From 41ed7ce462b180ed180cc8ac082cdd8b47e276f5 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 12 Dec 2019 14:31:04 -0500 Subject: [PATCH] "pip install damask" either locally or from PyPI after upload --- Makefile | 6 +- env/DAMASK.csh | 5 - env/DAMASK.sh | 1 - env/DAMASK.zsh | 1 - python/MANIFEST.in | 2 + python/damask/LICENSE | 15 +- python/damask/README | 14 +- python/damask/README.md | 13 + python/damask/VERSION | 2 +- python/damask/__init__.py | 14 +- python/damask/environment.py | 27 -- python/damask/result/marc2vtk.py | 743 ------------------------------- python/damask/solver/__init__.py | 5 - python/damask/solver/abaqus.py | 34 -- python/damask/solver/marc.py | 89 ---- python/damask/solver/solver.py | 6 - python/makeDistribution.sh | 12 + python/setup.py | 11 +- python/tests/conftest.py | 5 +- 19 files changed, 75 insertions(+), 930 deletions(-) mode change 120000 => 100644 python/damask/LICENSE mode change 120000 => 100644 python/damask/README create mode 100644 python/damask/README.md mode change 120000 => 100644 python/damask/VERSION delete mode 100644 python/damask/environment.py delete mode 100644 python/damask/result/marc2vtk.py delete mode 100644 python/damask/solver/__init__.py delete mode 100644 python/damask/solver/abaqus.py delete mode 100644 python/damask/solver/marc.py delete mode 100644 python/damask/solver/solver.py create mode 100644 python/makeDistribution.sh diff --git a/Makefile b/Makefile index b24e3d36b..64c83f5f7 100644 --- a/Makefile +++ b/Makefile @@ -4,7 +4,7 @@ SHELL = /bin/sh ######################################################################################## DAMASK_ROOT = $(shell python -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))") .PHONY: all -all: grid mesh processing +all: grid mesh python processing .PHONY: grid grid: build/grid @@ -36,3 +36,7 @@ clean: processing: @./installation/symlink_Processing.py ${MAKEFLAGS} +.PHONY: python +python: + @pip install --user ./python + diff --git a/env/DAMASK.csh b/env/DAMASK.csh index d223d885a..6ccb5cca4 100644 --- a/env/DAMASK.csh +++ b/env/DAMASK.csh @@ -61,8 +61,3 @@ if ( $?prompt ) then endif setenv DAMASK_NUM_THREADS $DAMASK_NUM_THREADS -if ( ! $?PYTHONPATH ) then - setenv PYTHONPATH $DAMASK_ROOT/python -else - setenv PYTHONPATH $DAMASK_ROOT/python:$PYTHONPATH -endif diff --git a/env/DAMASK.sh b/env/DAMASK.sh index 1b4bea86a..ff38cf981 100644 --- a/env/DAMASK.sh +++ b/env/DAMASK.sh @@ -94,7 +94,6 @@ if [ ! -z "$PS1" ]; then fi export DAMASK_NUM_THREADS -export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN BRANCH; do unset "${var}" diff --git a/env/DAMASK.zsh b/env/DAMASK.zsh index 5449007f9..3df2658cd 100644 --- a/env/DAMASK.zsh +++ b/env/DAMASK.zsh @@ -88,7 +88,6 @@ if [ ! -z "$PS1" ]; then fi export DAMASK_NUM_THREADS -export PYTHONPATH=$DAMASK_ROOT/python:$PYTHONPATH for var in BASE STAT SOLVER PROCESSING FREE DAMASK_BIN BRANCH; do unset "${var}" diff --git a/python/MANIFEST.in b/python/MANIFEST.in index bb6d21f36..cd47f5e61 100644 --- a/python/MANIFEST.in +++ b/python/MANIFEST.in @@ -1 +1,3 @@ +include damask/README include damask/VERSION +include damask/LICENSE diff --git a/python/damask/LICENSE b/python/damask/LICENSE deleted file mode 120000 index 30cff7403..000000000 --- a/python/damask/LICENSE +++ /dev/null @@ -1 +0,0 @@ -../../LICENSE \ No newline at end of file diff --git a/python/damask/LICENSE b/python/damask/LICENSE new file mode 100644 index 000000000..1ab20178c --- /dev/null +++ b/python/damask/LICENSE @@ -0,0 +1,14 @@ +Copyright 2011-19 Max-Planck-Institut für Eisenforschung GmbH + +DAMASK is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. + +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 General Public License for more details. + +You should have received a copy of the GNU General Public License +along with this