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DAMASK_EICMD
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Merge branch 'development' into 53-separate-mesh-for-different-solvers-3

This commit is contained in:
Martin Diehl 2019-02-16 10:25:42 +01:00
parent 61032b5fd8 0fd5476883
commit af83427e8c
30 changed files with 1111 additions and 2277 deletions
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63
.gitlab-ci.yml
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@ -7,9 +7,9 @@ stages:
- compilePETScGNU
- prepareSpectral
- spectral
- compileMarc2018_1
- compileMarc
- marc
- compileAbaqus2017
- compileAbaqus
- example
- performance
- createPackage
@ -51,39 +51,37 @@ variables:
# Names of module files to load
# ===============================================================================================
# ++++++++++++ Compiler ++++++++++++++++++++++++++++++++++++++++++++++
IntelCompiler16_0: "Compiler/Intel/16.0 Libraries/IMKL/2016"
IntelCompiler16_4: "Compiler/Intel/16.4 Libraries/IMKL/2016-4"
IntelCompiler17_0: "Compiler/Intel/17.0 Libraries/IMKL/2017"
IntelCompiler18_1: "Compiler/Intel/18.1 Libraries/IMKL/2018"
GNUCompiler7_3: "Compiler/GNU/7.3"
IntelCompiler16_4: "Compiler/Intel/16.4 Libraries/IMKL/2016"
IntelCompiler17_8: "Compiler/Intel/17.8 Libraries/IMKL/2017"
IntelCompiler18_4: "Compiler/Intel/18.4 Libraries/IMKL/2018"
GNUCompiler8_2: "Compiler/GNU/8.2"
# ------------ Defaults ----------------------------------------------
IntelCompiler: "$IntelCompiler18_1"
GNUCompiler: "$GNUCompiler7_3"
IntelCompiler: "$IntelCompiler18_4"
GNUCompiler: "$GNUCompiler8_2"
# ++++++++++++ MPI +++++++++++++++++++++++++++++++++++++++++++++++++++
MPICH3_2Intel18_1: "MPI/Intel/18.1/MPICH/3.2.1"
MPICH3_2GNU7_3: "MPI/GNU/7.3/MPICH/3.2.1"
IMPI2018Intel18_4: "MPI/Intel/18.4/IntelMPI/2018"
MPICH3_3GNU8_2: "MPI/GNU/8.2/MPICH/3.3"
# ------------ Defaults ----------------------------------------------
MPICH_Intel: "$MPICH3_2Intel18_1"
MPICH_GNU: "$MPICH3_2GNU7_3"
MPICH_Intel: "$IMPI2018Intel18_4"
MPICH_GNU: "$MPICH3_3GNU8_2"
# ++++++++++++ PETSc +++++++++++++++++++++++++++++++++++++++++++++++++
PETSc3_10_0MPICH3_2Intel18_1: "Libraries/PETSc/3.10.0/Intel-18.1-MPICH-3.2.1"
PETSc3_10_0MPICH3_2GNU7_3: "Libraries/PETSc/3.10.0/GNU-7.3-MPICH-3.2.1"
PETSc3_10_3IMPI2018Intel18_4: "Libraries/PETSc/3.10.3/Intel-18.4-IntelMPI-2018"
PETSc3_10_3MPICH3_3GNU8_2: "Libraries/PETSc/3.10.3/GNU-8.2-MPICH-3.3"
# ------------ Defaults ----------------------------------------------
PETSc_MPICH_Intel: "$PETSc3_10_0MPICH3_2Intel18_1"
PETSc_MPICH_GNU: "$PETSc3_10_0MPICH3_2GNU7_3"
PETSc_MPICH_Intel: "$PETSc3_10_3IMPI2018Intel18_4"
PETSc_MPICH_GNU: "$PETSc3_10_3MPICH3_3GNU8_2"
# ++++++++++++ FEM +++++++++++++++++++++++++++++++++++++++++++++++++++
Abaqus2017: "FEM/Abaqus/2017"
Abaqus2019: "FEM/Abaqus/2019"
MSC2018_1: "FEM/MSC/2018.1"
MSC2017: "FEM/MSC/2017"
# ------------ Defaults ----------------------------------------------
Abaqus: "$Abaqus2017"
Abaqus: "$Abaqus2019"
MSC: "$MSC2018_1"
IntelMarc: "$IntelCompiler17_0"
IntelMarc: "$IntelCompiler17_8"
IntelAbaqus: "$IntelCompiler16_4"
# ++++++++++++ Documentation +++++++++++++++++++++++++++++++++++++++++
Doxygen1_8_13: "Documentation/Doxygen/1.8.13"
Doxygen1_8_15: "Documentation/Doxygen/1.8.15"
# ------------ Defaults ----------------------------------------------
Doxygen: "$Doxygen1_8_13"
Doxygen: "$Doxygen1_8_15"
###################################################################################################
@ -158,6 +156,13 @@ Post_AverageDown:
- master
- release
Post_ASCIItable:
stage: postprocessing
script: ASCIItable/test.py
except:
- master
- release
Post_General:
stage: postprocessing
script: PostProcessing/test.py
@ -383,9 +388,9 @@ TextureComponents:
###################################################################################################
Marc_compileIfort2018_1:
stage: compileMarc2018_1
stage: compileMarc
script:
- module load $IntelCompiler17_0 $MSC2018_1
- module load $IntelMarc $MSC
- Marc_compileIfort/test.py -m 2018.1
except:
- master
@ -430,11 +435,11 @@ J2_plasticBehavior:
- release
###################################################################################################
Abaqus_compile2017:
stage: compileAbaqus2017
Abaqus_compile:
stage: compileAbaqus
script:
- module load $IntelCompiler16_4 $Abaqus2017
- Abaqus_compileIfort/test.py -a 2017
- module load $IntelAbaqus $Abaqus
- Abaqus_compileIfort/test.py
except:
- master
- release

