"pip install damask" either locally or from PyPI after upload
This commit is contained in:
Philip Eisenlohr
parent
19bc686327
commit
41ed7ce462
6
Makefile
6
Makefile
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@ -4,7 +4,7 @@ SHELL = /bin/sh
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########################################################################################
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DAMASK_ROOT = $(shell python -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))")
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.PHONY: all
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all: grid mesh processing
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all: grid mesh python processing
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.PHONY: grid
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grid: build/grid
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@ -36,3 +36,7 @@ clean:
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processing:
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@./installation/symlink_Processing.py ${MAKEFLAGS}
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.PHONY: python
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python:
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@pip install --user ./python
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@ -61,8 +61,3 @@ if ( $?prompt ) then
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endif
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setenv DAMASK_NUM_THREADS $DAMASK_NUM_THREADS
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if ( ! $?PYTHONPATH ) then
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setenv PYTHONPATH $DAMASK_ROOT/python
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else
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setenv PYTHONPATH $DAMASK_ROOT/python:$PYTHONPATH
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endif
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@ -94,7 +94,6 @@ if [ ! -z "$PS1" ]; then
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fi
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export DAMASK_NUM_THREADS
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export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
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for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN BRANCH; do
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unset "${var}"
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@ -88,7 +88,6 @@ if [ ! -z "$PS1" ]; then
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fi
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export DAMASK_NUM_THREADS
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export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH
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for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN BRANCH; do
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unset "${var}"
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@ -1 +1,3 @@
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include damask/README
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include damask/VERSION
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include damask/LICENSE
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@ -1 +0,0 @@
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../../LICENSE
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@ -0,0 +1,14 @@
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Copyright 2011-19 Max-Planck-Institut für Eisenforschung GmbH
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DAMASK is free software: you can redistribute it and/or modify
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it under the terms of the GNU General Public License as published by
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the Free Software Foundation, either version 3 of the License, or
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(at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU General Public License for more details.
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You should have received a copy of the GNU General Public License
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along with this program. If not, see <http://www.gnu.org/licenses/>.
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@ -1 +0,0 @@
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../../README
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@ -0,0 +1,13 @@
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DAMASK - The Düsseldorf Advanced Material Simulation Kit
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Visit damask.mpie.de for installation and usage instructions
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CONTACT INFORMATION
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Max-Planck-Institut für Eisenforschung GmbH
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Max-Planck-Str. 1
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40237 Düsseldorf
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Germany
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Email: DAMASK@mpie.de
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https://damask.mpie.de
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https://magit1.mpie.de
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@ -0,0 +1,13 @@
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DAMASK - The Düsseldorf Advanced Material Simulation Kit
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Visit damask.mpie.de for installation and usage instructions
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CONTACT INFORMATION
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Max-Planck-Institut für Eisenforschung GmbH
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Max-Planck-Str. 1
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40237 Düsseldorf
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Germany
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Email: DAMASK@mpie.de
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https://damask.mpie.de
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https://magit1.mpie.de
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@ -1 +0,0 @@
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../../VERSION
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@ -0,0 +1 @@
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0.9.0
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@ -1,15 +1,13 @@
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"""Main aggregator."""
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import os
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with open(os.path.join(os.path.dirname(__file__),'VERSION')) as f:
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version = f.readline()[1:-1]
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name = 'damask'
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with open(os.path.join(os.path.dirname(__file__),'VERSION')) as f:
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version = f.readline().strip()
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# classes
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from .environment import Environment # noqa
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from .asciitable import ASCIItable # noqa
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from .table import Table # noqa
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from .asciitable import ASCIItable # noqa
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from .config import Material # noqa
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from .colormaps import Colormap, Color # noqa
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@ -17,10 +15,12 @@ from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa
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from .dadf5 import DADF5 # noqa
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from .geom import Geom # noqa
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from .solver import Solver # noqa
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from .test import Test # noqa
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from .util import extendableOption # noqa
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# functions in modules
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from . import mechanics # noqa
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from . import mechanics # noqa
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# clean temporary variables
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del os
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del f
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@ -1,27 +0,0 @@
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import os
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import re
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class Environment():
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__slots__ = [ \
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'options',
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]
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def __init__(self):
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self.options = {}
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self.get_options()
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def relPath(self,relative = '.'):
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return os.path.join(self.rootDir(),relative)
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def rootDir(self):
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return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../'))
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def get_options(self):
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with open(self.relPath(self.rootDir()+'/CONFIG')) as configFile:
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for line in configFile:
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l = re.sub('^set ', '', line).strip() # remove "set" (tcsh) when setting variables
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if l and not l.startswith('#'):
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items = re.split(r'\s*=\s*',l)
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if len(items) == 2:
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self.options[items[0].upper()] = \
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re.sub('\$\{*DAMASK_ROOT\}*',self.rootDir(),os.path.expandvars(items[1])) # expand all shell variables and DAMASK_ROOT
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@ -1,743 +0,0 @@
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# -*- coding: UTF-8 no BOM -*-
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# This tool converts a msc.marc result file into the vtk format that
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# can be viewed by Paraview software (Kitware), or MayaVi (needs xml-vtk, or ...
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#
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# About the vtk format: http://www.vtk.org/VTK/project/about.html
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# Some example vtk files: http://people.sc.fsu.edu/~jburkardt/data/vtk/vtk.html
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# www.paraview.org
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import os,sys,re
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import numpy as np
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import py_post # MSC closed source module to access marc result files
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class MARC_POST():
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def __init__(self):
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self.projdir='./'
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def opent16(self,incr=None):
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self.fpath=os.path.join(self.projdir,self.postname)
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print('Trying to open ',self.fpath,' ...')