program. If not, see . diff --git a/python/damask/README b/python/damask/README deleted file mode 120000 index 3830a4118..000000000 --- a/python/damask/README +++ /dev/null @@ -1 +0,0 @@ -../../README \ No newline at end of file diff --git a/python/damask/README b/python/damask/README new file mode 100644 index 000000000..7fc372881 --- /dev/null +++ b/python/damask/README @@ -0,0 +1,13 @@ +DAMASK - The Düsseldorf Advanced Material Simulation Kit +Visit damask.mpie.de for installation and usage instructions + +CONTACT INFORMATION + +Max-Planck-Institut für Eisenforschung GmbH +Max-Planck-Str. 1 +40237 Düsseldorf +Germany + +Email: DAMASK@mpie.de +https://damask.mpie.de +https://magit1.mpie.de diff --git a/python/damask/README.md b/python/damask/README.md new file mode 100644 index 000000000..7fc372881 --- /dev/null +++ b/python/damask/README.md @@ -0,0 +1,13 @@ +DAMASK - The Düsseldorf Advanced Material Simulation Kit +Visit damask.mpie.de for installation and usage instructions + +CONTACT INFORMATION + +Max-Planck-Institut für Eisenforschung GmbH +Max-Planck-Str. 1 +40237 Düsseldorf +Germany + +Email: DAMASK@mpie.de +https://damask.mpie.de +https://magit1.mpie.de diff --git a/python/damask/VERSION b/python/damask/VERSION deleted file mode 120000 index 558194c5a..000000000 --- a/python/damask/VERSION +++ /dev/null @@ -1 +0,0 @@ -../../VERSION \ No newline at end of file diff --git a/python/damask/VERSION b/python/damask/VERSION new file mode 100644 index 000000000..ac39a106c --- /dev/null +++ b/python/damask/VERSION @@ -0,0 +1 @@ +0.9.0 diff --git a/python/damask/__init__.py b/python/damask/__init__.py index 2cd26cf1c..34a1bbbdd 100644 --- a/python/damask/__init__.py +++ b/python/damask/__init__.py @@ -1,15 +1,13 @@ """Main aggregator.""" import os -with open(os.path.join(os.path.dirname(__file__),'VERSION')) as f: - version = f.readline()[1:-1] - name = 'damask' +with open(os.path.join(os.path.dirname(__file__),'VERSION')) as f: + version = f.readline().strip() # classes -from .environment import Environment # noqa -from .asciitable import ASCIItable # noqa from .table import Table # noqa +from .asciitable import ASCIItable # noqa from .config import Material # noqa from .colormaps import Colormap, Color # noqa @@ -17,10 +15,12 @@ from .orientation import Symmetry, Lattice, Rotation, Orientation # noqa from .dadf5 import DADF5 # noqa from .geom import Geom # noqa -from .solver import Solver # noqa from .test import Test # noqa from .util import extendableOption # noqa # functions in modules -from . import mechanics # noqa +from . import mechanics # noqa +# clean temporary variables +del os +del f diff --git a/python/damask/environment.py b/python/damask/environment.py deleted file mode 100644 index ef07cd264..000000000 --- a/python/damask/environment.py +++ /dev/null @@ -1,27 +0,0 @@ -import os -import re - -class Environment(): - __slots__ = [ \ - 'options', - ] - - def __init__(self): - self.options = {} - self.get_options() - - def relPath(self,relative = '.'): - return os.path.join(self.rootDir(),relative) - - def rootDir(self): - return os.path.normpath(os.path.join(os.path.realpath(__file__),'../../../')) - - def get_options(self): - with open(self.relPath(self.rootDir()+'/CONFIG')) as configFile: - for line in configFile: - l = re.sub('^set ', '', line).strip() # remove "set" (tcsh) when setting variables - if l and not l.startswith('#'): - items = re.split(r'\s*=\s*',l) - if len(items) == 2: - self.options[items[0].upper()] = \ - re.sub('\$\{*DAMASK_ROOT\}*',self.rootDir(),os.path.expandvars(items[1])) # expand all shell variables and DAMASK_ROOT diff --git a/python/damask/result/marc2vtk.py b/python/damask/result/marc2vtk.py deleted file mode 100644 index f712bd963..000000000 --- a/python/damask/result/marc2vtk.py +++ /dev/null @@ -1,743 +0,0 @@ -# -*- coding: UTF-8 no BOM -*- - -# This tool converts a msc.marc result file into the vtk format that -# can be viewed by Paraview software (Kitware), or MayaVi (needs xml-vtk, or ... -# -# About the vtk format: http://www.vtk.org/VTK/project/about.html -# Some example vtk files: http://people.sc.fsu.edu/~jburkardt/data/vtk/vtk.html -# www.paraview.org - -import os,sys,re -import numpy as np - -import py_post # MSC closed source module to access marc result files - -class MARC_POST(): - def __init__(self): - self.projdir='./' - - def opent16(self,incr=None): - self.fpath=os.path.join(self.projdir,self.postname) - print('Trying to open ',self.fpath,' ...') - self.p=py_post.post_open(self.fpath) - if self.p is None: - print('Could not open %s.'%self.postname); #return 'err'#; sys.exit(1) - raise Exception('Could not open t16') - print('Postfile %s%s is open ...'%(self.projdir,self.postname)) - self.maxincr=self.p.increments() - print('and has %i increments'%self.maxincr) - if incr is None: - self.p.moveto(self.maxincr-1) - else: - self.p.moveto(incr+1) - print('moved to increment ', self.p.increment) - self.p.extrapolation('translate') # linear, translate, average. query with p.extrapolate - print('extrapolation method is ', self.p.extrapolate) - print('collecting model information') - self.t16info(printFlag=0) - print('t16 is open') - self.p - - def t16info(self, printFlag=1 - ): - if not self.p: - self.p=self.opent16()#post_open(self.postname) - print(self.p) - oldincr=self.p.position - if oldincr==0: - self.p.moveto(1) - - self.nnodes=self.p.nodes() #self.p.node(self.nnodes) crashes; only to nnodes-1 possible - self.nodes=range(0,self.nnodes) - self.nscals=self.p.node_scalars(); #print 'nscals', nscals - self.nscal_list=['']*self.nscals - self.nel=self.p.elements() - self.elscals=self.p.element_scalars() - self.elscal_list=['']*self.elscals - self.eltens=self.p.element_tensors() - self.elten_list=['']*self.eltens - for i in range(0,self.nscals): - self.nscal_list[i]=self.p.node_scalar_label(i) - for i in range (0,self.elscals): - self.elscal_list[i]=self.p.element_scalar_label(i) - if printFlag==1: print(i, self.elscal_list[i]) - for i in range (0,self.eltens): - self.elten_list[i]=self.p.element_tensor_label(i) - if printFlag==1: print(i, self.elten_list[i]) - for i in range(0,self.p.element_tensors()): - if printFlag==1: print('Element Tensor: ', i, self.p.element_tensor_label(i)) - if printFlag==1: print('') - for i in range(0,self.p.element_scalars()): - if printFlag==1: print('Element Scalar: ', i, self.p.element_scalar_label(i)) - if oldincr==0: - self.p.moveto(0) - - def closet16(self): - print('Trying to close FEM result file ...') - try: - if self.p: - self.p.close() - print('FEM result file closed.') - self.p=None - else: - print('post object not open?') - except: - print('ERROR. Could not close FEM result file.') - - def getLabelNr(self, label=None, type='Scalar'): - if type[0]=='S' or type[0]=='s': # element scalar - labelNr=self.elscal_list.index(label) - elif type[0]=='N': # node scalar - labelNr=self.nscal_list.index(label) - elif type[0]=='T' or type[0]=='t': # tensor - labelNr=self.elten_list.index(label) - print('Found label %s at index %i'%(label,labelNr)) - return labelNr - - - def writeNodes2VTK(self, fobj): - self.points=[] - self.VTKcnt=200 # number of values per line in vtk file - fobj.write('POINTS %i'%self.p.nodes()+' float\n') - self.nodes_dict={} # store the node IDs in case of holes in the numbering - for iNd in self.nodes: - nd=self.p.node(iNd) - disp=self.p.node_displacement(iNd) - nd_xyz=[nd.x+disp[0], nd.y+disp[1], nd.z+disp[2]] - self.points.append(nd_xyz) # for pyvtk - fobj.write('%f %f %f \n'% - (nd.x+disp[0], nd.y+disp[1], nd.z+disp[2])) - self.nodes_dict[nd.id-1]=iNd - 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') - self.cells=[] #for