27
CMakeLists.txt
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@ -445,6 +445,33 @@ elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
# Additional options
# -fdefault-integer-8: Use it to set precision to 8 bytes for integer, don't use it for the standard case of pInt=4 (there is no -fdefault-integer-4)
###################################################################################################
# PGI Compiler
###################################################################################################
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "PGI")
if (OPTIMIZATION STREQUAL "OFF")
set (OPTIMIZATION_FLAGS "-O0" )
elseif (OPTIMIZATION STREQUAL "DEFENSIVE")
set (OPTIMIZATION_FLAGS "-O2")
elseif (OPTIMIZATION STREQUAL "AGGRESSIVE")
set (OPTIMIZATION_FLAGS "-O3")
endif ()
#------------------------------------------------------------------------------------------------
# Fine tuning compilation options
set (COMPILE_FLAGS "${COMPILE_FLAGS} -Mpreprocess")
# preprocessor
set (STANDARD_CHECK "-Mallocatable=03")
#------------------------------------------------------------------------------------------------
# Runtime debugging
set (DEBUG_FLAGS "${DEBUG_FLAGS} -g")
# Includes debugging information in the object module; sets the optimization level to zero unless a -⁠O option is present on the command line
else ()
message (FATAL_ERROR "Compiler type (CMAKE_Fortran_COMPILER_ID) not recognized")
endif ()

2
CONFIG
View File

@ -8,6 +8,6 @@ set DAMASK_NUM_THREADS = 4
set MSC_ROOT = /opt/msc
set MARC_VERSION = 2018.1
set ABAQUS_VERSION = 2017
set ABAQUS_VERSION = 2019
set DAMASK_HDF5 = OFF

2
PRIVATE

@ -1 +1 @@
Subproject commit beb9682fff7d4d6c65aba12ffd04c7441dc6ba6b
Subproject commit 18ba1ba6a5e9ba446dc9311acf2acf2781614db1

1
README
View File

@ -10,3 +10,4 @@ Germany
Email: DAMASK@mpie.de
https://damask.mpie.de
https://magit1.mpie.de

2
VERSION
View File

@ -1 +1 @@
v2.0.2-1674-g683dee82
v2.0.2-1689-g1a471bcd

2
processing/post/addCumulative.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/addDerivative.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

7
processing/post/addLinked.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys
@ -21,7 +21,7 @@ Add data of selected column(s) from (first) row of linked ASCIItable that shares
parser.add_option('--link',
dest = 'link', nargs = 2,
type = 'string', metavar = 'string string',
help = 'column labels containing linked values')
help = 'column labels of table and linked table containing linking values')
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar = '<string LIST>',
@ -105,7 +105,8 @@ for name in filenames:
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
try:
table.data_append(data[np.argwhere(np.all((map(float,table.data[myLink:myLink+myLinkDim]) - index)==0,axis=1))[0]]) # add data of first matching line
table.data_append(data[np.argwhere(np.all((list(map(float,table.data[myLink:myLink+myLinkDim])) - index)==0,
axis=1))[0]]) # add data of first matching line
except IndexError:
table.data_append(np.nan*np.ones_like(data[0])) # or add NaNs
outputAlive = table.data_write() # output processed line

2
processing/post/addTable.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/blowUp.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys

2
processing/post/vtk_addGridData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_addPointcloudData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_addRectilinearGridData.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,vtk

2
processing/post/vtk_pointcloud.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk

2
processing/post/vtk_rectilinearGrid.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,vtk