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self.p=py_post.post_open(self.fpath)
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if self.p is None:
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print('Could not open %s.'%self.postname); #return 'err'#; sys.exit(1)
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raise Exception('Could not open t16')
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print('Postfile %s%s is open ...'%(self.projdir,self.postname))
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self.maxincr=self.p.increments()
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print('and has %i increments'%self.maxincr)
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if incr is None:
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self.p.moveto(self.maxincr-1)
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else:
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self.p.moveto(incr+1)
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print('moved to increment ', self.p.increment)
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self.p.extrapolation('translate') # linear, translate, average. query with p.extrapolate
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print('extrapolation method is ', self.p.extrapolate)
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print('collecting model information')
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self.t16info(printFlag=0)
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print('t16 is open')
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self.p
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def t16info(self, printFlag=1
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):
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if not self.p:
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self.p=self.opent16()#post_open(self.postname)
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print(self.p)
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oldincr=self.p.position
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if oldincr==0:
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self.p.moveto(1)
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self.nnodes=self.p.nodes() #self.p.node(self.nnodes) crashes; only to nnodes-1 possible
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self.nodes=range(0,self.nnodes)
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self.nscals=self.p.node_scalars(); #print 'nscals', nscals
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self.nscal_list=['']*self.nscals
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self.nel=self.p.elements()
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self.elscals=self.p.element_scalars()
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self.elscal_list=['']*self.elscals
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self.eltens=self.p.element_tensors()
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self.elten_list=['']*self.eltens
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for i in range(0,self.nscals):
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self.nscal_list[i]=self.p.node_scalar_label(i)
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for i in range (0,self.elscals):
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self.elscal_list[i]=self.p.element_scalar_label(i)
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if printFlag==1: print(i, self.elscal_list[i])
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for i in range (0,self.eltens):
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self.elten_list[i]=self.p.element_tensor_label(i)
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if printFlag==1: print(i, self.elten_list[i])
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for i in range(0,self.p.element_tensors()):
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if printFlag==1: print('Element Tensor: ', i, self.p.element_tensor_label(i))
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if printFlag==1: print('')
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for i in range(0,self.p.element_scalars()):
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if printFlag==1: print('Element Scalar: ', i, self.p.element_scalar_label(i))
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if oldincr==0:
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self.p.moveto(0)
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def closet16(self):
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print('Trying to close FEM result file ...')
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try:
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if self.p:
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self.p.close()
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print('FEM result file closed.')
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self.p=None
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else:
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print('post object not open?')
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except:
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print('ERROR. Could not close FEM result file.')
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def getLabelNr(self, label=None, type='Scalar'):
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if type[0]=='S' or type[0]=='s': # element scalar
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labelNr=self.elscal_list.index(label)
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elif type[0]=='N': # node scalar
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labelNr=self.nscal_list.index(label)
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elif type[0]=='T' or type[0]=='t': # tensor
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labelNr=self.elten_list.index(label)
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print('Found label %s at index %i'%(label,labelNr))
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return labelNr
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def writeNodes2VTK(self, fobj):
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self.points=[]
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self.VTKcnt=200 # number of values per line in vtk file
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fobj.write('POINTS %i'%self.p.nodes()+' float\n')
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self.nodes_dict={} # store the node IDs in case of holes in the numbering
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for iNd in self.nodes:
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nd=self.p.node(iNd)
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disp=self.p.node_displacement(iNd)
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nd_xyz=[nd.x+disp[0], nd.y+disp[1], nd.z+disp[2]]
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self.points.append(nd_xyz) # for pyvtk
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fobj.write('%f %f %f \n'%
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(nd.x+disp[0], nd.y+disp[1], nd.z+disp[2]))
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self.nodes_dict[nd.id-1]=iNd
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fobj.write('\n')
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print('Nodes written to VTK: %i'%self.p.nodes())
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def writeElements2VTK(self, fobj):
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fobj.write('\nCELLS %i %i'%(self.p.elements(),self.p.elements()*9)+'\n')
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self.cells=[] #for pyvtk
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for iEl in range(0,self.nel):
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el=self.p.element(iEl)
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cell_nodes=[] # for pyvtk
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ndlist=el.items
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for k in [0, 1, 2, 3, 4, 5, 6, 7]: # FOR CELL TYPE VTK_HEXAHEDRON
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node=ndlist[k]-1
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cell_nodes.append(self.nodes_dict[node])
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self.cells.append(cell_nodes) # for pyvtk
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for e in self.cells:
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fobj.write('8 ')
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for n in e:
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fobj.write('%6i '%n)
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fobj.write('\n')
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fobj.write('\nCELL_TYPES %i'%self.p.elements()+'\n')
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cnt=0
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for iEl in range(0,self.nel):
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cnt=cnt+1
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#fobj.write('11\n') #VTK_VOXEL
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fobj.write('12 ') #VTK_HEXAHEDRON
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if cnt>self.VTKcnt:
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fobj.write('\n');cnt=0
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fobj.write('\n')
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print('Elements written to VTK: %i'%self.p.elements())
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def writeElScalars2NodesVTK(self,fobj):
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fobj.write('\nPOINT_DATA %i\n'%self.p.nodes())
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nScal=12
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nComponents=1+nScal
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fobj.write('SCALARS scalars float %i\n'%nComponents)
