Merge branch 'development' into HMS

This commit is contained in:
Fengbo Han 2018-02-07 11:44:17 +01:00
commit 9249e7db2b
84 changed files with 3104 additions and 5831 deletions

2
.gitignore vendored
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@ -1,4 +1,3 @@
.noH5py
*.pyc
*.mod
*.o
@ -8,3 +7,4 @@
bin
PRIVATE
build
system_report.txt

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@ -124,6 +124,7 @@ endif ()
# Predefined sets for OPTIMIZATION/OPENMP based on BUILD_TYPE
if ("${CMAKE_BUILD_TYPE}" STREQUAL "DEBUG" OR "${CMAKE_BUILD_TYPE}" STREQUAL "SYNTAXONLY" )
set (DEBUG_FLAGS "${DEBUG_FLAGS} -DDEBUG")
set (PARALLEL "OFF")
set (OPTI "OFF")
elseif ("${CMAKE_BUILD_TYPE}" STREQUAL "RELEASE")

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@ -1,9 +1,17 @@
#!/usr/bin/env bash
OUTFILE="system_report.txt"
echo generating $OUTFILE
#==================================================================================================
# Execute this script (type './DAMASK_prerequisites.sh')
# and send system_report.txt to damask@mpie.de for support
#==================================================================================================
OUTFILE="system_report.txt"
echo ===========================================
echo + Generating $OUTFILE
echo + Send to damask@mpie.de for support
echo ===========================================
echo date +"%m-%d-%y" >$OUTFILE
# redirect STDOUT and STDERR to logfile
# https://stackoverflow.com/questions/11229385/redirect-all-output-in-a-bash-script-when-using-set-x^
@ -13,6 +21,10 @@ exec > $OUTFILE 2>&1
# https://stackoverflow.com/questions/59895/getting-the-source-directory-of-a-bash-script-from-within
DAMASK_ROOT="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
echo System report for \'$(hostname)\' created on $(date '+%Y-%m-%d %H:%M:%S') by \'$(whoami)\'
echo XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
echo
echo ==============================================================================================
echo DAMASK settings
echo ==============================================================================================
@ -30,19 +42,24 @@ echo System
echo ==============================================================================================
uname -a
echo
echo PATH: $PATH
echo LD_LIBRARY_PATH: $LD_LIBRARY_PATH
echo PYTHONPATH: $PYTHONPATH
echo SHELL: $SHELL
echo
echo ==============================================================================================
echo Python
echo ==============================================================================================
DEFAULT_PYTHON=python2.7
for executable in python python2 python3 python2.7; do
if [[ "$(which $executable)x" != "x" ]]; then
if which $executable &> /dev/null; then
echo $executable version: $($executable --version 2>&1)
else
echo $executable does not exist
fi
done
echo Location of $DEFAULT_PYTHON: $(ls -la $(which $DEFAULT_PYTHON))
echo Details on $DEFAULT_PYTHON: $(ls -la $(which $DEFAULT_PYTHON))
echo
for module in numpy scipy;do
echo ----------------------------------------------------------------------------------------------
@ -69,7 +86,7 @@ echo ===========================================================================
echo GCC
echo ==============================================================================================
for executable in gcc g++ gfortran ;do
if [[ "$(which $executable)x" != "x" ]]; then
if which $executable &> /dev/null; then
echo $(which $executable) version: $($executable --version 2>&1)
else
echo $executable does not exist
@ -80,7 +97,7 @@ echo ===========================================================================
echo Intel Compiler Suite
echo ==============================================================================================
for executable in icc icpc ifort ;do
if [[ "$(which $executable)x" != "x" ]]; then
if which $executable &> /dev/null; then
echo $(which $executable) version: $($executable --version 2>&1)
else
echo $executable does not exist
@ -91,7 +108,7 @@ echo ===========================================================================
echo MPI Wrappers
echo ==============================================================================================
for executable in mpicc mpiCC mpicxx mpicxx mpifort mpif90 mpif77; do
if [[ "$(which $executable)x" != "x" ]]; then
if which $executable &> /dev/null; then
echo $(which $executable) version: $($executable --show 2>&1)
else
echo $executable does not exist