47
processing/pre/geom_grainGrowth.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys,math
@ -49,7 +49,7 @@ parser.set_defaults(d = 1,
(options, filenames) = parser.parse_args()
options.immutable = map(int,options.immutable)
options.immutable = list(map(int,options.immutable))
getInterfaceEnergy = lambda A,B: np.float32((A*B != 0)*(A != B)*1.0) # 1.0 if A & B are distinct & nonzero, 0.0 otherwise
struc = ndimage.generate_binary_structure(3,1) # 3D von Neumann neighborhood
@ -70,9 +70,9 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.croak(['grid a b c: {}'.format(' x '.join(map(str,info['grid']))),
'size x y z: {}'.format(' x '.join(map(str,info['size']))),
'origin x y z: {}'.format(' : '.join(map(str,info['origin']))),
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'origin x y z: {}'.format(' : '.join(list(map(str,info['origin'])))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
@ -102,9 +102,9 @@ for name in filenames:
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d),dtype=np.float32) \
/np.power(2.0*np.pi*options.d*options.d,(3.0 - np.count_nonzero(info['grid'] == 1))/2.,dtype=np.float32)
gauss[:,:,:grid[2]/2:-1] = gauss[:,:,1:(grid[2]+1)/2] # trying to cope with uneven (odd) grid size
gauss[:,:grid[1]/2:-1,:] = gauss[:,1:(grid[1]+1)/2,:]
gauss[:grid[0]/2:-1,:,:] = gauss[1:(grid[0]+1)/2,:,:]
gauss[:,:,:grid[2]//2:-1] = gauss[:,:,1:(grid[2]+1)//2] # trying to cope with uneven (odd) grid size
gauss[:,:grid[1]//2:-1,:] = gauss[:,1:(grid[1]+1)//2,:]
gauss[:grid[0]//2:-1,:,:] = gauss[1:(grid[0]+1)//2,:,:]
gauss = np.fft.rfftn(gauss).astype(np.complex64)
for smoothIter in range(options.N):
@ -119,9 +119,9 @@ for name in filenames:
microstructure,i,axis=0), j,axis=1), k,axis=2)))
# periodically extend interfacial energy array by half a grid size in positive and negative directions
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2]
periodic_interfaceEnergy = np.tile(interfaceEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2]
# transform bulk volume (i.e. where interfacial energy remained zero), store index of closest boundary voxel
index = ndimage.morphology.distance_transform_edt(periodic_interfaceEnergy == 0.,
@ -148,15 +148,15 @@ for name in filenames:
ndimage.morphology.binary_dilation(interfaceEnergy > 0.,
structure = struc,
iterations = int(round(options.d*2.))-1),# fat boundary
periodic_bulkEnergy[grid[0]/2:-grid[0]/2, # retain filled energy on fat boundary...
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2], # ...and zero everywhere else
periodic_bulkEnergy[grid[0]//2:-grid[0]//2, # retain filled energy on fat boundary...
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2], # ...and zero everywhere else
0.)).astype(np.complex64) *
gauss).astype(np.float32)
periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the smoothed bulk energy
periodic_diffusedEnergy = np.tile(diffusedEnergy,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # periodically extend the smoothed bulk energy
# transform voxels close to interface region
@ -164,15 +164,15 @@ for name in filenames:
return_distances = False,
return_indices = True) # want index of closest bulk grain
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # periodically extend the microstructure
periodic_microstructure = np.tile(microstructure,(3,3,3))[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # periodically extend the microstructure
microstructure = periodic_microstructure[index[0],
index[1],
index[2]].reshape(2*grid)[grid[0]/2:-grid[0]/2,
grid[1]/2:-grid[1]/2,
grid[2]/2:-grid[2]/2] # extent grains into interface region
index[2]].reshape(2*grid)[grid[0]//2:-grid[0]//2,
grid[1]//2:-grid[1]//2,
grid[2]//2:-grid[2]//2] # extent grains into interface region
# replace immutable microstructures with closest mutable ones
index = ndimage.morphology.distance_transform_edt(np.in1d(microstructure,options.immutable).reshape(grid),
@ -236,3 +236,4 @@ for name in filenames:
# --- output finalization --------------------------------------------------------------------------
table.close()

12
processing/pre/geom_toTable.py
View File

@ -1,4 +1,4 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import os,sys
@ -48,11 +48,11 @@ for name in filenames:
table.head_read()
info,extra_header = table.head_getGeom()
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
'size x y z: %s'%(' x '.join(map(str,info['size']))),
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
'homogenization: %i'%info['homogenization'],
'microstructures: %i'%info['microstructures'],
damask.util.croak(['grid a b c: {}'.format(' x '.join(list(map(str,info['grid'])))),
'size x y z: {}'.format(' x '.join(list(map(str,info['size'])))),
'origin x y z: {}'.format(' : '.join(list(map(str,info['origin'])))),
'homogenization: {}'.format(info['homogenization']),
'microstructures: {}'.format(info['microstructures']),
])
errors = []