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fobj.write('LOOKUP_TABLE default\n')
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idxScal=self.nscal_list.index('Displacement Z')
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for iNd in self.nodes:
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fobj.write('%f '%(self.p.node_scalar(iNd,idxScal)))
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for iEl in range(0,self.nel):
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el=self.p.element(iEl)
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ndlist=el.items
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if (iNd+1) in ndlist:
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idx=ndlist.index(iNd+1)
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for iV in range(0,nScal):
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elData=self.p.element_scalar(iEl,35+iV)
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fobj.write('%f '%(elData[idx].value))
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break
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fobj.write('\n')
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fobj.write('\n')
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def writeNodeScalars2VTK(self,fobj):
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fobj.write('\nPOINT_DATA %i\n'%self.p.nodes())
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self.pointDataScalars=[]
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for idxNdScal in range(-3,self.nscals): #now include node x,y,z
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if idxNdScal>=0:
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datalabel=self.nscal_list[idxNdScal]
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datalabel=re.sub("\s",'_',datalabel)
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else:
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if idxNdScal==-3: datalabel='node.x'
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if idxNdScal==-2: datalabel='node.y'
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if idxNdScal==-1: datalabel='node.z'
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fobj.write('SCALARS %s float %i\n'%(datalabel,1))#nComponents))
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fobj.write('LOOKUP_TABLE default\n')
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cnt=0
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for iNd in range(0,self.nnodes):
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cnt=cnt+1
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if idxNdScal>=0:
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ndData=self.p.node_scalar(iNd,idxNdScal)
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else:
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nd=self.p.node(iNd)
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if idxNdScal==-3: ndData=nd.x
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if idxNdScal==-2: ndData=nd.y
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if idxNdScal==-1: ndData=nd.z
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fobj.write('%E '%(ndData))
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if cnt>self.VTKcnt:
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fobj.write('\n')
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cnt=0
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fobj.write('\n')
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fobj.write('\n')
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def writeElementData2VTK(self,fobj):
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self.sig_vMises=[]
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self.sig33=[]
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idx_sig_vMises=self.getLabelNr('Equivalent Von Mises Stress')
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idx_sig33=self.getLabelNr('Comp 33 of Cauchy Stress')
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fobj.write('\nCELL_DATA %i\n'%self.p.elements())
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for idxElScal in range(0,self.elscals):
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datalabel=self.elscal_list[idxElScal]
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datalabel=re.sub("\s",'_',datalabel)
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fobj.write('\n\nSCALARS %s float %i\n'%(datalabel,1))
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fobj.write('LOOKUP_TABLE default\n')
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cnt=0
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for iEl in range(0,self.nel):
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cnt=cnt+1
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elData=self.p.element_scalar(iEl,idxElScal)
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avgScal=0.0
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if datalabel in ['phi1', 'PHI','phi2']: # Euler angles should not be averaged
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avgScal=avgScal+elData[0].value
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else:
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for IP in range(0,8):
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avgScal=avgScal+elData[IP].value
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avgScal=avgScal/8.
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fobj.write('%E '%(avgScal))
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if idxElScal==idx_sig_vMises:
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self.sig_vMises.append(avgScal)
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elif idxElScal==idx_sig33:
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self.sig33.append(avgScal)
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if cnt>self.VTKcnt:
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fobj.write('\n')
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cnt=0
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fobj.write('\n')
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def get_avg_el_scal(self,idxElScal):
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result=[]
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datalabel=self.elscal_list[idxElScal]
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print('Collecting %s from all elements'%datalabel)
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for iEl in range(0,self.nel):
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elData=self.p.element_scalar(iEl,idxElScal)
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avgScal=0.0
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for IP in range(0,8):
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avgScal=avgScal+elData[IP].value
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avgScal=avgScal/8.
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result.append(avgScal)
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return result
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def writeUniaxiality2VTK(self,fobj):
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datalabel='uniaxiality_sig_vMises_durch_sig33'
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fobj.write('SCALARS %s float %i\n'%(datalabel,1))
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fobj.write('LOOKUP_TABLE default\n')
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cnt=0
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for iEl in range(0,self.nel):
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cnt=cnt+1
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if abs(self.sig_vMises[iEl])<1e-5:
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datum=0.
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else:
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datum=self.sig33[iEl]/self.sig_vMises[iEl]
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fobj.write('%E '%(datum))
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if cnt>self.VTKcnt:
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fobj.write('\n')
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cnt=0
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fobj.write('\n')
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def stress_per_element(self):
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self.stress=[]
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for iEl in range(0,self.nel):
|
||||
sig=self.avg_elten(2,elID=iEl)
|
||||
self.stress.append(sig[0])
|
||||
|
||||
def mean_stress_per_element(self):
|
||||
self.mean_stress=[]
|
||||
for iEl in range(0,self.nel):
|
||||
sig=self.stress[iEl]
|
||||
self.mean_stress.append(self.meanStress(sig))
|
||||
|
||||
def triaxiality_per_element(self):
|
||||
# classical triaxiality
|
||||
# 1/3 : uniax tension
|
||||
self.triaxiality=[]
|
||||
for iEl in range(0,self.nel):
|
||||
t=self.mean_stress[iEl]/self.sig_vMises[iEl]
|
||||
self.triaxiality.append(t)
|
||||
|
||||
def moreElData2VTK(self,fobj,data=[],label='datalabel'):
|
||||
fobj.write('SCALARS %s float %i\n'%(label,1))
|
||||
fobj.write('LOOKUP_TABLE default\n')
|
||||
cnt=0
|
||||
for iEl in range(0,self.nel):
|
||||
cnt=cnt+1
|
||||
fobj.write('%E '%(data[iEl]))
|
||||
if cnt>self.VTKcnt:
|
||||
fobj.write('\n')
|
||||
cnt=0
|
||||
fobj.write('\n')
|
||||
|
||||
def calc_lode_parameter(self):
|
||||
self.lode=[]
|
||||
try:
|
||||
self.stress
|
||||
except:
|
||||
self.stress_per_element()
|
||||
for iEl in range(0,self.nel):
|
||||
sig=self.stress[iEl]
|
||||
lode=self.stress2lode(sig)
|
||||
self.lode.append(lode)
|
||||
|
||||
def stress2lode(self,stress):
|
||||
[pStress,pAxes]=self.princStress(stress)
|
||||
s1=pStress[0]
|
||||
s2=pStress[1]
|
||||
s3=pStress[2]
|
||||
lode=(2*s2-s1-s3) / ( s1 - s3 )
|
||||
return lode
|
||||
|
||||
def princStress(self, stress):
|
||||
"""
|
||||
Function to compute 3D principal stresses and sort them.