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@ -1,6 +1,6 @@
Copyright 2011-17 Max-Planck-Institut für Eisenforschung GmbH
This program is free software: you can redistribute it and/or modify
DAMASK is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

@ -1 +1 @@
Subproject commit 55a263fc30c40c16ef337be050f8901dd2747390
Subproject commit 5fc3188c86ea1f4159db87529ac3e3169fb56e5d

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@ -1 +1 @@
v2.0.1-960-geddc2a6
v2.0.1-1035-gd80a255

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@ -1 +1,23 @@
# Save by abaqususer on Thu May 12 10:22:10 2011
# Save by m.diehl on 2017_12_06-18.38.26; build 2017 2016_09_27-23.54.59 126836
from abaqus import *
upgradeMdb(
'/nethome/storage/raid4/m.diehl/DAMASK/examples/AbaqusStandard/SX_PX_compression-6.9-1.cae'
,
'/nethome/storage/raid4/m.diehl/DAMASK/examples/AbaqusStandard/SX_PX_compression.cae')
# Save by m.diehl on 2017_12_06-18.38.26; build 2017 2016_09_27-23.54.59 126836
from part import *
from material import *
from section import *
from assembly import *
from step import *
from interaction import *
from load import *
from mesh import *
from optimization import *
from job import *
from sketch import *
from visualization import *
from connectorBehavior import *
mdb.jobs['Job_sx-px'].setValues(description='compression', userSubroutine=
'$HOME/DAMASK/src/DAMASK_abaqus_std.f')
# Save by m.diehl on 2017_12_06-18.39.44; build 2017 2016_09_27-23.54.59 126836

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@ -49,7 +49,7 @@ maxVolDiscrepancy_RGC 1.0e-5 # maximum allowable relative volume discr
volDiscrepancyMod_RGC 1.0e+12
discrepancyPower_RGC 5.0
fixed_seed 0 # put any number larger than zero, integer, if you want to have a pseudo random distribution
random_seed 0 # any integer larger than zero seeds the random generator, otherwise random seeding
## spectral parameters ##
err_div_tolAbs 1.0e-3 # absolute tolerance for fulfillment of stress equilibrium

