt.Key_Home: 'Home',
- Qt.Key_Left: 'Left',
- Qt.Key_Up: 'Up',
- Qt.Key_Right: 'Right',
- Qt.Key_Down: 'Down',
- Qt.Key_SysReq: 'Snapshot',
- Qt.Key_Insert: 'Insert',
- Qt.Key_Delete: 'Delete',
- Qt.Key_Help: 'Help',
- Qt.Key_0: '0',
- Qt.Key_1: '1',
- Qt.Key_2: '2',
- Qt.Key_3: '3',
- Qt.Key_4: '4',
- Qt.Key_5: '5',
- Qt.Key_6: '6',
- Qt.Key_7: '7',
- Qt.Key_8: '8',
- Qt.Key_9: '9',
- Qt.Key_A: 'a',
- Qt.Key_B: 'b',
- Qt.Key_C: 'c',
- Qt.Key_D: 'd',
- Qt.Key_E: 'e',
- Qt.Key_F: 'f',
- Qt.Key_G: 'g',
- Qt.Key_H: 'h',
- Qt.Key_I: 'i',
- Qt.Key_J: 'j',
- Qt.Key_K: 'k',
- Qt.Key_L: 'l',
- Qt.Key_M: 'm',
- Qt.Key_N: 'n',
- Qt.Key_O: 'o',
- Qt.Key_P: 'p',
- Qt.Key_Q: 'q',
- Qt.Key_R: 'r',
- Qt.Key_S: 's',
- Qt.Key_T: 't',
- Qt.Key_U: 'u',
- Qt.Key_V: 'v',
- Qt.Key_W: 'w',
- Qt.Key_X: 'x',
- Qt.Key_Y: 'y',
- Qt.Key_Z: 'z',
- Qt.Key_Asterisk: 'asterisk',
- Qt.Key_Plus: 'plus',
- Qt.Key_Minus: 'minus',
- Qt.Key_Period: 'period',
- Qt.Key_Slash: 'slash',
- Qt.Key_F1: 'F1',
- Qt.Key_F2: 'F2',
- Qt.Key_F3: 'F3',
- Qt.Key_F4: 'F4',
- Qt.Key_F5: 'F5',
- Qt.Key_F6: 'F6',
- Qt.Key_F7: 'F7',
- Qt.Key_F8: 'F8',
- Qt.Key_F9: 'F9',
- Qt.Key_F10: 'F10',
- Qt.Key_F11: 'F11',
- Qt.Key_F12: 'F12',
- Qt.Key_F13: 'F13',
- Qt.Key_F14: 'F14',
- Qt.Key_F15: 'F15',
- Qt.Key_F16: 'F16',
- Qt.Key_F17: 'F17',
- Qt.Key_F18: 'F18',
- Qt.Key_F19: 'F19',
- Qt.Key_F20: 'F20',
- Qt.Key_F21: 'F21',
- Qt.Key_F22: 'F22',
- Qt.Key_F23: 'F23',
- Qt.Key_F24: 'F24',
- Qt.Key_NumLock: 'Num_Lock',
- Qt.Key_ScrollLock: 'Scroll_Lock',
- }
-
-def _qt_key_to_key_sym(key):
- """ Convert a Qt key into a vtk keysym.
-
- This is essentially copied from the c++ implementation in
- GUISupport/Qt/QVTKInteractorAdapter.cxx.