|
||||
|
||||
from: http://geodynamics.org/svn/cig/short/3D/PyLith/trunk/playpen/postproc/vtkcff.py
|
||||
"""
|
||||
stressMat=np.array(stress)
|
||||
(princStress, princAxes) = np.linalg.eigh(stressMat)
|
||||
idx = princStress.argsort()
|
||||
princStressOrdered = princStress[idx]
|
||||
princAxesOrdered = princAxes[:,idx]
|
||||
return princStressOrdered, princAxesOrdered
|
||||
|
||||
def avg_elten(self,
|
||||
idxElTen, mat=0, elID=None):
|
||||
tensum=np.zeros((3,3));
|
||||
T=np.zeros((3,3));
|
||||
pts=0;
|
||||
avg=np.zeros((3,3));
|
||||
|
||||
if elID is None:
|
||||
averaged_elements=range(0,self.nel)
|
||||
else:
|
||||
averaged_elements=[elID]
|
||||
for i in averaged_elements:
|
||||
if mat==0 or int(self.p.element_scalar(i,4)[0].value)==mat:
|
||||
T=self.p.element_tensor(i,idxElTen)
|
||||
for k in range (0,8):
|
||||
tensum[0][0] = tensum[0][0] + T[k].t11
|
||||
tensum[0][1] = tensum[0][1] + T[k].t12
|
||||
tensum[0][2] = tensum[0][2] + T[k].t13
|
||||
tensum[1][1] = tensum[1][1] + T[k].t22
|
||||
tensum[1][2] = tensum[1][2] + T[k].t23
|
||||
tensum[2][2] = tensum[2][2] + T[k].t33
|
||||
pts=pts+1
|
||||
avg=tensum/pts
|
||||
avg=self.fillComponents(avg)
|
||||
del [T]
|
||||
return (avg,tensum,pts)
|
||||
|
||||
def fillComponents(self,
|
||||
halftensor
|
||||
):
|
||||
halftensor[1][0]=halftensor[0][1]
|
||||
halftensor[2][0]=halftensor[0][2]
|
||||
halftensor[2][1]=halftensor[1][2]
|
||||
return halftensor
|
||||
|
||||
def vMises(self,tensor33):
|
||||
t=tensor33
|
||||
s=(t[0,0]-t[1,1])**2+(t[1,1]-t[2,2])**2+(t[0,0]-t[2,2])**2+\
|
||||
6*(t[0,1]**2+t[1,2]**2+t[2,0]**2)
|
||||
vM=np.sqrt(s/2.)
|
||||
return vM
|
||||
|
||||
def meanStress(self,tensor33):
|
||||
t=tensor33
|
||||
s=t[0,0]+t[1,1]+t[2,2]
|
||||
ms=s/3.
|
||||
return ms
|
||||
|
||||
def invariants(self,tensor33):
|
||||
t=tensor33
|
||||
I1=t[0,0]+t[1,1]+t[2,2]
|
||||
I2=t[0,0]*t[1,1]+t[1,1]*t[2,2]+t[0,0]*t[2,2]-\
|
||||
t[0,1]**2-t[1,2]**2-t[0,2]**2
|
||||
I3=t[0,0]*t[1,1]*t[2,2]+\
|
||||
2*t[0,1]*t[1,2]*t[2,0]-\
|
||||
t[2,2]*t[0,1]**2-t[0,0]*t[1,2]**2-t[1,1]*t[0,2]**2
|
||||
return [ I1, I2, I3 ]
|
||||
|
||||
|
||||
class VTK_WRITER():
|
||||
"""
|
||||
The resulting vtk-file can be imported in Paraview 3.12
|
||||
|
||||
Then use Filters: Cell Data to Point Data + Contour
|
||||
to plot semi-transparent iso-surfaces.
