Merge branch 'adri' into 'master'

amfe v1.0.7

See merge request !11

tbox/src/wDss.h

@@ -23,7 +23,6 @@
 #include "wLinearSolver.h"
 #include <mkl_dss.h>
 #include <Eigen/Sparse>
-#include <limits>
 
 namespace tbox
 {
@@ -48,7 +47,7 @@ public:
     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 double getError() override { return -1.; }
     virtual int getIterations() override { return 1; }
 
     virtual void write(std::ostream &out) const override;

tbox/src/wMumps.h

@@ -23,7 +23,6 @@
 #include "wLinearSolver.h"
 #include <dmumps_c.h>
 #include <Eigen/Sparse>
-#include <limits>
 
 namespace tbox
 {
@@ -61,7 +60,7 @@ public:
     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 double getError() override { return -1.; }
     virtual int getIterations() override { return 1; }
 
     virtual void write(std::ostream &out) const override;

tbox/src/wPardiso.h

@@ -22,7 +22,6 @@
 
 #include "wLinearSolver.h"
 #include <Eigen/PardisoSupport>
-#include <limits>
 
 namespace tbox
 {
@@ -46,7 +45,7 @@ public:
     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 double getError() override { return -1.; }
     virtual int getIterations() override { return 1; }
 
     virtual void write(std::ostream &out) const override;

tbox/src/wSparseLu.h

@@ -20,7 +20,6 @@
 #include "tbox.h"
 #include "wLinearSolver.h"
 #include <Eigen/Sparse>
-#include <limits>
 
 namespace tbox
 {
@@ -46,7 +45,7 @@ public:
     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 double getError() override { return -1.; }
     virtual int getIterations() override { return 1; }
 
     virtual void write(std::ostream &out) const override;

tbox/utils.py

@@ -34,28 +34,25 @@ def myrange(start, stop, step):
 def plot(x, y, cfg):
     """Plot using matplotlib
     """
-    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)
-        if 'xlabel' in cfg:
-            plt.xlabel(cfg['xlabel'], fontdict=font)
-        if 'ylabel' in cfg:
-            plt.ylabel(cfg['ylabel'], fontdict=font)
-        if 'title' in cfg:
-            plt.title(cfg['title'], fontdict=font)
-        if 'xlim' in cfg:
-            plt.xlim(cfg['xlim'])
-        if 'ylim' in cfg:
-            plt.ylim(cfg['ylim'])
-        if 'invert' in cfg and cfg['invert']:
-            plt.gca().invert_yaxis()
-        # display
-        plt.show()
+    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)
+    if 'xlabel' in cfg:
+        plt.xlabel(cfg['xlabel'], fontdict=font)
+    if 'ylabel' in cfg:
+        plt.ylabel(cfg['ylabel'], fontdict=font)
+    if 'title' in cfg:
+        plt.title(cfg['title'], fontdict=font)
+    if 'xlim' in cfg:
+        plt.xlim(cfg['xlim'])
+    if 'ylim' in cfg:
+        plt.ylim(cfg['ylim'])
+    if 'invert' in cfg and cfg['invert']:
+        plt.gca().invert_yaxis()
+    # display
+    plt.show()
 
 def sort(id, data):
     """Sort data array against id (line connectivity list)

tboxVtk/cutter.py

@@ -2,13 +2,13 @@
 # -*- 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.
@@ -29,13 +29,12 @@ class Cutter:
         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
+        """Cut the physical group ided "tag" with a plane defined by point "cutO" and normal "cutN"
+        """
         # create a threshold containing the physical group (tag) to cut
         thresh = vtk.vtkThreshold()
-        thresh.ThresholdBetween(tag,tag)
+        thresh.SetLowerThreshold(tag)
+        thresh.SetUpperThreshold(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()
@@ -51,10 +50,9 @@ class Cutter:
         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".
+        """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()

tboxVtk/lineExtractor.py

@@ -55,7 +55,8 @@ class LineExtractor:
 
         # create a threshold containing the physical group (tag) to cut
         thresh = vtk.vtkThreshold()
-        thresh.ThresholdBetween(tag,tag)
+        thresh.SetLowerThreshold(tag)
+        thresh.SetUpperThreshold(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()