- """
-
- if key not in _keysyms:
- return None
-
- return _keysyms[key]
-
-
-if __name__ == "__main__":
- print(PyQtImpl)
- QVTKRenderWidgetConeExample()
diff --git a/tboxVtk/qt5vtk6/README.txt b/tboxVtk/qt5vtk6/README.txt
deleted file mode 100644
index 2671b8f9..00000000
--- a/tboxVtk/qt5vtk6/README.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-Interface PyQt5 / vtk
-=====================
-This file is missing in vtk6.3.0
-location (in vtk7): python-2.7.12\Lib\site-packages\vtk\qt5
\ No newline at end of file
diff --git a/tboxVtk/qt5vtk6/__init__.py b/tboxVtk/qt5vtk6/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/tboxVtk/reader.py b/tboxVtk/reader.py
deleted file mode 100644
index 41227027..00000000
--- a/tboxVtk/reader.py
+++ /dev/null
@@ -1,45 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-# @brief VTK Reader
-# @authors Adrien Crovato
-
-try:
- import vtk
-except:
- raise Exception('VTK not found. Aborting!\n')
-
-class Reader:
- def __init__(self):
- self.reader = vtk.vtkXMLUnstructuredGridReader()
-
- def open(self, fname):
- import os.path
- extensions = ['.pvtu','.vtu','.vtk']
- extension = None
- for extension_tmp in extensions:
- if os.path.isfile(fname+extension_tmp):
- extension = extension_tmp
- break
- if extension is None: raise Exception("file %s.pvtu/.vtu/.vtk not found!\n" %fname)
- self.reader.SetFileName(fname+extension)
- self.reader.Update()
-
- def close(self):
- print('No need to do that apparently...\n')
- #self.reader.CloseFile()
diff --git a/tboxVtk/src/CMakeLists.txt b/tboxVtk/src/CMakeLists.txt
deleted file mode 100644
index e2e639b5..00000000
--- a/tboxVtk/src/CMakeLists.txt
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# CMake input file of tboxw.so
-
-FILE(GLOB SRCS *.h *.cpp *.inl *.hpp)
-
-ADD_LIBRARY(tboxVtk SHARED ${SRCS})
-MACRO_DebugPostfix(tboxVtk)
-
-TARGET_INCLUDE_DIRECTORIES(tboxVtk PUBLIC ${PROJECT_SOURCE_DIR}/tboxVtk/src)
-
-# ------------------------------------------------------------------------
-# "new" way to link against VTK >=6 using COMPONENTS
-# https://vtk.org/Wiki/VTK/Build_System_Migration
-
-
-# 1. first, look for all available VTK libraries
-FIND_PACKAGE(VTK REQUIRED NO_MODULE)
-IF(${VTK_VERSION} VERSION_LESS 6.0)
- MESSAGE(FATAL_ERROR "VTK>=6 required!")
-ENDIF()
-MESSAGE(STATUS "VTK_LIBRARIES1 = ${VTK_LIBRARIES}") # display all VTK libs
-
-# list of required components
-SET(REQVTKCMP vtkIOXML)
-
-# check whether MPI has been compiled
-IF(TARGET vtkParallelMPI) # NOTE: this test also works with a previous single-COMPONENT search
- SET(REQVTKCMP ${REQVTKCMP} vtkParallelMPI vtkIOParallelXML)
- TARGET_COMPILE_DEFINITIONS(tboxVtk PUBLIC "-DVTK_HAS_MPI")
- MESSAGE(STATUS "vtkParallelMPI available!")
-ELSE()
- MESSAGE(STATUS "vtkParallelMPI NOT available!")
-ENDIF()
-
-# 2. second, perform a new search with a limited number of components
-# NOTE: you may just disable the following line to link against ALL vtk libraries!
-FIND_PACKAGE(VTK REQUIRED COMPONENTS ${REQVTKCMP} NO_MODULE)
-
-# debug
-MESSAGE(STATUS "VTK_DEFINITIONS = ${VTK_DEFINITIONS}")
-MESSAGE(STATUS "VTK_REQUIRED_CXX_FLAGS = ${VTK_REQUIRED_CXX_FLAGS}")
-MESSAGE(STATUS "VTK_REQUIRED_EXE_LINKER_FLAGS = ${VTK_REQUIRED_EXE_LINKER_FLAGS}")
-MESSAGE(STATUS "VTK_REQUIRED_SHARED_LINKER_FLAGS = ${VTK_REQUIRED_SHARED_LINKER_FLAGS}")