|
||||
"""
|
||||
|
||||
def __init__(self):
|
||||
self.p=MARC_POST() # self.p
|
||||
|
||||
def openFile(self, filename='test.vtp'):
|
||||
self.f=open(filename,'w+')
|
||||
self.fname=filename
|
||||
|
||||
def writeFirstLines(self,
|
||||
vtkFile=None,
|
||||
version='2.0',
|
||||
comment='Test',
|
||||
dformat='ASCII', # BINARY | [ASCII]
|
||||
dtype='UNSTRUCTURED_GRID' # UNSTRUCTURED GRID
|
||||
):
|
||||
if vtkFile is None:
|
||||
vtkFile=self.f
|
||||
# First Line contains Data format version
|
||||
self.versionVTK=version
|
||||
vtkFile.write('# vtk DataFile Version %s\n'%self.versionVTK)
|
||||
# Comment goes to 2nd line and has maximum 256 chars
|
||||
vtkFile.write(comment+'\n')
|
||||
vtkFile.write(dformat+'\n')
|
||||
vtkFile.write('DATASET '+dtype+'\n')
|
||||
|
||||
|
||||
def marc2vtkBatch(self):
|
||||
for iori in range(1,63):
|
||||
self.p.postname='indent_fric0.3_R2.70_cA146.0_h0.320_ori%03i_OST_h19d.t16'%(iori)
|
||||
if os.path.exists(self.p.postname):
|
||||
self.marc2vtk(mode='fast', batchMode=1)
|
||||
|
||||
def marc2vtk(self, label=None, mode='fast',
|
||||
batchMode=0,
|
||||
incRange=None,
|
||||
incStepMult=1.):
|
||||
if batchMode==0:
|
||||
try:
|
||||
self.p
|
||||
except:
|
||||
self.p=MARC_POST()
|
||||
### ---- CHANGE dir/job/model to process here
|
||||
os.chdir('M:/nicu');
|
||||
jobname='ori001'
|
||||
self.p.postname='indent_fric0.3_R0.25_cA90.0_h0.010_4320els_'+jobname+'.t16'
|
||||
### ----
|
||||
|
||||
self.p.opent16()
|
||||
self.p.t16info()
|
||||
|
||||
incMax=self.p.p.increments();
|
||||
if incRange is None:
|
||||
incStep=5
|
||||
incRange=range(0,incMax+1,incStep)
|
||||
self.vtkPath=os.getcwd()+'/vtk_%s/'%self.p.postname
|
||||
if not os.path.exists(self.vtkPath):
|
||||
os.mkdir(self.vtkPath)
|
||||
for inc in incRange:
|
||||
print('Increment: %i'%inc)
|
||||
self.p.p.moveto(inc)
|
||||
t=self.p.p.time
|
||||
sys.stdout.write('inc:%i, time:%.3f\n'%(self.p.p.increment,t))
|
||||
self.incStr='inc%03i'%(inc*incStepMult)
|
||||
self.openFile(filename=self.vtkPath+self.p.postname[0:-4]+'_'+
|
||||
self.incStr+'.vtk')
|
||||
self.writeFirstLines(comment=self.p.postname,
|
||||
dtype='UNSTRUCTURED_GRID')
|
||||
self.p.writeNodes2VTK(fobj=self.f)
|
||||
self.p.writeElements2VTK(fobj=self.f)
|
||||
self.p.writeNodeScalars2VTK(fobj=self.f)
|
||||
self.p.writeElementData2VTK(fobj=self.f)
|
||||
# insert generation and writing of derived post values
|
||||
# *here*
|
||||
|
||||
self.f.close()
|
||||
print('Increment (self.p.p.increment): %i'%self.p.p.increment)
|
||||
print('Data written.')
|
||||
print(self.p.postname+' ready.')
|
||||
|
||||
|
||||
def scaleBar(self, length=1.0, posXYZ=[0., 0., 0.]):
|
||||
self.fsb=open('micronbar_l%.1f.vtp'%length,'w+')
|
||||
self.writeFirstLines(self.fsb, comment='micronbar')
|
||||
pts=np.array([])
|
||||
width=length*1.
|
||||
height=length*1.
|
||||
wVec=np.array([0., width, 0.])
|
||||
lVec=np.array([length,0.,0.])
|
||||
hVec=np.array([0.,0.,height])
|
||||
posXYZ=posXYZ-0.5*wVec-0.5*lVec#-0.5*hVec # CENTERING Y/N
|
||||
posXYZ=np.array(posXYZ)
|
||||
pts=[posXYZ, posXYZ+lVec,
|
||||
posXYZ+wVec,
|
||||
posXYZ+wVec+lVec]
|
||||
pts.extend([pts[0]+hVec,pts[1]+hVec,pts[2]+hVec,pts[3]+hVec])
|
||||
print(len(pts), pts)
|
||||
self.fsb.write('POINTS %i float\n'%len(pts))
|
||||
for npts in range(0,len(pts)):
|
||||
self.fsb.write('%f %f %f\n'%(pts[npts][0], pts[npts][1], pts[npts][2]))
|
||||
if 1: #Triad
|
||||
nCells=3
|
||||
ptsPerCell=2 # Lines (Type=3)
|
||||
cellSize=(ptsPerCell+1)*nCells
|
||||
self.fsb.write('CELLS %i %i\n'%(nCells,cellSize))
|
||||
self.fsb.write('2 0 1\n') #X-Line
|
||||
self.fsb.write('2 0 2\n') #Y-Line
|
||||
self.fsb.write('2 0 4\n') #Z-Line
|
||||
self.fsb.write('CELL_TYPES %i\n'%(nCells))
|
||||
self.fsb.write('3\n3\n3\n')#Line
|
||||
else: # Cube, change posXYZ
|
||||
nCells=1
|
||||
ptsPerCell=2 # Lines (Type=3)
|
||||
cellSize=(ptsPerCell+1)*nCells
|
||||
self.fsb.write('CELLS %i %i\n'%(nCells,cellSize))
|
||||
self.fsb.write('2 0 1\n') #Line
|
||||
self.fsb.write('CELL_TYPES %i\n'%(nCells))
|
||||
self.fsb.write('3\n')#Line
|
||||
|
||||
self.fsb.write('\n')
|
||||
self.fsb.close()
|
||||
print(self.fsb)
|
||||
|
||||
def example_unstructured(self):
|
||||