94
img/COPYING Normal file
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@ -0,0 +1,94 @@
Creative Commons Attribution-NoDerivatives 4.0 International Public License
By exercising the Licensed Rights (defined below), You accept and agree to be bound by the terms and conditions of this Creative Commons Attribution-NoDerivatives 4.0 International Public License ("Public License"). To the extent this Public License may be interpreted as a contract, You are granted the Licensed Rights in consideration of Your acceptance of these terms and conditions, and the Licensor grants You such rights in consideration of benefits the Licensor receives from making the Licensed Material available under these terms and conditions.
Section 1 Definitions.
Adapted Material means material subject to Copyright and Similar Rights that is derived from or based upon the Licensed Material and in which the Licensed Material is translated, altered, arranged, transformed, or otherwise modified in a manner requiring permission under the Copyright and Similar Rights held by the Licensor. For purposes of this Public License, where the Licensed Material is a musical work, performance, or sound recording, Adapted Material is always produced where the Licensed Material is synched in timed relation with a moving image.
Copyright and Similar Rights means copyright and/or similar rights closely related to copyright including, without limitation, performance, broadcast, sound recording, and Sui Generis Database Rights, without regard to how the rights are labeled or categorized. For purposes of this Public License, the rights specified in Section 2(b)(1)-(2) are not Copyright and Similar Rights.
Effective Technological Measures means those measures that, in the absence of proper authority, may not be circumvented under laws fulfilling obligations under Article 11 of the WIPO Copyright Treaty adopted on December 20, 1996, and/or similar international agreements.
Exceptions and Limitations means fair use, fair dealing, and/or any other exception or limitation to Copyright and Similar Rights that applies to Your use of the Licensed Material.
Licensed Material means the artistic or literary work, database, or other material to which the Licensor applied this Public License.
Licensed Rights means the rights granted to You subject to the terms and conditions of this Public License, which are limited to all Copyright and Similar Rights that apply to Your use of the Licensed Material and that the Licensor has authority to license.
Licensor means the individual(s) or entity(ies) granting rights under this Public License.
Share means to provide material to the public by any means or process that requires permission under the Licensed Rights, such as reproduction, public display, public performance, distribution, dissemination, communication, or importation, and to make material available to the public including in ways that members of the public may access the material from a place and at a time individually chosen by them.
Sui Generis Database Rights means rights other than copyright resulting from Directive 96/9/EC of the European Parliament and of the Council of 11 March 1996 on the legal protection of databases, as amended and/or succeeded, as well as other essentially equivalent rights anywhere in the world.
You means the individual or entity exercising the Licensed Rights under this Public License. Your has a corresponding meaning.
Section 2 Scope.
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Subject to the terms and conditions of this Public License, the Licensor hereby grants You a worldwide, royalty-free, non-sublicensable, non-exclusive, irrevocable license to exercise the Licensed Rights in the Licensed Material to:
reproduce and Share the Licensed Material, in whole or in part; and
produce and reproduce, but not Share, Adapted Material.
Exceptions and Limitations. For the avoidance of doubt, where Exceptions and Limitations apply to Your use, this Public License does not apply, and You do not need to comply with its terms and conditions.
Term. The term of this Public License is specified in Section 6(a).
Media and formats; technical modifications allowed. The Licensor authorizes You to exercise the Licensed Rights in all media and formats whether now known or hereafter created, and to make technical modifications necessary to do so. The Licensor waives and/or agrees not to assert any right or authority to forbid You from making technical modifications necessary to exercise the Licensed Rights, including technical modifications necessary to circumvent Effective Technological Measures. For purposes of this Public License, simply making modifications authorized by this Section 2(a)(4) never produces Adapted Material.
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Offer from the Licensor Licensed Material. Every recipient of the Licensed Material automatically receives an offer from the Licensor to exercise the Licensed Rights under the terms and conditions of this Public License.
No downstream restrictions. You may not offer or impose any additional or different terms or conditions on, or apply any Effective Technological Measures to, the Licensed Material if doing so restricts exercise of the Licensed Rights by any recipient of the Licensed Material.
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Section 3 License Conditions.
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If You Share the Licensed Material, You must:
retain the following if it is supplied by the Licensor with the Licensed Material:
identification of the creator(s) of the Licensed Material and any others designated to receive attribution, in any reasonable manner requested by the Licensor (including by pseudonym if designated);
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if You include all or a substantial portion of the database contents in a database in which You have Sui Generis Database Rights, then the database in which You have Sui Generis Database Rights (but not its individual contents) is Adapted Material; and
You must comply with the conditions in Section 3(a) if You Share all or a substantial portion of the contents of the database.
For the avoidance of doubt, this Section 4 supplements and does not replace Your obligations under this Public License where the Licensed Rights include other Copyright and Similar Rights.
Section 5 Disclaimer of Warranties and Limitation of Liability.
Unless otherwise separately undertaken by the Licensor, to the extent possible, the Licensor offers the Licensed Material as-is and as-available, and makes no representations or warranties of any kind concerning the Licensed Material, whether express, implied, statutory, or other. This includes, without limitation, warranties of title, merchantability, fitness for a particular purpose, non-infringement, absence of latent or other defects, accuracy, or the presence or absence of errors, whether or not known or discoverable. Where disclaimers of warranties are not allowed in full or in part, this disclaimer may not apply to You.
To the extent possible, in no event will the Licensor be liable to You on any legal theory (including, without limitation, negligence) or otherwise for any direct, special, indirect, incidental, consequential, punitive, exemplary, or other losses, costs, expenses, or damages arising out of this Public License or use of the Licensed Material, even if the Licensor has been advised of the possibility of such losses, costs, expenses, or damages. Where a limitation of liability is not allowed in full or in part, this limitation may not apply to You.
The disclaimer of warranties and limitation of liability provided above shall be interpreted in a manner that, to the extent possible, most closely approximates an absolute disclaimer and waiver of all liability.
Section 6 Term and Termination.
This Public License applies for the term of the Copyright and Similar Rights licensed here. However, if You fail to comply with this Public License, then Your rights under this Public License terminate automatically.
Where Your right to use the Licensed Material has terminated under Section 6(a), it reinstates:
automatically as of the date the violation is cured, provided it is cured within 30 days of Your discovery of the violation; or
upon express reinstatement by the Licensor.
For the avoidance of doubt, this Section 6(b) does not affect any right the Licensor may have to seek remedies for Your violations of this Public License.
For the avoidance of doubt, the Licensor may also offer the Licensed Material under separate terms or conditions or stop distributing the Licensed Material at any time; however, doing so will not terminate this Public License.
Sections 1, 5, 6, 7, and 8 survive termination of this Public License.
Section 7 Other Terms and Conditions.
The Licensor shall not be bound by any additional or different terms or conditions communicated by You unless expressly agreed.
Any arrangements, understandings, or agreements regarding the Licensed Material not stated herein are separate from and independent of the terms and conditions of this Public License.
Section 8 Interpretation.
For the avoidance of doubt, this Public License does not, and shall not be interpreted to, reduce, limit, restrict, or impose conditions on any use of the Licensed Material that could lawfully be made without permission under this Public License.
To the extent possible, if any provision of this Public License is deemed unenforceable, it shall be automatically reformed to the minimum extent necessary to make it enforceable. If the provision cannot be reformed, it shall be severed from this Public License without affecting the enforceability of the remaining terms and conditions.
No term or condition of this Public License will be waived and no failure to comply consented to unless expressly agreed to by the Licensor.
Nothing in this Public License constitutes or may be interpreted as a limitation upon, or waiver of, any privileges and immunities that apply to the Licensor or You, including from the legal processes of any jurisdiction or authority.