-MESSAGE(STATUS "VTK_USE_FILE = ${VTK_USE_FILE}")
-MESSAGE(STATUS "VTK_INCLUDE_DIR = ${VTK_INCLUDE_DIR}")
-MESSAGE(STATUS "VTK_LIBRARIES = ${VTK_LIBRARIES}")
-
-TARGET_INCLUDE_DIRECTORIES(tboxVtk PUBLIC ${VTK_INCLUDE_DIRS})
-TARGET_COMPILE_DEFINITIONS(tboxVtk PUBLIC ${VTK_DEFINITIONS})
-TARGET_LINK_LIBRARIES(tboxVtk ${VTK_LIBRARIES} tbox)
-
-SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
-
diff --git a/tboxVtk/src/tboxVtk.h b/tboxVtk/src/tboxVtk.h
deleted file mode 100644
index 3146b3a5..00000000
--- a/tboxVtk/src/tboxVtk.h
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-// global header of the "tboxVtk" module
-
-#ifndef TBOXVTK_H
-#define TBOXVTK_H
-
-#if defined(WIN32)
-#ifdef tboxVtk_EXPORTS
-#define TBOXVTK_API __declspec(dllexport)
-#else
-#define TBOXVTK_API __declspec(dllimport)
-#endif
-#else
-#define TBOXVTK_API
-#endif
-
-#include "tbox.h"
-
-/**
- * @brief Namespace for tboxVtk module
- */
-namespace tboxVtk
-{
-// Msh utilities
-class vtkExport;
-
-// Kim's old classes (to be cleaned)
-class vtkExport_KIM2CLEAN;
-} // namespace tboxVtk
-
-#endif //TBOXVTK_H
diff --git a/tboxVtk/src/wVtkExport.cpp b/tboxVtk/src/wVtkExport.cpp
deleted file mode 100644
index 322eff82..00000000
--- a/tboxVtk/src/wVtkExport.cpp
+++ /dev/null
@@ -1,260 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#include "wVtkExport.h"
-#include "wNode.h"
-#include "wElement.h"
-#include "wResults.h"
-#include "wTag.h"
-
-#include <vtkSmartPointer.h>
-#include <vtkUnstructuredGrid.h>
-#include <vtkXMLUnstructuredGridWriter.h>
-#include <vtkPoints.h>
-#include <vtkHexahedron.h>
-#include <vtkTetra.h>
-#include <vtkQuad.h>
-#include <vtkTriangle.h>
-#include <vtkLine.h>
-#include <vtkVertex.h>
-#include <vtkDoubleArray.h>
-#include <vtkIntArray.h>
-#include <vtkPointData.h>
-#include <vtkCellData.h>
-
-using namespace tbox;
-using namespace tboxVtk;
-
-using vtkWriterP = vtkSmartPointer<vtkXMLUnstructuredGridWriter>;
-using vtkPtsP = vtkSmartPointer<vtkPoints>;
-using vtkHexaP = vtkSmartPointer<vtkHexahedron>;
-using vtkTetraP = vtkSmartPointer<vtkTetra>;
-using vtkQuadP = vtkSmartPointer<vtkQuad>;
-using vtkTriP = vtkSmartPointer<vtkTriangle>;
-using vtkLineP = vtkSmartPointer<vtkLine>;
-using vtkVtxP = vtkSmartPointer<vtkVertex>;
-using vtkDblArrP = vtkSmartPointer<vtkDoubleArray>;
-using vtkIntArrP = vtkSmartPointer<vtkIntArray>;
-
-VtkExport::VtkExport(std::shared_ptr<MshData> _msh) : MshExport(_msh)
-{
- grid = vtkSmartPointer<vtkUnstructuredGrid>::New();
- create();
-}
-
-VtkExport::~VtkExport()
-{
- std::cout << "~VtkExport()\n";
-}
-
-/**
- * @brief Save mesh on disk
- * @authors Adrien Crovato
- */
-void VtkExport::save(std::string const &fname) const
-{
- // Update point position
- grid->GetPoints()->Reset();
- for (auto n : msh->nodes)
- grid->GetPoints()->InsertPoint(n->no - 1, n->pos(0), n->pos(1), n->pos(2));
- grid->GetPoints()->Modified();
-
- // Define writer
- std::string wname = fname + ".vtu";
- vtkWriterP writer = vtkWriterP::New();
- writer->SetFileName(wname.c_str());
- writer->SetInputData(grid);
- // Write binary or ascii
- if (binary)
- {
- std::cout << "writing binary file: " << wname << "... " << std::flush;
- writer->SetDataModeToBinary();
- }
- else
- {
- std::cout << "writing ascii file: " << wname << "... " << std::flush;