self.openFile(filename='example_unstructured_grid.vtk')
|
||||
self.f.write("""
|
||||
# vtk DataFile Version 2.0
|
||||
example_unstruct_grid
|
||||
ASCII
|
||||
|
||||
POINTS 12 float
|
||||
0 0 0
|
||||
1 0 0
|
||||
1 1 0
|
||||
0 1 0
|
||||
0 0 1
|
||||
1 0 1
|
||||
1 1 1
|
||||
0 1 1
|
||||
0 0 1.9
|
||||
1 0 1.9
|
||||
1 1 1.9
|
||||
0 1 1.9
|
||||
|
||||
|
||||
CELLS 2 18
|
||||
8 0 1 2 3 4 5 6 7
|
||||
8 4 5 6
|
||||
7 8 9 10 11
|
||||
|
||||
CELL_TYPES 2
|
||||
12
|
||||
12
|
||||
|
||||
POINT_DATA 12
|
||||
SCALARS nodex float 1
|
||||
LOOKUP_TABLE default
|
||||
2.34E+12
|
||||
2.00
|
||||
0.00
|
||||
1.62
|
||||
5.03
|
||||
1.02
|
||||
1.50
|
||||
0.00
|
||||
3 5 6 23423423423423423423.23423423""")
|
||||
self.f.close()
|
||||
|
||||
|
||||
|
||||
def writeNodes2VTK(self, fobj):
|
||||
self.VTKcnt=200 # how many numbers per line in vtk file
|
||||
fobj.write('POINTS %i'%self.p.nodes()+' float\n')
|
||||
for iNd in self.nodes:
|
||||
nd=self.p.node(iNd)
|
||||
disp=self.p.node_displacement(iNd)
|
||||
fobj.write('%f %f %f \n'%
|
||||
(nd.x+disp[0], nd.y+disp[1], nd.z+disp[2]))
|
||||
fobj.write('\n')
|
||||
print('Nodes written to VTK: %i'%self.p.nodes())
|
||||
|
||||
def writeElements2VTK(self, fobj):
|
||||
fobj.write('\nCELLS %i %i'%(self.p.elements(),self.p.elements()*9)+'\n')
|
||||
for iEl in range(0,self.nel):
|
||||
el=self.p.element(iEl)
|
||||
fobj.write('8 ')
|
||||
ndlist=el.items
|
||||
for k in [0, 1, 2, 3, 4, 5, 6, 7]: # FOR CELL TYPE VTK_HEXAHEDRON
|
||||
fobj.write('%6i '%(ndlist[k]-1))
|
||||
fobj.write('\n')
|
||||
fobj.write('\nCELL_TYPES %i'%self.p.elements()+'\n')
|
||||
cnt=0
|
||||
for iEl in range(0,self.nel):
|
||||
cnt=cnt+1
|
||||
fobj.write('12 ') #VTK_HEXAHEDRON
|
||||
if cnt>self.VTKcnt:
|
||||
fobj.write('\n');cnt=0
|
||||
fobj.write('\n')
|
||||
print('Elements written to VTK: %i'%self.p.elements())
|
||||
|
||||
def writeElScalars2NodesVTK(self,fobj):
|
||||
fobj.write('\nPOINT_DATA %i\n'%self.p.nodes())
|
||||
nScal=12
|
||||
nComponents=1+nScal
|
||||
fobj.write('SCALARS scalars float %i\n'%nComponents)
|
||||
fobj.write('LOOKUP_TABLE default\n')
|
||||
idxScal=self.nscal_list.index('Displacement Z')
|
||||
for iNd in self.nodes:
|
||||
fobj.write('%f '%(self.p.node_scalar(iNd,idxScal)))
|
||||
for iEl in range(0,self.nel):
|
||||
el=self.p.element(iEl)
|
||||
ndlist=el.items
|
||||
if (iNd+1) in ndlist:
|
||||
idx=ndlist.index(iNd+1)
|
||||
for iV in range(0,nScal):
|
||||
elData=self.p.element_scalar(iEl,35+iV)
|
||||
fobj.write('%f '%(elData[idx].value))
|
||||
break
|
||||
fobj.write('\n')
|
||||
fobj.write('\n')
|
||||
|
||||
def writeNodeScalars2VTK(self,fobj):
|
||||
fobj.write('\nPOINT_DATA %i\n'%self.p.nodes())
|
||||
for idxNdScal in range(-3,self.nscals): # include node x,y,z
|
||||
if idxNdScal>=0:
|
||||
datalabel=self.nscal_list[idxNdScal]
|
||||
datalabel=re.sub("\s",'_',datalabel)
|
||||
else:
|
||||
if idxNdScal==-3: datalabel='node.x'
|
||||
if idxNdScal==-2: datalabel='node.y'
|
||||
if idxNdScal==-1: datalabel='node.z'
|
||||
fobj.write('SCALARS %s float %i\n'%(datalabel,1))#nComponents))
|
||||
fobj.write('LOOKUP_TABLE default\n')
|
||||
cnt=0
|
||||
for iNd in range(0,self.nnodes):
|
||||
cnt=cnt+1
|
||||
if idxNdScal>=0:
|
||||
ndData=self.p.node_scalar(iNd,idxNdScal)
|
||||
else:
|
||||
nd=self.p.node(iNd)
|
||||
if idxNdScal==-3: ndData=nd.x
|
||||
if idxNdScal==-2: ndData=nd.y
|
||||
if idxNdScal==-1: ndData=nd.z
|
||||
fobj.write('%E '%(ndData))
|
||||
if cnt>self.VTKcnt:
|
||||
fobj.write('\n')
|
||||
cnt=0
|
||||
fobj.write('\n')
|
||||
fobj.write('\n')
|
||||
|
||||
def writeElementData2VTK(self,fobj):
|
||||
fobj.write('\nCELL_DATA %i\n'%self.p.elements())
|
||||
for idxElScal in range(0,self.elscals):
|
||||
datalabel=self.elscal_list[idxElScal]
|
||||
datalabel=re.sub("\s",'_',datalabel)
|
||||
fobj.write('\n\nSCALARS %s float %i\n'%(datalabel,1))#nComponents))
|
||||
fobj.write('LOOKUP_TABLE default\n')
|
||||
cnt=0
|
||||
for iEl in range(0,self.nel):
|
||||
cnt=cnt+1
|
||||
elData=self.p.element_scalar(iEl,idxElScal)
|
||||
avgScal=0.0
|
||||
if datalabel in ['phi1', 'PHI','phi2']:
|
||||
avgScal=avgScal+elData[0].value
|
||||
else:
|
||||
for IP in range(0,8):
|
||||
avgScal=avgScal+elData[IP].value
|
||||
avgScal=avgScal/8.
