added minRes to regridding function and writing out of new geometry file
updated f2py wrapper to enable the use of init functions. added 2 new error messages to io
This commit is contained in:
Krishna Komerla
parent
15c8a6b0ac
commit
06be437bc9
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@ -0,0 +1,64 @@
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#!/usr/bin/env python
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import numpy,os,damask,string,sys,subprocess,re
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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 [file[s]]', description = """
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Add column(s) with derived values according to user defined arithmetic operation between column(s).
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Columns can be specified either by label or index.
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Example: distance to IP coordinates -- "math.sqrt( #ip.x#**2 + #ip.y#**2 + #ip.z#**2 )"
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""" + string.replace('$Id: addCalculation.py 1355 2012-02-23 13:53:12Z MPIE\p.eisenlohr $','\n','\\n')
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)
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parser.add_option('-l','--load', '--loadcase', dest='loadcase', type='string', \
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help='PathToLoadFile/NameOfLoadFile.load. "PathToLoadFile" will be the working directory.')
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parser.add_option('-g','--geom', '--geometry', dest='geometry', type='string', \
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help='PathToGeomFile/NameOfGeomFile.load.')
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parser.set_defaults(loadcase= '')
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parser.set_defaults(geometry= '')
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(options,filenames) = parser.parse_args()
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out=subprocess.Popen(['DAMASK_spectral.exe', '-l', '%s'%options.loadcase, '-g', '%s'%options.geometry],stderr=subprocess.PIPE)
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stderr = out.communicate()
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stderrLines = string.split(stderr[1],'\n')
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exitCode = int(stderrLines[-2])
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print 'exit code', exitCode
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if exitCode==2:
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start = int(re.search('\d',stderrLines[0]).group(0))
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print 'restart at ', start
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#------------regridding----------------------------------------------
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#--------------------------------------------------------------------
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damask.core.prec.prec_init()
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damask.core.damask_interface.damask_interface_init(options.loadcase,options.geometry)
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damask.core.io.io_init()
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damask.core.numerics.numerics_init()
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damask.core.debug.debug_init()
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damask.core.math.math_init()
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damask.core.fesolving.fe_init()
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damask.core.mesh.mesh_init(1,1)
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damask.core.mesh.mesh_regrid()
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@ -1339,6 +1339,10 @@ subroutine IO_error(error_ID,e,i,g,ext_msg)
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msg = 'updating of gamma operator not possible if it is pre calculated'
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case (880_pInt)
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msg = 'mismatch of microstructure count and a*b*c in geom file'
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case (890_pInt)
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msg = 'invalid input for regridding a 2D model'
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case (891_pInt)
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msg = 'invalid input for regridding a 3D model'
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!* Error messages related to parsing of Abaqus input file
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@ -14,18 +14,36 @@
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python module core ! in
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interface ! in :core
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module prec
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subroutine prec_init
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end subroutine prec_init
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end module prec
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module damask_interface ! in :damask_interface:DAMASK_spectral_interface.f90
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subroutine damask_interface_init(loadcaseParameterIn,geometryParameterIn) ! in :damask_interface:DAMASK_spectral_interface.f90
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character(len=1024), intent(in) :: loadcaseParameterIn
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character(len=1024), intent(in) :: geometryParameterIn
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end subroutine damask_interface_init
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end module damask_interface
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module io
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subroutine io_init
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end subroutine io_init
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end module io
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module numerics
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subroutine numerics_init
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end subroutine numerics_init
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end module numerics
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module debug
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subroutine debug_init
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end subroutine debug_init
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end module debug
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module math ! in :math:math.f90
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subroutine math_init
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end subroutine math_init
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subroutine volume_compare(res,geomdim,defgrad,nodes,volume_mismatch) ! in :math:math.f90
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! input variables
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@ -176,15 +194,23 @@ python module core ! in
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end subroutine math_nearestNeighborSearch
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end module math
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module mesh ! in :mesh:mesh.f90
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module fesolving
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subroutine fe_init
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end subroutine fe_init
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end module fesolving
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function mesh_regrid(resNewInput) ! in :mesh:mesh.f90
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module mesh ! in :mesh:mesh.f90
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subroutine mesh_init(ip,element)
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integer, parameter :: ip = 1
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integer, parameter :: element = 1
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end subroutine mesh_init
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function mesh_regrid(resNewInput,minRes) ! in :mesh:mesh.f90
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integer, dimension(3) :: mesh_regrid
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integer, dimension(3), intent(in), optional :: resNewInput
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integer, dimension(3), intent(in), optional :: minRes
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end function mesh_regrid
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end module mesh
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end interface
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end python module core
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111
code/mesh.f90
111
code/mesh.f90
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@ -777,7 +777,7 @@ function mesh_spectral_getHomogenization(fileUnit)
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integer(pInt) :: mesh_spectral_getHomogenization
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character(len=1024) :: line, &
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keyword
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integer(pInt) :: i, j
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integer(pInt) :: i
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logical :: gotHomogenization = .false.