17
processing/pre/seeds_fromDistribution.py
View File

@ -1,10 +1,11 @@
#!/usr/bin/env python2.7
#!/usr/bin/env python3
# -*- coding: UTF-8 no BOM -*-
import threading,time,os,sys,random
import numpy as np
from optparse import OptionParser
from cStringIO import StringIO
from io import StringIO
import binascii
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
@ -96,7 +97,7 @@ class myThread (threading.Thread):
perturbedGeomVFile = StringIO()
perturbedSeedsVFile.reset()
perturbedGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
' -g '+' '.join(map(str, options.grid)),streamIn=perturbedSeedsVFile)[0])
' -g '+' '.join(list(map(str, options.grid))),streamIn=perturbedSeedsVFile)[0])
perturbedGeomVFile.reset()
#--- evaluate current seeds file ----------------------------------------------------------------------
@ -214,7 +215,7 @@ options = parser.parse_args()[0]
damask.util.report(scriptName,options.seedFile)
if options.randomSeed is None:
options.randomSeed = int(os.urandom(4).encode('hex'), 16)
options.randomSeed = int(binascii.hexlify(os.urandom(4)),16)
damask.util.croak(options.randomSeed)
delta = (options.scale/options.grid[0],options.scale/options.grid[1],options.scale/options.grid[2])
baseFile=os.path.splitext(os.path.basename(options.seedFile))[0]
@ -240,17 +241,17 @@ if os.path.isfile(os.path.splitext(options.seedFile)[0]+'.seeds'):
for line in initialSeedFile: bestSeedsVFile.write(line)
else:
bestSeedsVFile.write(damask.util.execute('seeds_fromRandom'+\
' -g '+' '.join(map(str, options.grid))+\
' -g '+' '.join(list(map(str, options.grid)))+\
' -r {:d}'.format(options.randomSeed)+\
' -N '+str(nMicrostructures))[0])
bestSeedsUpdate = time.time()
# ----------- tessellate initial seed file to get and evaluate geom file
bestSeedsVFile.reset()
bestSeedsVFile.seek(0)
initialGeomVFile = StringIO()
initialGeomVFile.write(damask.util.execute('geom_fromVoronoiTessellation '+
' -g '+' '.join(map(str, options.grid)),bestSeedsVFile)[0])
initialGeomVFile.reset()
' -g '+' '.join(list(map(str, options.grid))),bestSeedsVFile)[0])
initialGeomVFile.seek(0)
initialGeomTable = damask.ASCIItable(initialGeomVFile,None,labeled=False,readonly=True)
initialGeomTable.head_read()
info,devNull = initialGeomTable.head_getGeom()

13
python/damask/solver/abaqus.py
View File

@ -2,7 +2,7 @@
from .solver import Solver
import damask
import subprocess,re
import subprocess
class Abaqus(Solver):
@ -15,14 +15,13 @@ class Abaqus(Solver):
def return_run_command(self,model):
env=damask.Environment()
shortVersion = re.sub('[\.,-]', '',self.version)
try:
cmd='abq'+shortVersion
subprocess.check_output(['abq'+shortVersion,'information=release'])
cmd='abq'+self.version
subprocess.check_output([cmd,'information=release'])
except OSError: # link to abqXXX not existing
cmd='abaqus'
process = subprocess.Popen(['abaqus','information=release'],stdout = subprocess.PIPE,stderr = subprocess.PIPE)
detectedVersion = process.stdout.readlines()[1].split()[1]
detectedVersion = process.stdout.readlines()[1].split()[1].decode('utf-8')
if self.version != detectedVersion:
raise Exception('found Abaqus version %s, but requested %s'%(detectedVersion,self.version))
return '%s -job %s -user %s/src/DAMASK_abaqus interactive'%(cmd,model,env.rootDir())
raise Exception('found Abaqus version {}, but requested {}'.format(detectedVersion,self.version))
return '{} -job {} -user {}/src/DAMASK_abaqus interactive'.format(cmd,model,env.rootDir())

10
src/C_routines.c
View File

@ -6,9 +6,11 @@
#include <sys/stat.h>
#include <stdio.h>
#include <string.h>
#include <signal.h>
/* http://stackoverflow.com/questions/30279228/is-there-an-alternative-to-getcwd-in-fortran-2003-2008 */
int isdirectory_c(const char *dir){
struct stat statbuf;
if(stat(dir, &statbuf) != 0) /* error */
@ -44,3 +46,11 @@ void gethostname_c(char hostname[], int *stat){
int chdir_c(const char *dir){
return chdir(dir);
}
void signalusr1_c(void (*handler)(int)){
signal(SIGUSR1, handler);
}
void signalusr2_c(void (*handler)(int)){
signal(SIGUSR2, handler);
}

29
src/DAMASK_abaqus.f
View File

@ -40,16 +40,25 @@ subroutine DAMASK_interface_init
character(len=256) :: wd
call date_and_time(values = dateAndTime)
write(6,'(/,a)') ' <<<+- DAMASK_abaqus_std -+>>>'
write(6,'(/,a)') ' Roters et al., Computational Materials Science, 2018'
write(6,'(/,a)') ' Version: '//DAMASKVERSION
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',&
dateAndTime(2),'/',&
dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':',&
dateAndTime(6),':',&
dateAndTime(7)
write(6,'(/,a)') ' <<<+- DAMASK_interface init -+>>>'
write(6,'(/,a)') ' <<<+- DAMASK_abaqus -+>>>'
write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
write(6,'(a,/)') ' Version: '//DAMASKVERSION
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
#if __INTEL_COMPILER >= 1800
write(6,*) 'Compiled with: ', compiler_version()
write(6,*) 'Compiler options: ', compiler_options()
#else
write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
', build date :', __INTEL_COMPILER_BUILD_DATE
#endif
write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
call getoutdir(wd, lenOutDir)
ierr = CHDIR(wd)