|
||||
fobj.write('%E '%(avgScal))
|
||||
if cnt>self.VTKcnt:
|
||||
fobj.write('\n')
|
||||
cnt=0
|
||||
fobj.write('\n')
|
||||
|
||||
|
||||
def example1(self):
|
||||
self.openFile()
|
||||
self.writeFirstLines()
|
||||
self.f.write("""DATASET POLYDATA
|
||||
POINTS 8 float
|
||||
0.0 0.0 0.0
|
||||
1.0 0.0 0.0
|
||||
1.0 1.0 0.0
|
||||
0.0 1.0 0.0
|
||||
0.0 0.0 1.0
|
||||
1.0 0.0 1.0
|
||||
1.0 1.0 1.0
|
||||
0.0 1.0 1.0
|
||||
POLYGONS 6 30
|
||||
4 0 1 2 3
|
||||
4 4 5 6 7
|
||||
4 0 1 5 4
|
||||
4 2 3 7 6
|
||||
4 0 4 7 3
|
||||
4 1 2 6 5
|
||||
|
||||
CELL_DATA 6
|
||||
SCALARS cell_scalars int 1
|
||||
LOOKUP_TABLE default
|
||||
0
|
||||
1
|
||||
2
|
||||
3
|
||||
4
|
||||
5
|
||||
NORMALS cell_normals float
|
||||
0 0 -1
|
||||
0 0 1
|
||||
0 -1 0
|
||||
0 1 0
|
||||
-1 0 0
|
||||
1 0 0
|
||||
FIELD FieldData 2
|
||||
cellIds 1 6 int
|
||||
0 1 2 3 4 5
|
||||
faceAttributes 2 6 float
|
||||
0.0 1.0 1.0 2.0 2.0 3.0 3.0 4.0 4.0 5.0 5.0 6.0
|
||||
|
||||
POINT_DATA 8
|
||||
SCALARS sample_scalars float 1
|
||||
LOOKUP_TABLE my_table
|
||||
0.0
|
||||
1.0
|
||||
2.0
|
||||
3.0
|
||||
4.0
|
||||
5.0
|
||||
6.0
|
||||
7.0
|
||||
LOOKUP_TABLE my_table 8
|
||||
0.0 0.0 0.0 1.0
|
||||
1.0 0.0 0.0 1.0
|
||||
0.0 1.0 0.0 1.0
|
||||
1.0 1.0 0.0 1.0
|
||||
0.0 0.0 1.0 1.0
|
||||
1.0 0.0 1.0 1.0
|
||||
0.0 1.0 1.0 1.0
|
||||
1.0 1.0 1.0 1.0""")
|
||||
self.f.close()
|
||||
|
||||
|
||||
import pyvtk
|
||||
class marc_to_vtk():
|
||||
"""
|
||||
Anybody wants to implement it with pyvtk?
|
||||
|
||||
The advantage would be that pyvtk can also wirte the
|
||||
<xml>-VTK format and binary.
|
||||
These can be plotted with mayavi.
|
||||
"""
|
||||
|
||||
def __init__(self):
|
||||
self.p=[]#MARC_POST() # self.p
|
||||
|
||||
def run(self):
|
||||
vtk = pyvtk.VtkData(\
|
||||
pyvtk.UnstructuredGrid(self.p.points,
|
||||
hexahedron=self.p.cells),
|
||||
'm2v output')
|
||||
vtk.tofile('m2v_file')
|
||||
|
||||
|
|
@ -1,5 +0,0 @@
|
|||
"""Tools to control the various solvers."""
|
||||
|
||||
from .solver import Solver # noqa
|
||||
from .marc import Marc # noqa
|
||||
from .abaqus import Abaqus # noqa
|
||||
|
|
@ -1,34 +0,0 @@
|
|||
import subprocess
|
||||
|
||||
from .solver import Solver
|
||||
import damask
|
||||
|
||||
|
||||
class Abaqus(Solver):
|
||||
"""Wrapper to run DAMASK with Abaqus."""
|
||||
|
||||
def __init__(self,version=int(damask.Environment().options['ABAQUS_VERSION'])):
|
||||
"""
|
||||
Create a Abaqus solver object.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
version : integer
|
||||
Abaqus version
|
||||
|
||||
"""
|
||||
self.solver ='Abaqus'
|
||||
self.version = int(version)
|
||||
|
||||
def return_run_command(self,model):
|
||||
env=damask.Environment()
|
||||
try:
|
||||
cmd='abq'+self.version
|
||||
subprocess.check_output([cmd,'information=release'])
|
||||
except OSError: # link to abqXXX not existing
|
||||
cmd='abaqus'
|
||||
process = subprocess.Popen(['abaqus','information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
|
||||
detectedVersion = int(process.stdout.readlines()[1].split()[1].decode('utf-8'))
|
||||
if self.version != detectedVersion:
|
||||
raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
|
||||
return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,env.rootDir())
|
||||
|
|
@ -1,89 +0,0 @@
|
|||
import os
|
||||
import subprocess
|
||||
import shlex
|
||||
|
||||
from .solver import Solver
|
||||
import damask
|
||||
|
||||
class Marc(Solver):
|
||||
"""Wrapper to run DAMASK with MSCMarc."""