- writer->SetDataModeToAscii();
- }
- writer->Write();
- std::cout << "done!" << std::endl;
-}
-
-/**
- * @brief Save mesh and results on disk
- * @authors Adrien Crovato, Kim Liegeois
- */
-void VtkExport::save(std::string const &fname, Results const &r) const
-{
- // Create scalar field (at nodes)
- for (auto &p : r.scalars_at_nodes)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(1);
- data->SetNumberOfTuples(msh->nodes.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->nodes.size(); ++i)
- data->SetValue(msh->nodes[i]->no - 1, (*(p.second))[i]);
- grid->GetPointData()->AddArray(data);
- }
- // Create vector field (at nodes)
- for (auto &p : r.vectors_at_nodes)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(3);
- data->SetNumberOfTuples(msh->nodes.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->nodes.size(); ++i)
- data->SetTuple3(msh->nodes[i]->no - 1, (*(p.second))[i](0), (*(p.second))[i](1), (*(p.second))[i](2));
- grid->GetPointData()->AddArray(data);
- }
- // Create tensor field (at nodes)
- for (auto &p : r.tensors_at_nodes)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(9);
- data->SetNumberOfTuples(msh->nodes.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->nodes.size(); ++i)
- data->SetTuple9(msh->nodes[i]->no - 1, (*(p.second))[i](0, 0), (*(p.second))[i](0, 1), (*(p.second))[i](0, 2),
- (*(p.second))[i](1, 0), (*(p.second))[i](1, 1), (*(p.second))[i](1, 2),
- (*(p.second))[i](2, 0), (*(p.second))[i](2, 1), (*(p.second))[i](2, 2));
- grid->GetPointData()->AddArray(data);
- }
-
- // Create scalar field (at elements)
- for (auto &p : r.scalars_at_elems)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(1);
- data->SetNumberOfTuples(msh->elems.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->elems.size(); ++i)
- data->SetValue(msh->elems[i]->no - 1, (*(p.second))[i]);
- grid->GetCellData()->AddArray(data);
- }
- // Create vector field (at elems)
- for (auto &p : r.vectors_at_elems)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(3);
- data->SetNumberOfTuples(msh->elems.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->elems.size(); ++i)
- data->SetTuple3(msh->elems[i]->no - 1, (*(p.second))[i](0), (*(p.second))[i](1), (*(p.second))[i](2));
- grid->GetCellData()->AddArray(data);
- }
- // Create tensor field (at elems)
- for (auto &p : r.tensors_at_elems)
- {
- vtkDblArrP data = vtkDblArrP::New();
- data->SetNumberOfComponents(9);
- data->SetNumberOfTuples(msh->elems.size());
- data->SetName(p.first.c_str());
- for (size_t i = 0; i < msh->elems.size(); ++i)
- data->SetTuple9(msh->elems[i]->no - 1, (*(p.second))[i](0, 0), (*(p.second))[i](0, 1), (*(p.second))[i](0, 2),
- (*(p.second))[i](1, 0), (*(p.second))[i](1, 1), (*(p.second))[i](1, 2),
- (*(p.second))[i](2, 0), (*(p.second))[i](2, 1), (*(p.second))[i](2, 2));
- grid->GetCellData()->AddArray(data);
- }
-
- // Write to file
- save(fname);
-}
-
-/**
- * @brief Create data structure
- * @authors Adrien Crovato, Romain Boman
- */
-void VtkExport::create()
-{
- // Create points
- vtkPtsP points = vtkPtsP::New();
- points->SetNumberOfPoints(msh->nodes.size());
- for (auto n : msh->nodes)
- points->InsertPoint(n->no - 1, n->pos(0), n->pos(1), n->pos(2));
- grid->SetPoints(points);
-
- // Create elements
- for (auto e : msh->elems)
- {
