fixed wrong setting of coordinates in spectral solvers and removed old python scripts for setup of code and processing
This commit is contained in:
Martin Diehl
parent
f9c45fd931
commit
cc9eb685fe
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@ -187,8 +187,8 @@ subroutine AL_init(temperature)
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read (777,rec=1) temp3333_Real
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close (777)
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endif
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(&
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F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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call Utilities_constitutiveResponse(F,F,temperature,0.0_pReal,P,temp3333_Real2,&
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temp33_Real,.false.,math_I3)
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call DMDAVecRestoreArrayF90(da,solution_vec,xx_psc,ierr); CHKERRQ(ierr)
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@ -313,8 +313,8 @@ type(tSolutionState) function &
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!--------------------------------------------------------------------------------------------------
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! update coordinates and rate and forward last inc
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(&
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F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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Fdot = Utilities_calculateRate(math_rotate_backward33(f_aimDot,rotation_BC), &
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timeinc_old,guess,F_lastInc,reshape(F,[3,3,res(1),res(2),res(3)]))
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F_lambdaDot = Utilities_calculateRate(math_rotate_backward33(f_aimDot,rotation_BC), &
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@ -125,8 +125,7 @@ subroutine basic_init(temperature)
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read (777,rec=1) temp3333_Real
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close (777)
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endif
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,F),[3,1,mesh_NcpElems])
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call Utilities_constitutiveResponse(F,F,temperature,0.0_pReal,P,C,temp33_Real,.false.,math_I3) ! constitutive response with no deformation in no time to get reference stiffness
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if (restartInc == 1_pInt) then ! use initial stiffness as reference stiffness
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temp3333_Real = C
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@ -245,8 +244,7 @@ type(tSolutionState) function &
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C = C_lastInc
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else
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C_lastInc = C
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,F),[3,1,mesh_NcpElems])
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!--------------------------------------------------------------------------------------------------
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! calculate rate for aim
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@ -175,8 +175,8 @@ subroutine basicPETSc_init(temperature)
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read (777,rec=1) temp3333_Real
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close (777)
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endif
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(&
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F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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call Utilities_constitutiveResponse(&
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reshape(F(0:8,0:res(1)-1_pInt,0:res(2)-1_pInt,0:res(3)-1_pInt),[3,3,res(1),res(2),res(3)]),&
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reshape(F(0:8,0:res(1)-1_pInt,0:res(2)-1_pInt,0:res(3)-1_pInt),[3,3,res(1),res(2),res(3)]),&
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@ -264,16 +264,16 @@ type(tSolutionState) function &
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write (777,rec=1) C_lastInc
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close(777)
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endif
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(F,[3,3,res(1),res(2),res(3)])),&
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[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(&
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F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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if ( cutBack) then
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F_aim = F_aim_lastInc
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F = reshape(F_lastInc,[9,res(1),res(2),res(3)])
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C = C_lastInc
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else
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C_lastInc = C
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mesh_ipCoordinates = 0.0_pReal !reshape(mesh_deformedCoordsFFT(geomdim,&
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!reshape(F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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mesh_ipCoordinates = reshape(mesh_deformedCoordsFFT(geomdim,reshape(&
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F,[3,3,res(1),res(2),res(3)])),[3,1,mesh_NcpElems])
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!--------------------------------------------------------------------------------------------------
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! calculate rate for aim
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@ -1,105 +0,0 @@
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#!/usr/bin/env python
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import os,string,re
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import damask
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from optparse import OptionParser, OptionGroup, Option, SUPPRESS_HELP
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# -----------------------------
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class extendedOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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parser = OptionParser(option_class=extendedOption, usage='%prog [options] datafile[s]', description = """
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Writes version specific files for different MARC releases, adjustes the make file for the spectral solver and optionally compiles the spectral solver
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""" + string.replace('$Id$','\n','\\n')
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)
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parser.add_option('-c', '--compile', dest='spectralCompile', action='store_true', \
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help='compiles the spectral solver [%default]')
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parser.add_option('-o', '--options', dest='makeOptions', action='extend', type='string', \
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metavar="KEY=VALUE", \
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help='comma-separated list of options passed to Makefile when compiling spectral code %default')
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parser.set_defaults(spectralCompile = False)
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parser.set_defaults(makeOptions = ['F90=ifort'])
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(options, args) = parser.parse_args()
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architectures = {
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'marc': {
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'parent': 'DAMASK_marc.f90',
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'versions' : ['%%MARCVERSION%%','2010','2011','2012'],
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},
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}
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bin_link = { \
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'.' : [
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'DAMASK_spectral.exe',
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],
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}
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damaskEnv = damask.Environment('../../') # script location relative to root
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baseDir = damaskEnv.relPath('code/')
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for arch in architectures:
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me = architectures[arch]
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try:
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parentFile = open(baseDir+os.sep+me['parent'])
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parentContent = parentFile.readlines()
