Merge branch 'MiscImprovements' into 'development'
Misc improvements See merge request damask/DAMASK!76
This commit is contained in:
Vitesh
commit
0e77be2590
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@ -0,0 +1,83 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os
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import numpy as np
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import argparse
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# --------------------------------------------------------------------
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# MAIN
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# --------------------------------------------------------------------
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parser = argparse.ArgumentParser()
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#ToDo: We need to decide on a way of handling arguments of variable lentght
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#https://stackoverflow.com/questions/15459997/passing-integer-lists-to-python
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#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
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parser.add_argument('filenames', nargs='+',
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help='DADF5 files')
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parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
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help='name of subdirectory to hold output')
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options = parser.parse_args()
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options.labels = ['Fe','Fp','xi_sl']
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# --- loop over input files ------------------------------------------------------------------------
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for filename in options.filenames:
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results = damask.DADF5(filename)
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if not results.structured: continue
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delta = results.size/results.grid*0.5
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x, y, z = np.meshgrid(np.linspace(delta[2],results.size[2]-delta[2],results.grid[2]),
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np.linspace(delta[1],results.size[1]-delta[1],results.grid[1]),
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np.linspace(delta[0],results.size[0]-delta[0],results.grid[0]),
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indexing = 'ij')
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coords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
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for i,inc in enumerate(results.increments):
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print('Output step {}/{}'.format(i+1,len(results.increments)))
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header = '1 header\n'
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data = np.array([inc['inc'] for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])
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header+= 'inc'
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data = np.concatenate((data,np.array([j+1 for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])),1)
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header+=' node'
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coords = coords.reshape([np.product(results.grid),3])
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data = np.concatenate((data,coords),1)
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header+=' 1_pos 2_pos 3_pos'
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results.active['increments'] = [inc]
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for label in options.labels:
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for o in results.c_output_types:
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results.active['c_output_types'] = [o]
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for c in results.constituents:
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results.active['constituents'] = [c]
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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label = x[0].split('/')[-1]
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array = results.read_dataset(x,0)
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d = np.product(np.shape(array)[1:])
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array = np.reshape(array,[np.product(results.grid),d])
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data = np.concatenate((data,array),1)
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header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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try:
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os.mkdir(dirname)
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except FileExistsError:
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pass
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file_out = '{}_inc{:04d}.txt'.format(filename.split('.')[0],inc['inc'])
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np.savetxt(os.path.join(dirname,file_out),data,header=header,comments='')
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@ -21,6 +21,8 @@ parser = argparse.ArgumentParser()
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#parser.add_argument('--version', action='version', version='%(prog)s {}'.format(scriptID))
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parser.add_argument('filenames', nargs='+',
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help='DADF5 files')
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parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
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help='name of subdirectory to hold output')
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options = parser.parse_args()
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@ -80,12 +82,17 @@ for filename in options.filenames:
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if results.structured:
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writer = vtk.vtkXMLRectilinearGridWriter()
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dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
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try:
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os.mkdir(dirname)
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except FileExistsError:
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pass
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file_out = '{}_inc{:04d}.{}'.format(filename.split('.')[0],inc['inc'],writer.GetDefaultFileExtension())
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writer.SetCompressorTypeToZLib()
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writer.SetDataModeToBinary()
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writer.SetFileName(os.path.join(os.path.split(filename)[0],
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os.path.splitext(os.path.split(filename)[1])[0] +
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'_inc{:04d}'.format(i) + # ToDo: adjust to length of increments
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'.' + writer.GetDefaultFileExtension()))
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writer.SetFileName(os.path.join(dirname,file_out))
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if results.structured:
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writer.SetInputData(rGrid)
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@ -20,14 +20,14 @@ class DADF5():
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with h5py.File(filename,'r') as f:
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if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 1:
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if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 2:
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raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
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self.structured = 'grid' in f['mapping'].attrs.keys()
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self.structured = 'grid' in f['geometry'].attrs.keys()
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if self.structured:
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self.grid = f['mapping'].attrs['grid']
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self.size = f['mapping'].attrs['size']
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self.grid = f['geometry'].attrs['grid']
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self.size = f['geometry'].attrs['size']
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r=re.compile('inc[0-9]+')
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self.increments = [{'inc': int(u[3:]),
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@ -47,7 +47,8 @@ module CPFEM
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public :: &
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CPFEM_general, &
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CPFEM_initAll
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CPFEM_initAll, &
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CPFEM_results
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contains
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@ -633,4 +634,35 @@ subroutine CPFEM_general(mode, parallelExecution, ffn, ffn1, temperature_inp, dt
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end subroutine CPFEM_general
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!--------------------------------------------------------------------------------------------------
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!> @brief triggers writing of the results
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!--------------------------------------------------------------------------------------------------
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subroutine CPFEM_results(inc,time)
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use prec, only: &
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pInt
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#ifdef DAMASK_HDF5
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use results
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use HDF5_utilities
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#endif
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use constitutive, only: &
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constitutive_results
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use crystallite, only: &
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crystallite_results
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implicit none
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integer(pInt), intent(in) :: inc
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real(pReal), intent(in) :: time
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#ifdef DAMASK_HDF5
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call results_openJobFile
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call results_addIncrement(inc,time)
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call constitutive_results
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call crystallite_results
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call results_removeLink('current') ! ToDo: put this into closeJobFile
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call results_closeJobFile
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#endif
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end subroutine CPFEM_results
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end module CPFEM
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@ -290,6 +290,7 @@ subroutine CPFEM_age()
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end subroutine CPFEM_age
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!--------------------------------------------------------------------------------------------------
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!> @brief triggers writing of the results
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!--------------------------------------------------------------------------------------------------
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@ -45,7 +45,7 @@ contains
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!> @brief initializes the solver by interpreting the command line arguments. Also writes
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!! information on computation to screen
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!--------------------------------------------------------------------------------------------------
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subroutine DAMASK_interface_init()
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subroutine DAMASK_interface_init
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use, intrinsic :: &
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iso_fortran_env
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use, intrinsic :: &
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@ -130,11 +130,11 @@ subroutine DAMASK_interface_init()
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call MPI_Init_Thread(MPI_THREAD_FUNNELED,threadLevel,mpi_err)
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if (mpi_err /= 0) call quit(1)
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if (threadLevel<MPI_THREAD_FUNNELED) then
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write(6,'(a)') ' MPI library does not support OpenMP'
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write(6,'(/,a)') ' ERROR: MPI library does not support OpenMP'
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call quit(1)
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endif
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#endif
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call PETScInitialize(PETSC_NULL_CHARACTER,petsc_err) ! according to PETSc manual, that should be the first line in the code
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call PETScInitializeNoArguments(petsc_err) ! according to PETSc manual, that should be the first line in the code
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CHKERRQ(petsc_err) ! this is a macro definition, it is case sensitive
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call MPI_Comm_rank(PETSC_COMM_WORLD,worldrank,mpi_err)
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@ -144,11 +144,11 @@ subroutine DAMASK_interface_init()
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mainProcess: if (worldrank == 0) then
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if (output_unit /= 6) then
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write(output_unit,'(a)') ' STDOUT != 6'
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write(output_unit,'(/,a)') ' ERROR: STDOUT != 6'
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call quit(1)
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endif
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if (error_unit /= 0) then
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write(output_unit,'(a)') ' STDERR != 0'
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write(output_unit,'(/,a)') ' ERROR: STDERR != 0'
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call quit(1)
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endif
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else mainProcess
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@ -254,14 +254,14 @@ subroutine DAMASK_interface_init()
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call get_command_argument(i+1,arg)
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read(arg,*,iostat=stat) interface_restartInc
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if (interface_restartInc < 0 .or. stat /=0) then
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write(6,'(a)') ' Could not parse restart increment: '//trim(arg)
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write(6,'(/,a)') ' ERROR: Could not parse restart increment: '//trim(arg)
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call quit(1)
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endif
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end select
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enddo
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if (len_trim(loadcaseArg) == 0 .or. len_trim(geometryArg) == 0) then
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write(6,'(a)') ' Please specify geometry AND load case (-h for help)'
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write(6,'(/,a)') ' ERROR: Please specify geometry AND load case (-h for help)'