- if (e->type() == ELTYPE::HEX8)
- {
- vtkHexaP cell = vtkHexaP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else if (e->type() == ELTYPE::TETRA4)
- {
- vtkTetraP cell = vtkTetraP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else if (e->type() == ELTYPE::QUAD4)
- {
- vtkQuadP cell = vtkQuadP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else if (e->type() == ELTYPE::TRI3)
- {
- vtkTriP cell = vtkTriP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else if (e->type() == ELTYPE::LINE2)
- {
- vtkLineP cell = vtkLineP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else if (e->type() == ELTYPE::POINT1)
- {
- vtkVtxP cell = vtkVtxP::New();
- for (size_t i = 0; i < e->nodes.size(); ++i)
- cell->GetPointIds()->SetId(i, e->nodes[i]->no - 1);
- grid->InsertNextCell(cell->GetCellType(), cell->GetPointIds());
- }
- else
- {
- std::stringstream err;
- err << "tboxVtk::create: translation to VTK for element type "
- << e->type() << " is not supported yet!\n";
- throw std::runtime_error(err.str());
- }
- }
-
- // Create tags
- vtkIntArrP tag = vtkIntArrP::New();
- tag->SetName("tag");
- tag->SetNumberOfComponents(1);
- tag->SetNumberOfTuples(msh->elems.size());
- for (auto &ptag : msh->ptags)
- {
- for (size_t i = 0; i < ptag.second->elems.size(); ++i)
- tag->SetValue(ptag.second->elems[i]->no - 1, ptag.second->no);
- }
- grid->GetCellData()->AddArray(tag);
-}
-
-void VtkExport::write(std::ostream &out) const
-{
- out << "VtkExport on " << *msh << std::endl;
-}
\ No newline at end of file
diff --git a/tboxVtk/src/wVtkExport.h b/tboxVtk/src/wVtkExport.h
deleted file mode 100644
index 8dea4d0f..00000000
--- a/tboxVtk/src/wVtkExport.h
+++ /dev/null
@@ -1,58 +0,0 @@
-/*
- * Copyright 2020 University of Liège
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- * http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-#ifndef WVTKEXPORT_H
-#define WVTKEXPORT_H
-
-#include "tboxVtk.h"
-#include "wMshExport.h"
-#include <vector>
-#include <map>
-#include <vtkSmartPointer.h>
-#include <vtkUnstructuredGrid.h>
-
-namespace tboxVtk
-{
-
-/**
- * @todo [Long-term] implement a way to automatically update vtk data structure (grid) if internal data structure (msh) changes.
- * For now, the points and the data are always updated at each save operation.
- */
-
-/**
- * @brief Write mesh in VTK format
- * @authors Adrien Crovato, Romain Boman
- */
-class TBOXVTK_API VtkExport : public tbox::MshExport
-{
- vtkSmartPointer<vtkUnstructuredGrid> grid;
- void create();
-
-public:
- VtkExport(std::shared_ptr<tbox::MshData> _msh);
- virtual ~VtkExport();
-
- virtual void save(std::string const &fname) const override;
-#ifndef SWIG
- virtual void save(std::string const &fname, tbox::Results const &r) const override;
-#endif
-
- virtual void write(std::ostream &out) const override;
-};
-
-} // namespace tboxVtk
-
-#endif //WGMSHUTILS_H
diff --git a/tboxVtk/tests/models/model.geo b/tboxVtk/tests/models/model.geo
deleted file mode 100644
index 2543d346..00000000
--- a/tboxVtk/tests/models/model.geo
+++ /dev/null
@@ -1,14 +0,0 @@
-Point(1) = { 0, 0, 0, 0.1};
-Point(2) = { 1, 0, 0, 0.2};
-Point(3) = { 1, 1, 0, 0.3};
-Point(4) = { 0, 1, 0, 0.1};
-
-Line(1) = {1, 2};
-Line(2) = {2, 3};
-Line(3) = {3, 4};
-Line(4) = {4, 1};
-
-Line Loop(1) = {1, 2, 3, 4};
-Plane Surface(1) = {1};
-