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parentFile.close()
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except IOError:
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print 'unable to open',me['parent']
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continue
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for version in me['versions'][1:]:
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childFile = open(baseDir+os.sep+version.join(os.path.splitext(me['parent'])),'w')
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for line in parentContent:
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childFile.write(line.replace(me['versions'][0],version))
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childFile.close()
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# changing dirs in makefile
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makefile = open(os.path.join(baseDir,'Makefile'))
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content = makefile.readlines()
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makefile.close()
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makefile = open(os.path.join(baseDir,'Makefile'),'w')
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for line in content:
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m = re.match(r'(FFTW|IMKL|ACML|LAPACK)ROOT\s*\?=',line)
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if m:
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if m.group(1).lower() in damaskEnv.pathInfo:
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substitution = damaskEnv.pathInfo[m.group(1).lower()]
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else:
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substitution = ''
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line = '%sROOT ?= %s\n'%(m.group(1),substitution)
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makefile.write(line)
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makefile.close()
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# compiling spectral code
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if (options.spectralCompile):
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os.system('make --directory %s clean'%(baseDir))
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os.system('make --directory %s %s'%(baseDir,' '.join(options.makeOptions)))
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# processing symbolic linking list
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for dir in bin_link:
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for file in bin_link[dir]:
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src = os.path.abspath(os.path.join(baseDir,dir,file))
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if os.path.exists(src):
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sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),\
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{True: dir,
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False:os.path.splitext(file)[0]}[file == '']))
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if os.path.lexists(sym_link): os.remove(sym_link)
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os.symlink(src,sym_link)
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print sym_link,'-->',src
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@ -1,220 +0,0 @@
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#!/usr/bin/env python
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# Makes postprocessing routines acessible from everywhere.
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import os,sys,glob,string,subprocess
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from damask import Environment
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from optparse import OptionParser, Option
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# -----------------------------
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class extendableOption(Option):
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# -----------------------------
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# used for definition of new option parser action 'extend', which enables to take multiple option arguments
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# taken from online tutorial http://docs.python.org/library/optparse.html
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ACTIONS = Option.ACTIONS + ("extend",)
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STORE_ACTIONS = Option.STORE_ACTIONS + ("extend",)
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TYPED_ACTIONS = Option.TYPED_ACTIONS + ("extend",)
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ALWAYS_TYPED_ACTIONS = Option.ALWAYS_TYPED_ACTIONS + ("extend",)
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def take_action(self, action, dest, opt, value, values, parser):
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if action == "extend":
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lvalue = value.split(",")
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values.ensure_value(dest, []).extend(lvalue)
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else:
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Option.take_action(self, action, dest, opt, value, values, parser)
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########################################################
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# MAIN
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########################################################
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parser = OptionParser(option_class=extendableOption, usage='%prog options', description = """
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Sets up the pre and post processing tools of DAMASK
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""" + string.replace('$Id$','\n','\\n')
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)
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compilers = ['intel','ifort','intel32','gfortran','gnu95']
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parser.add_option('--F90', '--f90', dest='compiler', type='string', \
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help='name of F90 compiler')
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parser.set_defaults(compiler = {True:'ifort',False:'gfortran'}[\
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subprocess.call(['which', 'ifort'],\
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stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0])
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(options,filenames) = parser.parse_args()
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if options.compiler not in compilers:
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parser.error('compiler switch "--F90" has to be one out of: %s'%(', '.join(compilers)))
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f2py_compiler = {
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'gfortran': 'gnu95 --f90flags="-fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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'gnu95': 'gnu95 --f90flags="-fno-range-check -xf95-cpp-input -std=f2008 -fall-intrinsics -DSpectral -fdefault-real-8 -fdefault-double-8 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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'intel32': 'intel --f90flags="-fpp -stand f03 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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'intel': 'intelem --f90flags="-fpp -stand f03 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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'ifort': 'intelem --f90flags="-fpp -stand f03 -diag-disable 5268 -assume byterecl -DSpectral -real-size 64 -integer-size 32 -DFLOAT=8 -DINT=4 -I${DAMASK_ROOT}/lib"',
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}[options.compiler]
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compiler = {
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'gfortran': 'gfortran',
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'gnu95': 'gfortran',
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'intel32': 'ifort',
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'intel': 'ifort',
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'ifort': 'ifort',
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}[options.compiler]
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damaskEnv = Environment()
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baseDir = damaskEnv.relPath('processing/')
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codeDir = damaskEnv.relPath('code/')
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if 'ikml' in damaskEnv.pathInfo and damaskEnv.pathInfo['ikml'] != '':
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lib_lapack = '' # TODO!!
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elif 'acml' in damaskEnv.pathInfo and damaskEnv.pathInfo['acml'] != '':
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lib_lapack = '-L%s/%s64/lib -lacml'%(os.path.join(damaskEnv.pathInfo['acml']),compiler) # can we use linker flag?