81
src/DAMASK_interface.f90
View File

@ -12,9 +12,9 @@
module DAMASK_interface
use prec, only: &
pInt
implicit none
private
logical, public, protected :: SIGUSR1,SIGUSR2
integer(pInt), public, protected :: &
interface_restartInc = 0_pInt !< Increment at which calculation starts
character(len=1024), public, protected :: &
@ -42,6 +42,8 @@ contains
subroutine DAMASK_interface_init()
use, intrinsic :: &
iso_fortran_env
use :: &
iso_c_binding
#include <petsc/finclude/petscsys.h>
#if defined(__GFORTRAN__) && __GNUC__ < 5
===================================================================================================
@ -81,6 +83,8 @@ subroutine DAMASK_interface_init()
use PETScSys
use system_routines, only: &
signalusr1_C, &
signalusr2_C, &
getHostName, &
getCWD
@ -139,16 +143,27 @@ subroutine DAMASK_interface_init()
call date_and_time(values = dateAndTime)
write(6,'(/,a)') ' <<<+- DAMASK_interface init -+>>>'
write(6,'(a,/)') ' Roters et al., Computational Materials Science, 2018'
write(6,'(/,a)') ' Version: '//DAMASKVERSION
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',&
dateAndTime(2),'/',&
dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':',&
dateAndTime(6),':',&
dateAndTime(7)
write(6,'(/,a,i4.1)') ' MPI processes: ',worldsize
#include "compilation_info.f90"
write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
write(6,'(a,/)') ' Version: '//DAMASKVERSION
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
write(6,*) 'Compiled with: ', compiler_version()
write(6,*) 'Compiler options: ', compiler_options()
#elif defined(__INTEL_COMPILER)
write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
', build date :', __INTEL_COMPILER_BUILD_DATE
#elif defined(__PGI)
write(6,'(a,i4.4,a,i8.8)') ' Compiled with PGI fortran version :', __PGIC__,&
'.', __PGIC_MINOR__
#endif
write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
call get_command(commandLine)
chunkPos = IIO_stringPos(commandLine)
@ -215,9 +230,11 @@ subroutine DAMASK_interface_init()
call get_environment_variable('USER',userName)
! ToDo: https://stackoverflow.com/questions/8953424/how-to-get-the-username-in-c-c-in-linux
write(6,'(a,a)') ' Host name: ', trim(getHostName())
write(6,'(a,a)') ' User name: ', trim(userName)
write(6,'(a,a)') ' Command line call: ', trim(commandLine)
write(6,'(/,a,i4.1)') ' MPI processes: ',worldsize
write(6,'(a,a)') ' Host name: ', trim(getHostName())
write(6,'(a,a)') ' User name: ', trim(userName)
write(6,'(/a,a)') ' Command line call: ', trim(commandLine)
if (len(trim(workingDirArg)) > 0) &
write(6,'(a,a)') ' Working dir argument: ', trim(workingDirArg)
write(6,'(a,a)') ' Geometry argument: ', trim(geometryArg)
@ -229,6 +246,12 @@ subroutine DAMASK_interface_init()
if (interface_restartInc > 0_pInt) &
write(6,'(a,i6.6)') ' Restart from increment: ', interface_restartInc
call signalusr1_c(c_funloc(setSIGUSR1))
call signalusr2_c(c_funloc(setSIGUSR2))
SIGUSR1 = .false.
SIGUSR2 = .false.
end subroutine DAMASK_interface_init
@ -412,6 +435,35 @@ character(len=1024) function makeRelativePath(a,b)
end function makeRelativePath
!--------------------------------------------------------------------------------------------------
!> @brief sets global variable SIGUSR1 to .true. if program receives SIGUSR1
!--------------------------------------------------------------------------------------------------
subroutine setSIGUSR1(signal) bind(C)
use :: iso_c_binding
implicit none
integer(C_INT), value :: signal
SIGUSR1 = .true.
write(6,*) 'received signal ',signal, 'set SIGUSR1'
end subroutine setSIGUSR1
!--------------------------------------------------------------------------------------------------
!> @brief sets global variable SIGUSR2 to .true. if program receives SIGUSR2
!--------------------------------------------------------------------------------------------------
subroutine setSIGUSR2(signal) bind(C)
use :: iso_c_binding
implicit none
integer(C_INT), value :: signal
SIGUSR2 = .true.
write(6,*) 'received signal ',signal, 'set SIGUSR2'
end subroutine setSIGUSR2
!--------------------------------------------------------------------------------------------------
!> @brief taken from IO, check IO_stringValue for documentation
@ -469,7 +521,6 @@ pure function IIO_stringPos(string)
do while (verify(string(right+1:),SEP)>0)
left = right + verify(string(right+1:),SEP)
right = left + scan(string(left:),SEP) - 2
if ( string(left:left) == '#' ) exit
IIO_stringPos = [IIO_stringPos,int(left, pInt), int(right, pInt)]
IIO_stringPos(1) = IIO_stringPos(1)+1_pInt
enddo