-
diff --git a/tboxVtk/tests/vtkio.py b/tboxVtk/tests/vtkio.py
deleted file mode 100755
index 81a49b2d..00000000
--- a/tboxVtk/tests/vtkio.py
+++ /dev/null
@@ -1,44 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-
-import tboxVtk
-import tbox.gmsh as gmsh
-
-def main():
- msh = gmsh.MeshLoader("models/model.geo",__file__).execute()
- printtags(msh)
-
- vtkWriter = tboxVtk.VtkExport(msh)
- print(vtkWriter)
- vtkWriter.binary = False
- vtkWriter.save(msh.name)
-
-def printtags(mshdata):
- print("\n-ptags:")
- for t in list(mshdata.ptags.items()):
- print(t[1])
- print("\n-etags:")
- for t in list(mshdata.etags.items()):
- print(t[1])
- print("\n-partitions:")
- for t in list(mshdata.parts.items()):
- print(t[1])
-
-if __name__ == "__main__":
- main()
-
diff --git a/tlnos/_src/CMakeLists.txt b/tlnos/_src/CMakeLists.txt
index 1baf919b..32cc0790 100644
--- a/tlnos/_src/CMakeLists.txt
+++ b/tlnos/_src/CMakeLists.txt
@@ -12,10 +12,10 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/tlnos/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
)
SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
@@ -30,10 +30,10 @@ MACRO_DebugPostfix(_tlnosw)
FIND_PACKAGE(Trilinos REQUIRED)
INCLUDE_DIRECTORIES( ${PROJECT_SOURCE_DIR}/tlnos/src
- ${PROJECT_SOURCE_DIR}/tbox/src
- ${PROJECT_SOURCE_DIR}/fwk/src
- ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${Trilinos_INCLUDE_DIRS}
${Trilinos_TPL_INCLUDE_DIRS}
${MPI_INCLUDE_PATH})
@@ -42,3 +42,5 @@ SWIG_LINK_LIBRARIES(tlnosw
tlnos tbox fwk ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES} ${PYTHON_LIBRARIES}
)
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/tlnosw.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _tlnosw DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/tlnos/src/CMakeLists.txt b/tlnos/src/CMakeLists.txt
index 34b13919..ca02962e 100644
--- a/tlnos/src/CMakeLists.txt
+++ b/tlnos/src/CMakeLists.txt
@@ -77,5 +77,4 @@ LINK_DIRECTORIES (${Trilinos_LIBRARY_DIRS} ${Trilinos_TPL_LIBRARY_DIRS})
TARGET_LINK_LIBRARIES(tlnos tbox fwk ${Trilinos_LIBRARIES} ${Trilinos_TPL_LIBRARIES} ${MPI_LIBRARIES})
-#SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
-
+INSTALL(TARGETS tlnos DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/waves-config.cmake.in b/waves-config.cmake.in
deleted file mode 100644
index ffac3e3f..00000000
--- a/waves-config.cmake.in
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 2020 University of Liège
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-# Config file generator for the waves package
-# waves-config.cmake - find fwk and tbox modules given the location of waves
-# ----------------------------------------------------------------------------
-# output:
-# WAVES_FOUND : TRUE/FALSE
-# WAVES_INCLUDE_DIRS : where the Waves/*.h are [cached]
-# WAVES_SWIG_DIRS : where the Waves/*.i are [cached]
-# WAVES_LIBRARIES : where the Waves/*.so are [cached]
-# ----------------------------------------------------------------------------
-
-# Includes
-SET(WAVES_INCLUDE_DIRS "@WAVES_INCLUDE_DIRS@" CACHE STRING "Waves headers")
-SET(WAVES_SWIG_DIRS "@WAVES_SWIG_DIRS@" CACHE STRING "Waves swig interface")
-
-# These are IMPORTED targets created by wavesTargets.cmake
-GET_FILENAME_COMPONENT(WAVES_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" DIRECTORY)