|
||||
|
||||
def __init__(self,version=damask.Environment().options['MARC_VERSION']):
|
||||
"""
|
||||
Create a Marc solver object.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
version : float
|
||||
Marc version
|
||||
|
||||
"""
|
||||
self.solver ='Marc'
|
||||
self.version = damask.environment.Environment().options['MARC_VERSION']
|
||||
|
||||
|
||||
#--------------------------
|
||||
def libraryPath(self):
|
||||
|
||||
path_MSC = damask.environment.Environment().options['MSC_ROOT']
|
||||
path_lib = '{}/mentat{}/shlib/linux64'.format(path_MSC,self.version)
|
||||
|
||||
return path_lib if os.path.exists(path_lib) else ''
|
||||
|
||||
|
||||
#--------------------------
|
||||
def toolsPath(self):
|
||||
|
||||
path_MSC = damask.environment.Environment().options['MSC_ROOT']
|
||||
path_tools = '{}/marc{}/tools'.format(path_MSC,self.version)
|
||||
|
||||
return path_tools if os.path.exists(path_tools) else ''
|
||||
|
||||
|
||||
#--------------------------
|
||||
def submit_job(self,
|
||||
model,
|
||||
job = 'job1',
|
||||
logfile = False,
|
||||
compile = False,
|
||||
optimization ='',
|
||||
):
|
||||
|
||||
|
||||
damaskEnv = damask.environment.Environment()
|
||||
|
||||
user = os.path.join(damaskEnv.relPath('src'),'DAMASK_marc{}.{}'.format(self.version,'f90' if compile else 'marc'))
|
||||
if not os.path.isfile(user):
|
||||
raise FileNotFoundError("DAMASK4Marc ({}) '{}' not found".format(('source' if compile else 'binary'),user))
|
||||
|
||||
# Define options [see Marc Installation and Operation Guide, pp 23]
|
||||
script = 'run_damask_{}mp'.format(optimization)
|
||||
|
||||
cmd = os.path.join(self.toolsPath(),script) + \
|
||||
' -jid ' + model + '_' + job + \
|
||||
' -nprocd 1 -autorst 0 -ci n -cr n -dcoup 0 -b no -v no'
|
||||
|
||||
if compile: cmd += ' -u ' + user + ' -save y'
|
||||
else: cmd += ' -prog ' + os.path.splitext(user)[0]
|
||||
|
||||
print('job submission with{} compilation: {}'.format('' if compile else 'out',user))
|
||||
if logfile: log = open(logfile, 'w')
|
||||
print(cmd)
|
||||
process = subprocess.Popen(shlex.split(cmd),stdout = log,stderr = subprocess.STDOUT)
|
||||
log.close()
|
||||
process.wait()
|
||||
|
||||
#--------------------------
|
||||
def exit_number_from_outFile(self,outFile=None):
|
||||
import string
|
||||
exitnumber = -1
|
||||
fid_out = open(outFile,'r')
|
||||
for line in fid_out:
|
||||
if (string.find(line,'tress iteration') != -1):
|
||||
print(line)
|
||||
elif (string.find(line,'Exit number') != -1):
|
||||
substr = line[string.find(line,'Exit number'):len(line)]
|
||||
exitnumber = int(substr[12:16])
|
||||
|
||||
fid_out.close()
|
||||
return exitnumber
|
||||
|
|
@ -1,6 +0,0 @@
|
|||
class Solver():
|
||||
"""
|
||||
General class for solver specific functionality.
|
||||
|
||||
Sub-classed by the individual solvers.
|
||||
"""
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
#!/bin/bash
|
||||
|
||||
DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" >/dev/null 2>&1 && pwd )"
|
||||
cd $DIR
|
||||
|
||||
VERSION=$(head -n1 damask/VERSION)
|
||||
read -p "updated version [${VERSION}]: " UP
|
||||
echo ${UP:-$VERSION} > damask/VERSION
|
||||
|
||||
rm -rf dist/
|
||||
python3 setup.py sdist bdist_wheel
|
||||
python3 -m twine upload dist/*
|
||||
|
|
@ -2,7 +2,7 @@ import setuptools
|
|||
import os
|
||||
|
||||
with open(os.path.join(os.path.dirname(__file__),'damask/VERSION')) as f:
|
||||
version = f.readline()[1:-1]
|
||||
version = f.readline()
|
||||
|
||||
setuptools.setup(
|
||||
name="damask",
|
||||
|
|
@ -15,14 +15,17 @@ setuptools.setup(
|
|||
packages=setuptools.find_packages(),
|
||||
include_package_data=True,
|
||||
install_requires = [
|
||||
"numpy",
|
||||
"scipy",
|
||||
"pandas",
|
||||
"h5py",
|
||||
"vtk"
|
||||
"vtk",
|
||||
],
|
||||
license = 'GPL3',
|
||||
classifiers = [
|
||||
"Intended Audience :: Science/Research",
|
||||
"Topic :: Scientific/Engineering",
|
||||
"Programming Language :: Python :: 3",
|
||||
"License :: OSI Approved :: GPL3",
|
||||
"License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
|
||||
"Operating System :: OS Independent",
|
||||
],
|
||||
)
|
||||
|
|
|
|||
|
|
@ -2,8 +2,6 @@ import os
|
|||
|
||||
import pytest
|
||||
|
||||
import damask
|
||||
|
||||
def pytest_addoption(parser):
|
||||
parser.addoption("--update",
|
||||
action="store_true",
|
||||
|
|
@ -17,5 +15,4 @@ def update(request):
|
|||
@pytest.fixture
|
||||
def reference_dir_base():
|
||||
"""Directory containing reference results."""
|
||||
env = damask.Environment()
|
||||
return os.path.join(env.rootDir(),'python','tests','reference')
|
||||
return os.path.join(os.path.dirname(__file__),'reference')
|
||||
|
|
|
|||
Loading…
Reference in New Issue