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@ -5,11 +5,37 @@
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:svg="http://www.w3.org/2000/svg"
xmlns="http://www.w3.org/2000/svg"
xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd"
xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape"
viewBox="0 0 104.4 104.4"
height="104.4"
width="104.4"
version="1.1"
id="svg4314">
id="svg4314"
sodipodi:docname="DAMASK_QR-CodeBW.svg"
inkscape:version="0.92.1 r15371">
<title
id="title4483">DAMASK QR code</title>
<sodipodi:namedview
pagecolor="#ffffff"
bordercolor="#666666"
borderopacity="1"
objecttolerance="10"
gridtolerance="10"
guidetolerance="10"
inkscape:pageopacity="0"
inkscape:pageshadow="2"
inkscape:window-width="1920"
inkscape:window-height="1001"
id="namedview6"
showgrid="false"
inkscape:zoom="2.2605364"
inkscape:cx="52.200001"
inkscape:cy="52.200001"
inkscape:window-x="-9"
inkscape:window-y="-9"
inkscape:window-maximized="1"
inkscape:current-layer="svg4314" />
<metadata
id="metadata4320">
<rdf:RDF>
@ -18,8 +44,32 @@
<dc:format>image/svg+xml</dc:format>
<dc:type
rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
<dc:title></dc:title>
<dc:title>DAMASK QR code</dc:title>
<cc:license
rdf:resource="http://creativecommons.org/licenses/by-nd/4.0/" />
<dc:creator>
<cc:Agent>
<dc:title>Franz Roters</dc:title>
</cc:Agent>
</dc:creator>
<dc:subject>
<rdf:Bag>
<rdf:li>DAMASK; Crystal Plasticity; Multi-Physics</rdf:li>
</rdf:Bag>
</dc:subject>
<dc:description>link to https://damask.mpie.de</dc:description>
</cc:Work>
<cc:License
rdf:about="http://creativecommons.org/licenses/by-nd/4.0/">
<cc:permits
rdf:resource="http://creativecommons.org/ns#Reproduction" />
<cc:permits
rdf:resource="http://creativecommons.org/ns#Distribution" />
<cc:requires
rdf:resource="http://creativecommons.org/ns#Notice" />
<cc:requires
rdf:resource="http://creativecommons.org/ns#Attribution" />
</cc:License>
</rdf:RDF>
</metadata>
<defs