-INCLUDE("${WAVES_CMAKE_DIR}/wavesTargets.cmake")
-SET(WAVES_LIBRARIES "@WAVES_LIBRARIES@" CACHE STRING "Waves libs")
-SET_TARGET_PROPERTIES(${WAVES_LIBRARIES} PROPERTIES IMPORTED_GLOBAL TRUE)
-
-# handle the QUIETLY and REQUIRED arguments and set WAVES_FOUND to TRUE
-# if all listed variables are TRUE
-INCLUDE(FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(WAVES
- REQUIRED_VARS WAVES_INCLUDE_DIRS WAVES_SWIG_DIRS WAVES_LIBRARIES)
diff --git a/waves/CMakeLists.txt b/waves/CMakeLists.txt
index 6190a51e..3e2df53e 100644
--- a/waves/CMakeLists.txt
+++ b/waves/CMakeLists.txt
@@ -20,3 +20,14 @@ ADD_SUBDIRECTORY( _src )
# Add test dir
MACRO_AddTest(${CMAKE_CURRENT_SOURCE_DIR}/tests)
+
+# Add to install
+INSTALL(FILES ${CMAKE_CURRENT_LIST_DIR}/__init__.py
+ ${CMAKE_CURRENT_LIST_DIR}/srcs.py
+ ${CMAKE_CURRENT_LIST_DIR}/utils.py
+ ${CMAKE_CURRENT_LIST_DIR}/viewer.py
+ DESTINATION waves)
+INSTALL(DIRECTORY ${CMAKE_CURRENT_LIST_DIR}/tests
+ ${CMAKE_CURRENT_LIST_DIR}/models
+ DESTINATION waves)
+
\ No newline at end of file
diff --git a/waves/_src/CMakeLists.txt b/waves/_src/CMakeLists.txt
index 0373de8d..666aa00d 100644
--- a/waves/_src/CMakeLists.txt
+++ b/waves/_src/CMakeLists.txt
@@ -25,10 +25,10 @@ SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES CPLUSPLUS ON)
SET(SWINCFLAGS
-I${PROJECT_SOURCE_DIR}/waves/src
--I${PROJECT_SOURCE_DIR}/tbox/src
--I${PROJECT_SOURCE_DIR}/tbox/_src
--I${PROJECT_SOURCE_DIR}/fwk/src
--I${PROJECT_SOURCE_DIR}/fwk/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/src
+-I${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
)
SET_SOURCE_FILES_PROPERTIES(${ISRCS} PROPERTIES SWIG_FLAGS "${SWINCFLAGS}")
@@ -39,11 +39,14 @@ else()
endif()
MACRO_DebugPostfix(_wavesw)
-TARGET_INCLUDE_DIRECTORIES(_wavesw PRIVATE ${PROJECT_SOURCE_DIR}/fwk/_src
- ${PROJECT_SOURCE_DIR}/tbox/_src
+TARGET_INCLUDE_DIRECTORIES(_wavesw PRIVATE ${PROJECT_SOURCE_DIR}/ext/amfe/fwk/_src
+ ${PROJECT_SOURCE_DIR}/ext/amfe/tbox/_src
${PYTHON_INCLUDE_PATH}
)
SWIG_LINK_LIBRARIES(wavesw
waves tbox fwk ${PYTHON_LIBRARIES}
)
+
+INSTALL(FILES ${CMAKE_SWIG_OUTDIR}/wavesw.py DESTINATION ${CMAKE_INSTALL_PREFIX})
+INSTALL(TARGETS _wavesw DESTINATION ${CMAKE_INSTALL_PREFIX})
diff --git a/waves/exe/CMakeLists.txt b/waves/exe/CMakeLists.txt
index 4c8eadd1..00d9f3d2 100644
--- a/waves/exe/CMakeLists.txt
+++ b/waves/exe/CMakeLists.txt
@@ -17,4 +17,4 @@
FILE(GLOB SRCS *.h *.cpp *.inl *.hpp)
ADD_EXECUTABLE(waves1 ${SRCS})
MACRO_DebugPostfix(waves1)
-TARGET_LINK_LIBRARIES(waves1 waves) # tbox)
+TARGET_LINK_LIBRARIES(waves1 waves)
diff --git a/waves/src/CMakeLists.txt b/waves/src/CMakeLists.txt
index fd1745ca..9216fd83 100644
--- a/waves/src/CMakeLists.txt
+++ b/waves/src/CMakeLists.txt
@@ -22,5 +22,7 @@ TARGET_INCLUDE_DIRECTORIES(waves PUBLIC ${PROJECT_SOURCE_DIR}/waves/src)
TARGET_LINK_LIBRARIES(waves tbox fwk)
+INSTALL(TARGETS waves DESTINATION ${CMAKE_INSTALL_PREFIX})
+
SOURCE_GROUP(base REGULAR_EXPRESSION ".*\\.(cpp|inl|hpp|h)")
SOURCE_GROUP(schemes REGULAR_EXPRESSION ".+(TimeIntegration|Runge|Euler|Newmark).+")
diff --git a/waves_config.h.in b/waves_config.h.in
deleted file mode 100644
index a37b9446..00000000
--- a/waves_config.h.in
+++ /dev/null
@@ -1,2 +0,0 @@
-#cmakedefine WAVES_USE_MKL
-#cmakedefine WAVES_USE_MUMPS
--
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