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elif 'lapack' in damaskEnv.pathInfo and damaskEnv.pathInfo['lapack'] != '':
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lib_lapack = '-L%s -llapack'%(damaskEnv.pathInfo['lapack']) # see http://cens.ioc.ee/pipermail/f2py-users/2003-December/000621.html
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#define ToDo list
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bin_link = { \
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'pre' : [
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'marc_addUserOutput.py',
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'mentat_pbcOnBoxMesh.py',
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'mentat_spectralBox.py',
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'OIMang_hex2cub.py',
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'patchFromReconstructedBoundaries.py',
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'randomSeeding.py',
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'geom_fromAng.py',
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'geom_fromMinimalSurface.py',
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'geom_fromVoronoiTessellation.py',
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'geom_canvas.py',
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'geom_check.py',
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'geom_rescale.py',
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'geom_pack.py',
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'geom_unpack.py',
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'geom_translate.py',
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'geom_vicinityOffset.py',
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'geom_euclideanDistance.py'
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],
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'post' : [
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'3Dvisualize.py',
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'addCalculation.py',
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'addCauchy.py',
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'addCompatibilityMismatch.py',
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'addCurl.py',
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'addDeformedConfiguration.py',
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'addDeterminant.py',
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'addDeviator.py',
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'addDivergence.py',
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'addEhkl.py',
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'addEuclideanDistance.py',
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'addMises.py',
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'addNorm.py',
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'addPK2.py',
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'addSpectralDecomposition.py',
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'addStrainTensors.py',
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'averageDown.py',
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'binXY.py',
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'blowUp.py',
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'stddevDown.py',
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'deleteColumn.py',
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'deleteInfo.py',
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'filterTable.py',
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'mentat_colorMap.py',
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'nodesFromCentroids.py',
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'perceptualUniformColorMap.py',
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'postResults.py',
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'showTable.py',
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'spectral_parseLog.py',
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'table2ang',
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'tagLabel.py',
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],
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}
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compile = { \
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'pre' : [
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],
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'post' : [
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],
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}
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execute = { \
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'coreModule' : [
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'make tidy',
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# The following command is used to compile the fortran files and make the functions defined
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# in damask.core.pyf available for python in the module core.so
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# It uses the fortran wrapper f2py that is included in the numpy package to construct the
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# module core.so out of the fortran code in the f90 files
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# For the generation of the pyf file use the following lines:
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###########################################################################
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#'f2py -h damask.core.pyf' +\
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#' --overwrite-signature --no-lower prec.f90 DAMASK_spectral_interface.f90 math.f90 mesh.f90',
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###########################################################################
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'rm `readlink -f %s`' %(os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
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'f2py damask.core.pyf' +\
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' --build-dir ./' +\
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' -c --no-lower --fcompiler=%s'%(f2py_compiler) +\
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' %s'%'prec.f90'+\
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' %s'%'DAMASK_spectral_interface.f90'+\
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' %s'%'IO.f90'+\
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' %s'%'numerics.f90'+\
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' %s'%'debug.f90'+\
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' %s'%'math.f90'+\
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' %s'%'FEsolving.f90'+\
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' %s'%'mesh.f90'+\
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' %s'%'spectral_quit.f90'+\
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' -L%s/lib -lfftw3'%(damaskEnv.pathInfo['fftw'])+\
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' %s'%lib_lapack,
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'mv %s `readlink -f %s`' %(os.path.join(codeDir,'core.so'),os.path.join(damaskEnv.relPath('lib/damask'),'core.so')),
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]
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}
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for dir in compile: #there is nothing to compile at the moment
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for file in compile[dir]:
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src = os.path.abspath(os.path.join(baseDir,dir,file))
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if os.path.isfile(src):
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try:
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os.system('rm %s.exe'%(os.path.splitext(src)[0]))
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print 'removing %s.exe '%(os.path.splitext(src)[0])
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except:
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pass
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print 'compiling ',src,'using',compiler
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os.system('%s -O2 -o %s.exe %s'%(compiler,os.path.splitext(src)[0],src))
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os.chdir(codeDir) # needed for compilation with gfortran and f2py
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for tasks in execute:
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for cmd in execute[tasks]:
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try:
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print 'executing...:',cmd
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os.system(cmd)
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except:
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print 'failed..!'
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pass
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os.chdir(damaskEnv.relPath('processing/setup/'))
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modules = glob.glob('*.mod')
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for module in modules:
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print 'removing', module
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os.remove(module)
|
||||
|
||||
for dir in bin_link:
|
||||
for file in bin_link[dir]:
|
||||
src = os.path.abspath(os.path.join(baseDir,dir,file))
|
||||
if (file == ''):
|
||||
sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),dir))
|
||||
else:
|
||||
sym_link = os.path.abspath(os.path.join(damaskEnv.binDir(),os.path.splitext(file)[0]))
|
||||
print sym_link,'-->',src
|
||||
if os.path.lexists(sym_link):
|
||||
os.remove(sym_link)
|
||||
os.symlink(src,sym_link)
|
||||
|
||||
#check if compilation of core module was successful
|
||||
try:
|
||||
with open(damaskEnv.relPath('lib/damask/core.so')) as f: pass
|
||||
except IOError as e:
|
||||
print '*********\n* core.so not found, compilation of core modules was not successful\n*********'
|
||||
sys.exit()
|
||||
f.close
|
||||
Loading…
Reference in New Issue