From 4e62114403088b3d22944d0d52613b4c76ff7f09 Mon Sep 17 00:00:00 2001
From: Romain Boman <r.boman@uliege.be>
Date: Wed, 22 May 2024 12:38:32 +0200
Subject: [PATCH] add additional extractors (Metafor only)
---
models/Clidastes/50k/Point_5_L.off | 3 +
models/Clidastes/Clidastes_propython_50k.py | 23 ++++++
models/boneload.py | 2 +-
models/bonemodel.py | 84 ++++++++++++++++++---
4 files changed, 102 insertions(+), 10 deletions(-)
create mode 100644 models/Clidastes/50k/Point_5_L.off
diff --git a/models/Clidastes/50k/Point_5_L.off b/models/Clidastes/50k/Point_5_L.off
new file mode 100644
index 0000000..2e67a62
--- /dev/null
+++ b/models/Clidastes/50k/Point_5_L.off
@@ -0,0 +1,3 @@
+NOFF
+1 0 0
+47.137432 171.505753 9.123382
diff --git a/models/Clidastes/Clidastes_propython_50k.py b/models/Clidastes/Clidastes_propython_50k.py
index 172ea1b..bfe6ccb 100644
--- a/models/Clidastes/Clidastes_propython_50k.py
+++ b/models/Clidastes/Clidastes_propython_50k.py
@@ -100,6 +100,29 @@ def parms(d={}):
'method': 'T+N'
}
]
+ p['extractors'] = [
+ {
+ 'name': 'Point_1_L',
+ 'nodes': [9.737800, -107.443642, -41.476234],
+ 'variables': [ 'x0', 'y0', 'z0', 'sigvm' ]
+ },
+ {
+ 'name': 'Point_2_L',
+ 'nodes': [18.720367, -42.742260, -36.978378],
+ 'variables': 'sigvm'
+ },
+ {
+ 'name': 'Point_3_and_4_L',
+ 'nodes': [[33.984665, 40.152878, -24.569260],
+ [43.314785, 99.891335, -16.491674]],
+ 'variables': 'sigzz'
+ },
+ {
+ 'name': 'Point_5_L',
+ 'nodes': f'{path}/Point_5_L.off',
+ 'variables': [ 'sigvm', 'dx', 'dy', 'dz' ]
+ }
+ ]
# material properties
p['density'] = 1.662e-9 # [T\mm³]
diff --git a/models/boneload.py b/models/boneload.py
index 50f96a1..e4fb3ae 100644
--- a/models/boneload.py
+++ b/models/boneload.py
@@ -22,7 +22,7 @@ colors = vtk.vtkNamedColors()
def load_msh(meshfile):
- """loads a mesh in .off or .ply format
+ """loads a mesh in .off, .stl or .ply format
returns:
a list of node coordinates
a list of triangles defined by 3 node tags
diff --git a/models/bonemodel.py b/models/bonemodel.py
index 00d1c7a..a973806 100644
--- a/models/bonemodel.py
+++ b/models/bonemodel.py
@@ -8,11 +8,6 @@ from wrap import *
import boneload
import os
-# enable full parallelism
-StrVectorBase.useTBB()
-StrMatrixBase.useTBB()
-ContactInteraction.useTBB()
-
def parms(d={}):
"""default parameters of the model
"""
@@ -64,6 +59,7 @@ def parms(d={}):
]
p['loads'] = [] # additional loads
+ p['extractors'] = [] # additional extractors
p['food'] = 'fixteeth' # type of food: 'fixteeth' or 'cylinder'
@@ -146,6 +142,10 @@ def getMetafor(p={}):
for fix in p['fixations']:
create_group(fix['nodes'], nods_no, nods_pos, domain, groups, fix['name'])
+ # create groups of additional extractors
+ for extr in p['extractors']:
+ create_group(extr['nodes'], nods_no, nods_pos, domain, groups, extr['name'])
+
# --------------------------------------------------------------------------
# material
@@ -242,12 +242,22 @@ def getMetafor(p={}):
solver = DSSolver()
solman.setSolver(solver)
+ # enable full parallelism
+ StrVectorBase.useTBB()
+ StrMatrixBase.useTBB()
+ ContactInteraction.useTBB()
+
# history curves
+ # by default, extract all forces on all groups
valuesmanager = metafor.getValuesManager()
idx=1
valuesmanager.add(idx, MiscValueExtractor(metafor,EXT_T),'time'); idx+=1
