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FEM: Fenics, add Fenics tools module

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This commit is contained in:
joha2
2018-02-07 13:32:06 +01:00
committed by wmayer
parent ec719e98fd
commit b99cc55a6b
3 changed files with 124 additions and 0 deletions
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7
src/Mod/Fem/CMakeLists.txt
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@@ -108,6 +108,11 @@ SET(FemSolverZ88_SRCS
femsolver/z88/writer.py
)
SET(FemSolverFenics_SRCS
femsolver/fenics/__init__.py
femsolver/fenics/fenics_tools.py
)
SET(FemTests_SRCS
femtest/__init__.py
femtest/testfemcommon.py
@@ -191,6 +196,7 @@ SET(FemAllScripts
${FemSolverElmer_SRCS}
${FemSolverElmerEquations_SRCS}
${FemSolverZ88_SRCS}
${FemSolverFenics_SRCS}
${FemTests_SRCS}
${FemTestsFiles_SRCS}
${FemTestsCcx_SRCS}
@@ -218,6 +224,7 @@ INSTALL(FILES ${FemSolverCalculix_SRCS} DESTINATION Mod/Fem/femsolver/calculix)
INSTALL(FILES ${FemSolverElmer_SRCS} DESTINATION Mod/Fem/femsolver/elmer)
INSTALL(FILES ${FemSolverElmerEquations_SRCS} DESTINATION Mod/Fem/femsolver/elmer/equations)
INSTALL(FILES ${FemSolverZ88_SRCS} DESTINATION Mod/Fem/femsolver/z88)
INSTALL(FILES ${FemSolverFenics_SRCS} DESTINATION Mod/Fem/femsolver/fenics)
INSTALL(FILES ${FemTests_SRCS} DESTINATION Mod/Fem/femtest)
INSTALL(FILES ${FemTestsFiles_SRCS} DESTINATION Mod/Fem/femtest/testfiles)
INSTALL(FILES ${FemTestsCcx_SRCS} DESTINATION Mod/Fem/femtest/testfiles/ccx)

0
src/Mod/Fem/femsolver/fenics/__init__.py Normal file
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117
src/Mod/Fem/femsolver/fenics/fenics_tools.py Normal file
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@@ -0,0 +1,117 @@
# ***************************************************************************
# * *
# * Copyright (c) 2017 - Johannes Hartung <j.hartung@gmx.net> *
# * *
# * This program is free software; you can redistribute it and/or modify *
# * it under the terms of the GNU Lesser General Public License (LGPL) *
# * as published by the Free Software Foundation; either version 2 of *
# * the License, or (at your option) any later version. *
# * for detail see the LICENCE text file. *
# * *
# * This program is distributed in the hope that it will be useful, *
# * but WITHOUT ANY WARRANTY; without even the implied warranty of *
# * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
# * GNU Library General Public License for more details. *
# * *
# * You should have received a copy of the GNU Library General Public *
# * License along with this program; if not, write to the Free Software *
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 *
# * USA *
# * *
# ***************************************************************************
from __future__ import print_function
try:
import fenics
except:
print("No Fenics modules found, please install them.")
else:
class CellExpressionXDMF(fenics.Expression):
def __init__(self, xdmffilename, group_value_dict, group_priority_dict={}, default=0., check_marked=(lambda x: x == 1), **kwargs):
self.group_priority_dict = group_priority_dict
self.check_marked = check_marked
self.default = default
self.readXDMFfile(xdmffilename, group_value_dict)
def readXDMFfile(self, xdmffilename, group_value_dict):
"""
Initialization of CellExpressionXDMF by reading an XDMF file.
@param: xdmffilename: path to xdmf file
@param: group_value_dict: {"groupname":function(x)}
function(x) is a function which is evaluated at the marked positions of the cells
"""
xdmffile = fenics.XDMFFile(xdmffilename)
self.group_value_dict = group_value_dict
self.mesh = fenics.Mesh()
xdmffile.read(self.mesh)
self.markers = {}
self.dx = {}
for (key, value) in self.group_value_dict.iteritems():
# Fenics interface here: create cell function of type int for every group
# TODO: examine whether int is appropriate or this class could be generalized
self.markers[key] = fenics.CellFunction("int", self.mesh)
xdmffile.read(self.markers[key], key)
self.dx[key] = fenics.Measure("dx", domain=self.mesh, subdomain_data=self.markers[key])
xdmffile.close()
def eval_cell(self, values, x, cell):
values_list = []
for (key, func) in self.group_value_dict.iteritems():
if self.check_marked(self.markers[key][cell.index]):
values_list.append(func(x))
if values_list:
values[0] = values_list[0]
# TODO: improve for vectorial data
# TODO: fix value assignment for overlap
# according to priority, mean, or standard
# TODO: python classes much slower than JIT compilation
else:
values[0] = self.default
# def value_shape(self):
# return self.shape
class FacetFunctionXDMF(object):
def __init__(self, xdmffilename, group_value_dict):
"""
Initialization of FacetFunctionXDMF by reading an XDMF file.
@param: xdmffilename: path to xdmf file
@param: group_value_dict: {"groupname":{"type":"Dirichlet|Neumann|Robin", "value":u_D|du_N|(r,s), "marked":1}, ...}
If group_value_dict contains no "marked" entry for the groupname, "marked" is set to 1 by default.
"""
self.readXDMFFile(xdmffilename, group_value_dict)
def readXDMFFile(self, xdmffilename, group_value_dict):
xdmffile = fenics.XDMFFile(xdmffilename)
self.group_value_dict = group_value_dict
self.mesh = fenics.Mesh()
xdmffile.read(self.mesh)
self.markers = {}
self.marked = {}
self.ds = {}
self.bcs = {}
for (key, value) in self.group_value_dict.iteritems():
# Fenics interface here: create facet function of type size_t (positive int) for every group
# TODO: examine whether size_t is appropriate or this class could be generalized
self.markers[key] = fenics.FacetFunction("size_t", self.mesh)
xdmffile.read(self.markers[key], key)
self.marked[key] = value.get("marked", 1)
self.ds[key] = fenics.Measure("ds", domain=self.mesh, subdomain_data=self.markers[key])
self.bcs[key] = value
xdmffile.close()
def getDirichletBCs(self, vectorspace, *args, **kwargs):
dbcs = []
for (dict_key, dict_value) in self.bcs.iteritems():
if dict_value["type"] == 'Dirichlet':
bc = fenics.DirichletBC(vectorspace, dict_value["value"], self.markers[dict_key], dict_value.get("marked", 1), *args, **kwargs)
dbcs.append(bc)
return dbcs
# TODO: write some functions to return integrals for Neumann and Robin
# boundary conditions for the general case (i.e. vector, tensor)