pyvtk - for iEl in range(0,self.nel): - el=self.p.element(iEl) - cell_nodes=[] # for pyvtk - ndlist=el.items - for k in [0, 1, 2, 3, 4, 5, 6, 7]: # FOR CELL TYPE VTK_HEXAHEDRON - node=ndlist[k]-1 - cell_nodes.append(self.nodes_dict[node]) - self.cells.append(cell_nodes) # for pyvtk - for e in self.cells: - fobj.write('8 ') - for n in e: - fobj.write('%6i '%n) - 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('11\n') #VTK_VOXEL - 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()) - self.pointDataScalars=[] - for idxNdScal in range(-3,self.nscals): #now 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): - self.sig_vMises=[] - self.sig33=[] - idx_sig_vMises=self.getLabelNr('Equivalent Von Mises Stress') - idx_sig33=self.getLabelNr('Comp 33 of Cauchy Stress') - 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)) - 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']: # Euler angles should not be averaged - 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 idxElScal==idx_sig_vMises: - self.sig_vMises.append(avgScal) - elif idxElScal==idx_sig33: - self.sig33.append(avgScal) - if cnt>self.VTKcnt: - fobj.write('\n') - cnt=0 - fobj.write('\n') - - def get_avg_el_scal(self,idxElScal): - result=[] - datalabel=self.elscal_list[idxElScal] - print('Collecting %s from all elements'%datalabel) - for iEl in range(0,self.nel): - elData=self.p.element_scalar(iEl,idxElScal) - avgScal=0.0 - for IP in range(0,8): - avgScal=avgScal+elData[IP].value - avgScal=avgScal/8. - result.append(avgScal) - return result - - def writeUniaxiality2VTK(self,fobj): - datalabel='uniaxiality_sig_vMises_durch_sig33' - fobj.write('SCALARS %s float %i\n'%(datalabel,1)) - fobj.write('LOOKUP_TABLE default\n') - cnt=0 - for iEl in range(0,self.nel): - cnt=cnt+1 - if abs(self.sig_vMises[iEl])<1e-5: - datum=0. - else: - datum=self.sig33[iEl]/self.sig_vMises[iEl] - fobj.write('%E '%(datum)) - if cnt>self.VTKcnt: - fobj.write('\n') - cnt=0 - fobj.write('\n') - - def stress_per_element(self): - self.stress=[] - 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 - -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') - diff --git a/python/damask/solver/__init__.py b/python/damask/solver/__init__.py deleted file mode 100644 index 70f48eb26..000000000 --- a/python/damask/solver/__init__.py +++ /dev/null @@ -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 diff --git a/python/damask/solver/abaqus.py b/python/damask/solver/abaqus.py deleted file mode 100644 index 693ec1360..000000000 --- a/python/damask/solver/abaqus.py +++ /dev/null @@ -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()) diff --git a/python/damask/solver/marc.py b/python/damask/solver/marc.py deleted file mode 100644 index 971b2226b..000000000 --- a/python/damask/solver/marc.py +++ /dev/null @@ -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 diff --git a/python/damask/solver/solver.py b/python/damask/solver/solver.py deleted file mode 100644 index c1ca7ff69..000000000 --- a/python/damask/solver/solver.py +++ /dev/null @@ -1,6 +0,0 @@ -class Solver(): - """ - General class for solver specific functionality. - - Sub-classed by the individual solvers. - """ diff --git a/python/makeDistribution.sh b/python/makeDistribution.sh new file mode 100644 index 000000000..ed81257cf --- /dev/null +++ b/python/makeDistribution.sh @@ -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/* diff --git a/python/setup.py b/python/setup.py index 515401c59..f53a08513 100644 --- a/python/setup.py +++ b/python/setup.py @@ -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", ], ) diff --git a/python/tests/conftest.py b/python/tests/conftest.py index a0504c499..411c07a8c 100644 --- a/python/tests/conftest.py +++ b/python/tests/conftest.py @@ -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')