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call quit(1)
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endif
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@ -324,7 +324,7 @@ subroutine setWorkingDirectory(workingDirectoryArg)
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workingDirectory = trim(rectifyPath(workingDirectory))
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error = setCWD(trim(workingDirectory))
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if(error) then
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write(6,'(a20,a,a16)') ' Working directory "',trim(workingDirectory),'" does not exist'
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write(6,'(/,a)') ' ERROR: Working directory "'//trim(workingDirectory)//'" does not exist'
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call quit(1)
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endif
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@ -374,7 +374,7 @@ character(len=1024) function getGeometryFile(geometryParameter)
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inquire(file=trim(getGeometryFile), exist=file_exists)
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if (.not. file_exists) then
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write(6,'(a)') ' Geometry file does not exists ('//trim(getGeometryFile)//')'
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write(6,'(/,a)') ' ERROR: Geometry file does not exists ('//trim(getGeometryFile)//')'
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call quit(1)
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endif
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@ -399,7 +399,7 @@ character(len=1024) function getLoadCaseFile(loadCaseParameter)
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inquire(file=trim(getLoadCaseFile), exist=file_exists)
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if (.not. file_exists) then
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write(6,'(a)') ' Load case file does not exists ('//trim(getLoadCaseFile)//')'
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write(6,'(/,a)') ' ERROR: Load case file does not exists ('//trim(getLoadCaseFile)//')'
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call quit(1)
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endif
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@ -16,6 +16,7 @@
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!> @details Marc subroutines used:
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!> @details - hypela2
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!> @details - plotv
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!> @details - uedinc
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!> @details - flux
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!> @details - quit
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!> @details Marc common blocks included:
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@ -273,26 +274,20 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
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outdatedByNewInc = .false. ! no aging of state
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calcMode = .false. ! pretend last step was collection
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lastLovl = lovl ! pretend that this is NOT the first after a lovl change
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!$OMP CRITICAL (write2out)
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write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> start of analysis..! ',m(1),nn
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flush(6)
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!$OMP END CRITICAL (write2out)
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else if (inc - theInc > 1) then ! >> restart of broken analysis <<
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lastIncConverged = .false. ! no Jacobian backup
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outdatedByNewInc = .false. ! no aging of state
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calcMode = .true. ! pretend last step was calculation
|
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!$OMP CRITICAL (write2out)
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write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> restart of analysis..! ',m(1),nn
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flush(6)
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!$OMP END CRITICAL (write2out)
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else ! >> just the next inc <<
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lastIncConverged = .true. ! request Jacobian backup
|
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outdatedByNewInc = .true. ! request aging of state
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calcMode = .true. ! assure last step was calculation
|
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!$OMP CRITICAL (write2out)
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write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> new increment..! ',m(1),nn
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flush(6)
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!$OMP END CRITICAL (write2out)
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endif
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else if ( timinc < theDelta ) then ! >> cutBack <<
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lastIncConverged = .false. ! no Jacobian backup
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@ -300,10 +295,8 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
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terminallyIll = .false.
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cycleCounter = -1 ! first calc step increments this to cycle = 0
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calcMode = .true. ! pretend last step was calculation
|
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!$OMP CRITICAL (write2out)
|
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write(6,'(a,i6,1x,i2)') '<< HYPELA2 >> cutback detected..! ',m(1),nn
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flush(6)
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!$OMP END CRITICAL (write2out)
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endif ! convergence treatment end
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@ -365,7 +358,6 @@ subroutine hypela2(d,g,e,de,s,t,dt,ngens,m,nn,kcus,matus,ndi,nshear,disp, &
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lastLovl = lovl ! record lovl
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|
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call CPFEM_general(computationMode,usePingPong,ffn,ffn1,t(1),timinc,m(1),nn,stress,ddsdde)
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! Mandel: 11, 22, 33, SQRT(2)*12, SQRT(2)*23, SQRT(2)*13
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! Marc: 11, 22, 33, 12, 23, 13
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! Marc: 11, 22, 33, 12
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|
@ -407,6 +399,26 @@ subroutine flux(f,ts,n,time)
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end subroutine flux
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|
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|
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!--------------------------------------------------------------------------------------------------
|
||||
!> @brief sets user defined output variables for Marc
|
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!> @details select a variable contour plotting (user subroutine).
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine uedinc(inc,incsub)
|
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use prec, only: &
|
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pReal, &
|
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pInt
|
||||
use CPFEM, only: &
|
||||
CPFEM_results
|
||||
|
||||
implicit none
|
||||
integer, intent(in) :: inc, incsub
|
||||
#include QUOTE(PASTE(./MarcInclude/creeps,Marc4DAMASK)) ! creeps is needed for timinc (time increment)
|
||||
|
||||
call CPFEM_results(inc,cptim)
|
||||
|
||||
end subroutine uedinc
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief sets user defined output variables for Marc
|
||||
!> @details select a variable contour plotting (user subroutine).