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32
img/LICENSE Normal file
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@ -0,0 +1,32 @@
DAMASK logo: Copyright 2011 Philip Eisenlohr,
Max-Planck-Institut für Eisenforschung GmbH
DAMASK QR code: Copyright 2016 Franz Roters,
Max-Planck-Institut für Eisenforschung GmbH
These images are licensed according to the Attribution-NoDerivatives 4.0 International
(CC BY-ND 4.0) license.
You should have received a copy of the Attribution-NoDerivatives 4.0 International license
along with these images. If not, see <http://creativecommons.org/licenses/by-nd/4.0/>
The following is a human-readable summary of (and not a substitute for) the license:
You are free to:
Share — copy and redistribute the material in any medium or format for any purpose,
even commercially.
The licensor cannot revoke these freedoms as long as you follow the license terms.
Under the following terms:
Attribution — You must give appropriate credit, provide a link to the license, and
indicate if changes were made. You may do so in any reasonable manner, but not in
any way that suggests the licensor endorses you or your use.
NoDerivatives — If you remix, transform, or build upon the material, you may not
distribute the modified material.
No additional restrictions — You may not apply legal terms or technological measures
that legally restrict others from doing anything the license permits.

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@ -44,16 +44,6 @@ double_precision=BOTH
# The user will not be asked whether old job files of the same name should be deleted.
ask_delete=OFF
# You can compile DAMASK into a library to be used with abaqus
# it saves you from compiling the subroutine for each job
# in this case you do not have to specify a usersubroutine file
# however if you still do, the compiled version will override that in the library
# Procedure:
# 1. create a library directory, e.g. abqlib, in your prefered location
# 2. build the library replacing your_prefered_location/abqlib with the correct path to the directory created in 1.:
# abaqus make -l DAMASK_abaqus_std.f -dir your_prefered_location/abqlib
# abaqus make -l DAMASK_abaqus_exp.f -dir your_prefered_location/abqlib
# 3. uncomment the next line after replacing your_prefered_location/abqlib with the correct path to the directory created in 1.
# usub_lib_dir='your_prefered_location/abqlib'
# Remove the temporary names from the namespace

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@ -44,16 +44,6 @@ double_precision=BOTH
# The user will not be asked whether old job files of the same name should be deleted.
ask_delete=OFF
# You can compile DAMASK into a library to be used with abaqus
# it saves you from compiling the subroutine for each job
# in this case you do not have to specify a usersubroutine file
# however if you still do, the compiled version will override that in the library
# Procedure:
# 1. create a library directory, e.g. abqlib, in your prefered location
# 2. build the library replacing your_prefered_location/abqlib with the correct path to the directory created in 1.:
# abaqus make -l DAMASK_abaqus_std.f -dir your_prefered_location/abqlib
# abaqus make -l DAMASK_abaqus_exp.f -dir your_prefered_location/abqlib
# 3. uncomment the next line after replacing your_prefered_location/abqlib with the correct path to the directory created in 1.
# usub_lib_dir='your_prefered_location/abqlib'
# Remove the temporary names from the namespace

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@ -1,6 +1,6 @@
# DAMASK patching
This folder contains patches that modify the functionality of the current version of DAMASK prior to the corresponding inclusion in the official release.
This folder contains patches that modify the functionality of the current development version of DAMASK ahead of the corresponding adoption in the official release.
## Usage
@ -13,3 +13,13 @@ patch -p1 < installation/patch/nameOfPatch
* **fwbw_derivative** switches the default spatial derivative from continuous to forward/backward difference.
This generally reduces spurious oscillations in the result as the spatial accuracy of the derivative is then compatible with the underlying solution grid.
* **PETSc-3.8** adjusts all includes and calls to PETSc to follow the 3.8.x API.
This allows to use the most recent version of PETSc.
## Create patch
commit your changes
```bash
git format-patch PATH_TO_COMPARE --stdout >
```