for name, group in groups.items():
+ # skip the main mesh and its surface
if name in ['all','surf']: continue
+ # skip all additional extractors
+ if name in [e['name'] for e in p['extractors']]: continue
+ # muscles and loads should remain
for key, c in zip([TX,TY,TZ],['x','y','z']):
fname = f'{name}_F{c}'
valuesmanager.add(idx, DbNodalValueExtractor(group, Field1D(key,GF1)), SumOperator(), fname)
@@ -259,11 +269,63 @@ def getMetafor(p={}):
valuesmanager.add(idx, InteractionValueExtractor(ci, key), fname)
metafor.getTestSuiteChecker().checkExtractor(idx)
idx+=1
-
+
+ # add additional extractors
+
+ # conversion dicts
+ var2field_db = {
+ 'dx': Field1D(TX, RE),
+ 'dy': Field1D(TY, RE),
+ 'dz': Field1D(TZ, RE),
+ 'x0': Field1D(TX, AB),
+ 'y0': Field1D(TY, AB),
+ 'z0': Field1D(TZ, AB),
+ 'fx': Field1D(TX, GF1),
+ 'fy': Field1D(TY, GF1),
+ 'fz': Field1D(TZ, GF1)
+ }
+
+ var2field_if = {
+ 'sigvm': IF_EVMS,
+ 'sigxx': IF_SIG_XX,
+ 'sigyy': IF_SIG_YY,
+ 'sigzz': IF_SIG_ZZ,
+ 'sigxy': IF_SIG_XY,
+ 'sigyz': IF_SIG_YZ,
+ 'sigxz': IF_SIG_XZ,
+ 'epsxx': IF_GL_STRAIN_XX,
+ 'epsyy': IF_GL_STRAIN_YY,
+ 'epszz': IF_GL_STRAIN_ZZ,
+ 'epsxy': IF_GL_STRAIN_XY,
+ 'epsyz': IF_GL_STRAIN_YZ,
+ 'epsxz': IF_GL_STRAIN_XZ
+ }
+
+ for extr in p['extractors']:
+ # if only one variable is given, convert it to a list
+ if isinstance(extr['variables'], str):
+ extr['variables'] = [extr['variables']]
+
+ for var in extr['variables']:
+ fname = f'{extr["name"]}_{var}'
+ target = groups[extr['name']]
+ # nodal values
+ if var.lower() in var2field_db:
+ field = var2field_db[var.lower()]
+ valuesmanager.add(idx, DbNodalValueExtractor(target, field), fname)
+ elif var.lower() in var2field_if:
+ field = var2field_if[var.lower()]
+ valuesmanager.add(idx, IFNodalValueExtractor(target, field), fname)
+ else:
+ raise Exception(f'Unknown variable: {var}')
+ if target.getNumberOfMeshPoints() == 1:
+ metafor.getTestSuiteChecker().checkExtractor(idx)
+ idx+=1
+
return metafor
# ------------------------------------------------------------------------------
-# utility functions involing Metafor objects
+# utility functions involving Metafor objects
def import_mesh(domain, filename, use_gmshOld=True):
@@ -342,7 +404,7 @@ def create_group(mesh_file_or_coord, all_no, all_coords, domain, groups, gname=N
Then, the routine creates a group named "gname" (built from mesh_file_or_coord if None)
mesh_file_or_coord can be either:
- a filename
+ a filename (.off, .ply, .stl)
an array of points: [ [x1,y1,z1], [x2,y2,z2], ... ]
one single point: [x1,y1,z1]
"""
@@ -373,6 +435,10 @@ def create_group(mesh_file_or_coord, all_no, all_coords, domain, groups, gname=N
if gname is None:
gname, _ = os.path.splitext(os.path.basename(mesh_file_or_coord))
group = groupset.add(Group(groupset.getLargestNo()+1))
+
+ if gname in groups:
+ raise Exception(f'create_group: group "{gname}" already exists!')
+
groups[gname] = group
# add all the identified vertices to the group
@@ -397,7 +463,7 @@ class MuscleGroup:
def ply2mtf(domain, meshfile):
- """load a surface into Metafor's memory from a ply file
+ """load a surface into Metafor's memory from a mesh file (ply, off or stl)
"""
fullpath = os.path.join(os.path.dirname(__file__), meshfile)
nodes, tris = boneload.load_msh(fullpath)
--
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