31
src/DAMASK_marc.f90
View File

@ -53,17 +53,26 @@ subroutine DAMASK_interface_init
character(len=1024) :: wd
call date_and_time(values = dateAndTime)
write(6,'(/,a)') ' <<<+- DAMASK_Marc -+>>>'
write(6,'(/,a)') ' Roters et al., Computational Materials Science, 2018'
write(6,'(/,a)') ' Version: '//DAMASKVERSION
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',&
dateAndTime(2),'/',&
dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':',&
dateAndTime(6),':',&
dateAndTime(7)
write(6,'(/,a)') ' <<<+- DAMASK_interface init -+>>>'
#include "compilation_info.f90"
write(6,'(/,a)') ' <<<+- DAMASK_abaqus -+>>>'
write(6,'(/,a)') ' Roters et al., Computational Materials Science 158, 2018, 420-478'
write(6,'(a,/)') ' https://doi.org/10.1016/j.commatsci.2018.04.030'
write(6,'(a,/)') ' Version: '//DAMASKVERSION
! https://github.com/jeffhammond/HPCInfo/blob/master/docs/Preprocessor-Macros.md
#if __INTEL_COMPILER >= 1800
write(6,*) 'Compiled with: ', compiler_version()
write(6,*) 'Compiler options: ', compiler_options()
#else
write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version :', __INTEL_COMPILER,&
', build date :', __INTEL_COMPILER_BUILD_DATE
#endif
write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
write(6,'(a,2(i2.2,a),i4.4)') ' Date: ',dateAndTime(3),'/',dateAndTime(2),'/', dateAndTime(1)
write(6,'(a,2(i2.2,a),i2.2)') ' Time: ',dateAndTime(5),':', dateAndTime(6),':', dateAndTime(7)
inquire(5, name=wd) ! determine inputputfile
wd = wd(1:scan(wd,'/',back=.true.))
ierr = CHDIR(wd)

8
src/FEM_utilities.f90
View File

@ -162,7 +162,6 @@ subroutine utilities_init()
character(len=1024) :: petsc_optionsPhysics
integer(pInt) :: dimPlex
integer(pInt) :: headerID = 205_pInt
PetscInt, allocatable :: nEntities(:), nOutputCells(:), nOutputNodes(:)
PetscInt :: dim
PetscErrorCode :: ierr
@ -213,13 +212,6 @@ subroutine utilities_init()
nOutputCells(worldrank+1) = count(material_homog > 0_pInt)
call MPI_Allreduce(MPI_IN_PLACE,nOutputNodes,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)
call MPI_Allreduce(MPI_IN_PLACE,nOutputCells,worldsize,MPI_INT,MPI_SUM,PETSC_COMM_WORLD,ierr)
if (worldrank == 0_pInt) then
open(unit=headerID, file=trim(getSolverJobName())//'.header', &
form='FORMATTED', status='REPLACE')
write(headerID, '(a,i0)') 'dimension : ', dimPlex
write(headerID, '(a,i0)') 'number of nodes : ', sum(nOutputNodes)
write(headerID, '(a,i0)') 'number of cells : ', sum(nOutputCells)
endif
end subroutine utilities_init

2759
src/HDF5_utilities.f90
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File diff suppressed because it is too large Load Diff

10
src/compilation_info.f90
View File

@ -1,10 +0,0 @@
#if defined(__GFORTRAN__) || __INTEL_COMPILER >= 1800
write(6,*) 'Compiled with ', compiler_version()
write(6,*) 'With options ', compiler_options()
#else
write(6,'(a,i4.4,a,i8.8)') ' Compiled with Intel fortran version ', __INTEL_COMPILER,&
', build date ', __INTEL_COMPILER_BUILD_DATE
#endif
write(6,*) 'Compiled on ', __DATE__,' at ',__TIME__
write(6,*)
flush(6)

8
src/kinematics_thermal_expansion.f90
View File

@ -24,10 +24,10 @@ module kinematics_thermal_expansion
integer(pInt), dimension(:), allocatable, target, public :: &
kinematics_thermal_expansion_Noutput !< number of outputs per instance of this damage
! enum, bind(c) ! ToDo kinematics need state machinery to deal with sizePostResult
! enumerator :: undefined_ID, & ! possible remedy is to decouple having state vars from having output
! thermalexpansionrate_ID ! which means to separate user-defined types tState + tOutput...
! end enum
enum, bind(c) ! ToDo kinematics need state machinery to deal with sizePostResult
enumerator :: undefined_ID, & ! possible remedy is to decouple having state vars from having output
thermalexpansionrate_ID ! which means to separate user-defined types tState + tOutput...
end enum
public :: &
kinematics_thermal_expansion_init, &
kinematics_thermal_expansion_initialStrain, &