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@ -1,198 +0,0 @@
<?xml version="1.0"?>
<h5ds>
<!--Top level attributes-->
<history>
<type>attr</type>
<h5path>/</h5path>
<category></category>
<description>store cmd history</description>
</history>
<inc>
<type>attr</type>
<h5path>/</h5path>
<category></category>
<description></description>
</inc>
<!--Geometry section-->
<Vx>
<type>Scalar</type>
<h5path>/Geometry/Vx</h5path>
<category>Geometry</category>
<description>Vector along x define the spectral mesh</description>
</Vx>
<Vy>
<type>Scalar</type>
<h5path>/Geometry/Vy</h5path>
<category>Geometry</category>
<description>Vector along y defines the spectral mesh</description>
</Vy>
<Vz>
<type>Scalar</type>
<h5path>/Geometry/Vz</h5path>
<category>Geometry</category>
<description>Vector along z defines the spectral mesh</description>
</Vz>
<ip>
<type>Scalar</type>
<h5path>/Geometry/ip</h5path>
<category>Geometry</category>
<description></description>
</ip>
<node>
<type>Scalar</type>
<h5path>/Geometry/node</h5path>
<category>Geometry</category>
<description></description>
</node>
<grain>
<type>Scalar</type>
<h5path>/Geometry/grain</h5path>
<category>Geometry</category>
<description></description>
</grain>
<pos>
<type>Vector</type>
<h5path>/Geometry/pos</h5path>
<category>Geometry</category>
<description></description>
</pos>
<elem>
<type>Scalar</type>
<h5path>/Geometry/elem</h5path>
<category>Geometry</category>
<description></description>
</elem>
<!--Crystallite section-->
<phase>
<type>Scalar</type>
<h5path>/Crystallite/phase</h5path>
<category>Crystallite</category>
<description></description>
</phase>
<texture>
<type>Scalar</type>
<h5path>/Crystallite/texture</h5path>
<category>Crystallite</category>
<description></description>
</texture>
<volume>
<type>Scalar</type>
<h5path>/Crystallite/volume</h5path>
<category>Crystallite</category>
<description></description>
</volume>
<orientation>
<type>Vector</type>
<h5path>/Crystallite/orientation</h5path>
<category>Crystallite</category>
<description></description>
</orientation>
<eulerangles>
<type>Vector</type>
<h5path>/Crystallite/eulerangles</h5path>
<category>Crystallite</category>
<description>Bunnge Euler angles in degrees</description>
</eulerangles>
<grainrotation>
<type>Vector</type>
<h5path>/Crystallite/grainrotation</h5path>
<category>Crystallite</category>
<description></description>
</grainrotation>
<f>
<type>Tensor</type>
<h5path>/Crystallite/f</h5path>
<category>Crystallite</category>
<description>deformation gradient (F)</description>
</f>
<p>
<type>Tensor</type>
<h5path>/Crystallite/p</h5path>
<category>Crystallite</category>
<description>Pikola Kirkhoff stress</description>
</p>
<Cauchy>
<type>Tensor</type>
<h5path>/Crystallite/Cauchy</h5path>
<category>Crystallite</category>
<description>Cauchy stress tensor</description>
</Cauchy>
<lnV>
<type>Tensor</type>
<h5path>/Crystallite/lnV</h5path>
<category>Crystallite</category>
<description></description>
</lnV>
<MisesCauchy>
<type>Scalar</type>
<h5path>/Crystallite/MisesCauchy</h5path>
<category>Crystallite</category>
<description>von Mises equivalent of Cauchy stress</description>
</MisesCauchy>
<MiseslnV>
<type>Scalar</type>
<h5path>/Crystallite/MiseslnV</h5path>
<category>Crystallite</category>
<description>left von Mises strain</description>
</MiseslnV>
<!--Constitutive section-->
<resistance_slip>
<type>Vector</type>
<h5path>/Constitutive/resistance_slip</h5path>
<category>Constitutive</category>
<description></description>
</resistance_slip>
<shearrate_slip>
<type>Vector</type>
<h5path>/Constitutive/shearrate_slip</h5path>
<category>Constitutive</category>
<description></description>
</shearrate_slip>
<resolvedstress_slip>
<type>Vector</type>
<h5path>/Constitutive/resolvedstress_slip</h5path>
<category>Constitutive</category>
<description></description>
</resolvedstress_slip>
<totalshear>
<type>Scalar</type>
<h5path>/Constitutive/totalshear</h5path>
<category>Constitutive</category>
<description></description>
</totalshear>
<accumulatedshear_slip>
<type>Matrix</type>
<h5path>/Constitutive/accumulatedshear_slip</h5path>
<category>Constitutive</category>
<description>vector contains accumulated shear per slip system</description>
</accumulatedshear_slip>
<!--Derived section-->
</h5ds>