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integer(pInt) :: myUnit
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@ -822,7 +822,7 @@ end function mesh_spectral_getHomogenization
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!--------------------------------------------------------------------------------------------------
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!> @brief Performes a regridding from saved restart information
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!--------------------------------------------------------------------------------------------------
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function mesh_regrid(resNewInput)
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function mesh_regrid(resNewInput,minRes)
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use prec, only: &
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pInt, &
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pReal
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@ -830,18 +830,22 @@ function mesh_regrid(resNewInput)
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getSolverJobName
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use IO, only: &
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IO_read_jobBinaryFile ,&
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IO_write_jobBinaryFile
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IO_write_jobBinaryFile, &
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IO_write_jobFile, &
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IO_error
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use math, only: &
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math_nearestNeighborSearch, &
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deformed_FFT, &
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math_mul33x3
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integer(pInt), dimension(3) :: mesh_regrid
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character(len=1024):: formatString, N_Digits
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integer(pInt), dimension(3), optional, intent(in) :: resNewInput
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integer(pInt), dimension(3), optional, intent(in) :: minRes
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integer(pInt), dimension(3) :: mesh_regrid, ratio
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integer(pInt), dimension(3,2) :: possibleResNew
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integer(pInt):: maxsize, i, j, k, ielem, Npoints, NpointsNew, spatialDim
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integer(pInt), dimension(3) :: res, resNew
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integer(pInt), dimension(:), allocatable :: indices
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real(pReal), dimension(3) :: geomdim
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real(pReal), dimension(3) :: geomdim,geomdimNew
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real(pReal), dimension(3,3) :: Favg
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real(pReal), dimension(:,:), allocatable :: &
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coordinatesNew, &
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@ -869,9 +873,7 @@ function mesh_regrid(resNewInput)
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res = mesh_spectral_getResolution()
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geomdim = mesh_spectral_getDimension()
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Npoints = res(1)*res(2)*res(3)
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!---------------------------------------------------------
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allocate(F(res(1),res(2),res(3),3,3))
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call IO_read_jobBinaryFile(777,'convergedSpectralDefgrad',trim(getSolverJobName()),size(F))
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read (777,rec=1) F
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@ -897,24 +899,59 @@ function mesh_regrid(resNewInput)
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! ----For 2D /3D case----------------------------------
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if (res(3)== 1_pInt) then
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spatialDim = 2_pInt
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if (minRes(3) > 1_pInt) call IO_error(890_pInt)
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else
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spatialDim = 3_pInt
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if (minRes(3) <= 1_pInt) call IO_error(891_pInt)
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endif
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! ----determine/calculate new resolution--------------
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geomdimNew = math_mul33x3(Favg,geomdim)
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!---- Automatic detection based on current geom -----------------
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if (.not. present(resNewInput)) then
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resNew = res
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ratio = floor(real(res,pReal) * (geomdimNew/geomdim), pInt)
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possibleResNew = 1_pInt
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do i = 1_pInt, spatialDim
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if (mod(ratio(i),2) == 0_pInt) then
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possibleResNew(i,1:2) = [ratio(i),ratio(i) + 2_pInt]
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else
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if(all(resNewInput==0.0_pReal)) then
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mesh_regrid =[ 0,0,0]
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return !no automatic determination right now
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possibleResNew(i,1:2) = [ratio(i)-1_pInt, ratio(i) + 1_pInt]
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endif
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if (.not.present(minRes)) then
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possibleResNew = possibleResNew
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else
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do k = 1_pInt,3_pInt; do j = 1_pInt,3_pInt
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possibleResNew(j,k) = max(possibleResNew(j,k), minRes(j))
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enddo; enddo
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endif
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enddo
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k = huge(1_pInt)
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do i = 0_pInt, 2_pInt**spatialDim - 1
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j = possibleResNew(1,iand(i,1_pInt)/1_pInt + 1_pInt) &
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* possibleResNew(2,iand(i,2_pInt)/2_pInt + 1_pInt) &
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* possibleResNew(3,iand(i,4_pInt)/4_pInt + 1_pInt) &
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- Npoints
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if (j < k) then
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k = j
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resNew =[ possibleResNew(1,iand(i,1_pInt)/1_pInt + 1_pInt), &
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possibleResNew(2,iand(i,2_pInt)/2_pInt + 1_pInt), &
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possibleResNew(3,iand(i,4_pInt)/4_pInt + 1_pInt) ]