93
src/math.f90
View File

@ -118,6 +118,9 @@ module math
!---------------------------------------------------------------------------------------------------
public :: &
#if defined(__PGI)
norm2, &
#endif
math_init, &
math_qsort, &
math_expand, &
@ -351,20 +354,38 @@ end subroutine math_check
!--------------------------------------------------------------------------------------------------
!> @brief Quicksort algorithm for two-dimensional integer arrays
! Sorting is done with respect to array(1,:)
! and keeps array(2:N,:) linked to it.
! Sorting is done with respect to array(sort,:) and keeps array(/=sort,:) linked to it.
! default: sort=1
!--------------------------------------------------------------------------------------------------
recursive subroutine math_qsort(a, istart, iend)
recursive subroutine math_qsort(a, istart, iend, sortDim)
implicit none
integer(pInt), dimension(:,:), intent(inout) :: a
integer(pInt), intent(in) :: istart,iend
integer(pInt) :: ipivot
if (istart < iend) then
ipivot = qsort_partition(a,istart, iend)
call math_qsort(a, istart, ipivot-1_pInt)
call math_qsort(a, ipivot+1_pInt, iend)
integer(pInt), intent(in),optional :: istart,iend, sortDim
integer(pInt) :: ipivot,s,e,d
if(present(istart)) then
s = istart
else
s = lbound(a,2)
endif
if(present(iend)) then
e = iend
else
e = ubound(a,2)
endif
if(present(sortDim)) then
d = sortDim
else
d = 1
endif
if (s < e) then
ipivot = qsort_partition(a,s, e, d)
call math_qsort(a, s, ipivot-1_pInt, d)
call math_qsort(a, ipivot+1_pInt, e, d)
endif
!--------------------------------------------------------------------------------------------------
@ -373,37 +394,34 @@ recursive subroutine math_qsort(a, istart, iend)
!-------------------------------------------------------------------------------------------------
!> @brief Partitioning required for quicksort
!-------------------------------------------------------------------------------------------------
integer(pInt) function qsort_partition(a, istart, iend)
integer(pInt) function qsort_partition(a, istart, iend, sort)
implicit none
integer(pInt), dimension(:,:), intent(inout) :: a
integer(pInt), intent(in) :: istart,iend
integer(pInt) :: i,j,k,tmp
integer(pInt), intent(in) :: istart,iend,sort
integer(pInt), dimension(size(a,1)) :: tmp
integer(pInt) :: i,j
do
! find the first element on the right side less than or equal to the pivot point
! find the first element on the right side less than or equal to the pivot point
do j = iend, istart, -1_pInt
if (a(1,j) <= a(1,istart)) exit
if (a(sort,j) <= a(sort,istart)) exit
enddo
! find the first element on the left side greater than the pivot point
! find the first element on the left side greater than the pivot point
do i = istart, iend
if (a(1,i) > a(1,istart)) exit
if (a(sort,i) > a(sort,istart)) exit
enddo
if (i < j) then ! if the indexes do not cross, exchange values
do k = 1_pInt, int(size(a,1_pInt), pInt)
tmp = a(k,i)
a(k,i) = a(k,j)
a(k,j) = tmp
enddo
else ! if they do cross, exchange left value with pivot and return with the partition index
do k = 1_pInt, int(size(a,1_pInt), pInt)
tmp = a(k,istart)
a(k,istart) = a(k,j)
a(k,j) = tmp
enddo
cross: if (i >= j) then ! if the indices cross, exchange left value with pivot and return with the partition index
tmp = a(:,istart)
a(:,istart) = a(:,j)
a(:,j) = tmp
qsort_partition = j
return
endif
else cross ! if they do not cross, exchange values
tmp = a(:,i)
a(:,i) = a(:,j)
a(:,j) = tmp
endif cross
enddo
end function qsort_partition
@ -2707,4 +2725,19 @@ real(pReal) pure elemental function math_clip(a, left, right)
end function math_clip
#if defined(__PGI)
!--------------------------------------------------------------------------------------------------
!> @brief substitute for the norm2 intrinsic which is not available in PGI 18.10
!--------------------------------------------------------------------------------------------------
real(pReal) pure function norm2(v)
implicit none
real(pReal), intent(in), dimension(3) :: v
norm2 = sqrt(sum(v**2))
end function norm2
#endif
end module math