|
||||
|
|
|
|||
|
|
@ -77,6 +77,7 @@ program DAMASK_spectral
|
|||
use grid_mech_FEM
|
||||
use grid_damage_spectral
|
||||
use grid_thermal_spectral
|
||||
use HDF5_utilities
|
||||
use results
|
||||
|
||||
implicit none
|
||||
|
|
@ -155,8 +156,6 @@ program DAMASK_spectral
|
|||
write(6,'(/,a)') ' Shanthraj et al., Handbook of Mechanics of Materials, 2019'
|
||||
write(6,'(a)') ' https://doi.org/10.1007/978-981-10-6855-3_80'
|
||||
|
||||
call results_openJobFile()
|
||||
call results_closeJobFile()
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! initialize field solver information
|
||||
nActiveFields = 1
|
||||
|
|
@ -301,7 +300,7 @@ program DAMASK_spectral
|
|||
|
||||
reportAndCheck: if (worldrank == 0) then
|
||||
write (loadcase_string, '(i6)' ) currentLoadCase
|
||||
write(6,'(1x,a,i6)') 'load case: ', currentLoadCase
|
||||
write(6,'(/,1x,a,i6)') 'load case: ', currentLoadCase
|
||||
if (.not. newLoadCase%followFormerTrajectory) write(6,'(2x,a)') 'drop guessing along trajectory'
|
||||
if (newLoadCase%deformation%myType == 'l') then
|
||||
do j = 1_pInt, 3_pInt
|
||||
|
|
@ -351,7 +350,7 @@ program DAMASK_spectral
|
|||
write(6,'(2x,a,i5)') 'increments: ', newLoadCase%incs
|
||||
if (newLoadCase%outputfrequency < 1_pInt) errorID = 836_pInt ! non-positive result frequency
|
||||
write(6,'(2x,a,i5)') 'output frequency: ', newLoadCase%outputfrequency
|
||||
write(6,'(2x,a,i5,/)') 'restart frequency: ', newLoadCase%restartfrequency
|
||||
write(6,'(2x,a,i5)') 'restart frequency: ', newLoadCase%restartfrequency
|
||||
if (errorID > 0_pInt) call IO_error(error_ID = errorID, ext_msg = loadcase_string) ! exit with error message
|
||||
endif reportAndCheck
|
||||
loadCases = [loadCases,newLoadCase] ! load case is ok, append it
|
||||
|
|
@ -359,8 +358,9 @@ program DAMASK_spectral
|
|||
close(fileUnit)
|
||||
|
||||
call results_openJobFile
|
||||
call results_addAttribute('grid',grid,'mapping')
|
||||
call results_addAttribute('size',geomSize,'mapping')
|
||||
call HDF5_closeGroup(results_addGroup('geometry'))
|
||||
call results_addAttribute('grid',grid,'geometry')
|
||||
call results_addAttribute('size',geomSize,'geometry')
|
||||
call results_closeJobFile
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -66,9 +66,9 @@ subroutine results_init
|
|||
write(6,'(a)') ' https://doi.org/10.1007/s40192-018-0118-7'
|
||||
|
||||
resultsFile = HDF5_openFile(trim(getSolverJobName())//'.hdf5','w',.true.)
|
||||
call HDF5_addAttribute(resultsFile,'DADF5-version',0.1)
|
||||
call HDF5_addAttribute(resultsFile,'DADF5-version',0.2)
|
||||
call HDF5_addAttribute(resultsFile,'DADF5-major',0)
|
||||
call HDF5_addAttribute(resultsFile,'DADF5-minor',1)
|
||||
call HDF5_addAttribute(resultsFile,'DADF5-minor',2)
|
||||
call HDF5_addAttribute(resultsFile,'DAMASK',DAMASKVERSION)
|
||||
call get_command(commandLine)
|
||||
call HDF5_addAttribute(resultsFile,'call',trim(commandLine))
|
||||
|
|
@ -103,7 +103,7 @@ end subroutine results_closeJobFile
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief closes the results file
|
||||
!> @brief creates the group of increment and adds time as attribute to the file
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine results_addIncrement(inc,time)
|
||||
|
||||
|
|
@ -250,6 +250,8 @@ subroutine results_writeScalarDataset_real(group,dataset,label,description,SIuni
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
@ -277,6 +279,8 @@ subroutine results_writeVectorDataset_real(group,dataset,label,description,SIuni
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
@ -305,6 +309,8 @@ subroutine results_writeTensorDataset_real(group,dataset,label,description,SIuni
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
@ -333,6 +339,8 @@ subroutine results_writeVectorDataset_int(group,dataset,label,description,SIunit
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
@ -347,7 +355,7 @@ end subroutine results_writeVectorDataset_int
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief stores a vector dataset in a group
|
||||
!> @brief stores a tensor dataset in a group
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit)
|
||||
|
||||
|
|
@ -361,6 +369,8 @@ subroutine results_writeTensorDataset_int(group,dataset,label,description,SIunit
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
@ -375,7 +385,7 @@ end subroutine results_writeTensorDataset_int
|
|||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief stores a vector dataset in a group
|
||||
!> @brief stores a scalar dataset in a group
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine results_writeScalarDataset_rotation(group,dataset,label,description,lattice_structure)
|
||||
use rotations, only: &
|
||||
|
|
@ -391,6 +401,8 @@ subroutine results_writeScalarDataset_rotation(group,dataset,label,description,l
|
|||
|
||||
#ifdef PETSc
|
||||
call HDF5_write(groupHandle,dataset,label,.true.)
|
||||
#else
|
||||
call HDF5_write(groupHandle,dataset,label,.false.)
|
||||
#endif
|
||||
|
||||
if (HDF5_objectExists(groupHandle,label)) &
|
||||
|
|
|
|||
Loading…
Reference in New Issue