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endif
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enddo
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else
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if(all(resNewInput==0_pInt)) then
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resNew = res
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else
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resNew = resNewInput
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endif
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endif
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mesh_regrid = resNew
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NpointsNew = resNew(1)*resNew(2)*resNew(3)
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! ----Calculate regular new coordinates------------
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! ----Calculate regular new coordinates-----------------------------
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allocate(coordinatesNew(3,NpointsNew))
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ielem = 0_pInt
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do k=1_pInt,resNew(3); do j=1_pInt, resNew(2); do i=1_pInt, resNew(1)
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@ -923,14 +960,47 @@ function mesh_regrid(resNewInput)
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- geomdim/real(2_pInt*resNew,pReal))
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enddo; enddo; enddo
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!----- Nearest neighbour search -----------------------
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!----- Nearest neighbour search ------------------------------------
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allocate(indices(Npoints))
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call math_nearestNeighborSearch(spatialDim, Favg, geomdim, NpointsNew, Npoints, &
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coordinatesNew, coordinatesLinear, indices)
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deallocate(coordinatesNew)
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indices = indices / 3_pInt**spatialDim +1_pInt
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!---------------------------------------------------------------------------
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!----- write out indices--------------------------------------------
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write(N_Digits, '(a)') 1_pInt + int(log10(real(maxval(indices),pReal)),pInt)
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N_Digits = adjustl(N_Digits)
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formatString = '(I'//trim(N_Digits)//'.'//trim(N_Digits)//')'
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call IO_write_jobFile(777,'idx') ! make it a general open-write file
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write(777, '(A)') '1 header'
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write(777, '(A)') 'Numbered indices as per the large set'
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do i = 1_pInt, Npoints
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write(777,trim(formatString),advance='no') indices(i)
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if(mod(i,res(1)) == 0_pInt) write(777,'(A)') ''
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enddo
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close(777)
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do i = 1_pInt, Npoints
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indices(i) = indices(i) / 3_pInt**spatialDim +1_pInt ! +1 b'coz index count starts from '0'
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enddo
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!------Adjusting the point-to-grain association---------------------
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write(N_Digits, '(a)') 1_pInt + int(log10(real(NpointsNew,pReal)),pInt)
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N_Digits = adjustl(N_Digits)
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formatString = '(I'//trim(N_Digits)//'.'//trim(N_Digits)//')'
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call IO_write_jobFile(777,'geom')
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write(777, '(A)') '3 header'
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write(777, '(A, I8, A, I8, A, I8)') 'resolution a ', resNew(1), ' b ', resNew(2), ' c ', resNew(3)
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write(777, '(A, g17.10, A, g17.10, A, g17.10)') 'dimension x ', geomdim(1), ' y ', geomdim(2), ' z ', geomdim(3)
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write(777, '(A)') 'homogenization 1'
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do i = 1_pInt, NpointsNew
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write(777,trim(formatString),advance='no') mesh_element(4,indices(i))
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if(mod(i,resNew(1)) == 0_pInt) write(777,'(A)') ''
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enddo
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close(777)
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!-------------------------------------------------------------------
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allocate(material_phase (1,1, Npoints))
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allocate(material_phaseNew (1,1, NpointsNew))
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call IO_read_jobBinaryFile(777,'recordedPhase',trim(getSolverJobName()),size(material_phase))
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@ -1100,7 +1170,6 @@ function mesh_regrid(resNewInput)
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deallocate(indices)
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mesh_regrid = resNew
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end function mesh_regrid
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@ -1247,7 +1316,7 @@ subroutine mesh_spectral_build_elements(myUnit)
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integer(pInt), parameter :: maxNchunks = 7_pInt
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integer(pInt), dimension (1_pInt+2_pInt*maxNchunks) :: myPos
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integer(pInt), dimension(3) :: res
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integer(pInt) :: e, i, j, homog = 0_pInt, headerLength = 0_pInt, maxIntCount
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integer(pInt) :: e, i, homog = 0_pInt, headerLength = 0_pInt, maxIntCount
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integer(pInt), dimension(:), allocatable :: microstructures
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integer(pInt), dimension(1,1) :: dummySet = 0_pInt
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character(len=65536) :: line,keyword
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@ -2509,7 +2578,7 @@ integer(pInt), intent(in) :: myUnit
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integer(pInt), parameter :: maxNchunks = 5_pInt
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integer(pInt), dimension (1+2*maxNchunks) :: myPos
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integer(pInt) chunk, Nchunks
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character(len=300) line, keyword, damaskOption, v
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character(len=300) line, damaskOption, v
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mesh_periodicSurface = .false.
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