148
src/system_routines.f90
View File

@ -3,11 +3,17 @@
!> @brief provides wrappers to C routines
!--------------------------------------------------------------------------------------------------
module system_routines
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR, &
C_NULL_CHAR
implicit none
private
public :: &
signalusr1_C, &
signalusr2_C, &
isDirectory, &
getCWD, &
getHostName, &
@ -27,7 +33,7 @@ interface
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
character(kind=C_CHAR), dimension(1024), intent(out) :: str ! C string is an array
character(kind=C_CHAR), dimension(1024), intent(out) :: str ! C string is an array
integer(C_INT),intent(out) :: stat
end subroutine getCurrentWorkDir_C
@ -35,7 +41,7 @@ interface
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR
character(kind=C_CHAR), dimension(1024), intent(out) :: str ! C string is an array
character(kind=C_CHAR), dimension(1024), intent(out) :: str ! C string is an array
integer(C_INT),intent(out) :: stat
end subroutine getHostName_C
@ -46,31 +52,38 @@ interface
integer(C_INT) :: chdir_C
character(kind=C_CHAR), dimension(1024), intent(in) :: path ! C string is an array
end function chdir_C
subroutine signalusr1_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr1_C
subroutine signalusr2_C(handler) bind(C)
use, intrinsic :: ISO_C_Binding, only: &
C_FUNPTR
type(C_FUNPTR), intent(in), value :: handler
end subroutine signalusr2_C
end interface
contains
!--------------------------------------------------------------------------------------------------
!> @brief figures out if a given path is a directory (and not an ordinary file)
!--------------------------------------------------------------------------------------------------
logical function isDirectory(path)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR, &
C_NULL_CHAR
implicit none
character(len=*), intent(in) :: path
character(kind=C_CHAR), dimension(1024) :: strFixedLength
integer :: i
implicit none
character(len=*), intent(in) :: path
character(kind=C_CHAR), dimension(1024) :: strFixedLength ! C string as array
integer :: i
strFixedLength = repeat(C_NULL_CHAR,len(strFixedLength))
do i=1,len(path) ! copy array components
strFixedLength(i)=path(i:i)
enddo
isDirectory=merge(.True.,.False.,isDirectory_C(strFixedLength) /= 0_C_INT)
strFixedLength = repeat(C_NULL_CHAR,len(strFixedLength))
do i=1,len(path) ! copy array components
strFixedLength(i)=path(i:i)
enddo
isDirectory=merge(.True.,.False.,isDirectory_C(strFixedLength) /= 0_C_INT)
end function isDirectory
@ -79,29 +92,25 @@ end function isDirectory
!> @brief gets the current working directory
!--------------------------------------------------------------------------------------------------
character(len=1024) function getCWD()
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR, &
C_NULL_CHAR
implicit none
character(kind=C_CHAR), dimension(1024) :: charArray ! C string is an array
integer(C_INT) :: stat
integer :: i
implicit none
character(kind=C_CHAR), dimension(1024) :: charArray ! C string is an array
integer(C_INT) :: stat
integer :: i
call getCurrentWorkDir_C(charArray,stat)
if (stat /= 0_C_INT) then
getCWD = 'Error occured when getting currend working directory'
else
getCWD = repeat('',len(getCWD))
arrayToString: do i=1,len(getCWD)
if (charArray(i) /= C_NULL_CHAR) then
getCWD(i:i)=charArray(i)
else
exit
endif
enddo arrayToString
endif
call getCurrentWorkDir_C(charArray,stat)
if (stat /= 0_C_INT) then
getCWD = 'Error occured when getting currend working directory'
else
getCWD = repeat('',len(getCWD))
arrayToString: do i=1,len(getCWD)
if (charArray(i) /= C_NULL_CHAR) then
getCWD(i:i)=charArray(i)
else
exit
endif
enddo arrayToString
endif
end function getCWD
@ -110,51 +119,42 @@ end function getCWD
!> @brief gets the current host name
!--------------------------------------------------------------------------------------------------
character(len=1024) function getHostName()
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR, &
C_NULL_CHAR
implicit none
character(kind=C_CHAR), dimension(1024) :: charArray ! C string is an array
integer(C_INT) :: stat
integer :: i
implicit none
character(kind=C_CHAR), dimension(1024) :: charArray ! C string is an array
integer(C_INT) :: stat
integer :: i
call getHostName_C(charArray,stat)
if (stat /= 0_C_INT) then
getHostName = 'Error occured when getting host name'
else
getHostName = repeat('',len(getHostName))
arrayToString: do i=1,len(getHostName)
if (charArray(i) /= C_NULL_CHAR) then
getHostName(i:i)=charArray(i)
else
exit
endif
enddo arrayToString
endif
call getHostName_C(charArray,stat)
if (stat /= 0_C_INT) then
getHostName = 'Error occured when getting host name'
else
getHostName = repeat('',len(getHostName))
arrayToString: do i=1,len(getHostName)
if (charArray(i) /= C_NULL_CHAR) then
getHostName(i:i)=charArray(i)
else
exit
endif
enddo arrayToString
endif
end function getHostName
!--------------------------------------------------------------------------------------------------
!> @brief changes the current working directory
!--------------------------------------------------------------------------------------------------
logical function setCWD(path)
use, intrinsic :: ISO_C_Binding, only: &
C_INT, &
C_CHAR, &
C_NULL_CHAR
implicit none
character(len=*), intent(in) :: path
character(kind=C_CHAR), dimension(1024) :: strFixedLength ! C string is an array
integer :: i
implicit none
character(len=*), intent(in) :: path
character(kind=C_CHAR), dimension(1024) :: strFixedLength ! C string is an array
integer :: i
strFixedLength = repeat(C_NULL_CHAR,len(strFixedLength))
do i=1,len(path) ! copy array components
strFixedLength(i)=path(i:i)
enddo
setCWD=merge(.True.,.False.,chdir_C(strFixedLength) /= 0_C_INT)
strFixedLength = repeat(C_NULL_CHAR,len(strFixedLength))
do i=1,len(path) ! copy array components
strFixedLength(i)=path(i:i)
enddo
setCWD=merge(.True.,.False.,chdir_C(strFixedLength) /= 0_C_INT)
end function setCWD