View File

@ -1,31 +1,13 @@
# -*- coding: UTF-8 no BOM -*-
"""Main aggregator"""
import os,sys,time
h5py_flag = os.path.join(os.path.dirname(__file__),'../../.noH5py')
h5py_grace = 7200 # only complain once every 7200 sec (2 hours)
h5py_msg = "h5py module not found."
now = time.time()
import os
with open(os.path.join(os.path.dirname(__file__),'../../VERSION')) as f:
version = f.readline()[:-1]
from .environment import Environment # noqa
from .asciitable import ASCIItable # noqa
try:
from .h5table import H5Table # noqa
if os.path.exists(h5py_flag): os.remove(h5py_flag) # delete flagging file on success
except ImportError:
if os.path.exists(h5py_flag):
if now - os.path.getmtime(h5py_flag) > h5py_grace: # complain (again) every so-and-so often
sys.stderr.write(h5py_msg+'\n')
with open(h5py_flag, 'a'):
os.utime(h5py_flag,(now,now)) # update flag modification time to "now"
else:
open(h5py_flag, 'a').close() # create flagging file
sys.stderr.write(h5py_msg+'\n') # complain for the first time
from .config import Material # noqa
from .colormaps import Colormap, Color # noqa

View File

@ -1,146 +0,0 @@
# -*- coding: UTF-8 no BOM -*-
# ----------------------------------------------------------- #
# Ideally the h5py should be enough to serve as the data #
# interface for future DAMASK, but since we are still not #
# sure when this major shift will happen, it seems to be a #
# good idea to provide a interface class that help user ease #
# into using HDF5 as the new daily storage driver. #
# ----------------------------------------------------------- #
import os
import h5py
import numpy as np
import xml.etree.cElementTree as ET
# ---------------------------------------------------------------- #
# python 3 has no unicode object, this ensures that the code works #
# on Python 2&3 #
# ---------------------------------------------------------------- #
try:
test = isinstance('test', unicode)
except(NameError):
unicode = str
def lables_to_path(label, dsXMLPath=None):
"""Read the XML definition file and return the path."""
if dsXMLPath is None:
# use the default storage layout in DS_HDF5.xml
if "h5table.pyc" in __file__:
dsXMLPath = os.path.abspath(__file__).replace("h5table.pyc",
"DS_HDF5.xml")
else:
dsXMLPath = os.path.abspath(__file__).replace("h5table.py",
"DS_HDF5.xml")
# This current implementation requires that all variables
# stay under the root node, the nesting is defined through the
# h5path.
# Allow new derived data to be put under the root
tree = ET.parse(dsXMLPath)
try:
dataType = tree.find('{}/type'.format(label)).text
h5path = tree.find('{}/h5path'.format(label)).text
except:
dataType = "Scalar"
h5path = "/{}".format(label) # just put it under root
return (dataType, h5path)
class H5Table(object):
"""
Lightweight interface class for h5py
DESCRIPTION
-----------
Interface/wrapper class for manipulating data in HDF5 with DAMASK
specialized data structure.
--> try to maintain a minimal API design.
PARAMETERS
----------
h5f_path: str
Absolute path of the HDF5 file
METHOD
------
del_entry() -- Force delete attributes/group/datasets (dangerous)
get_attr() -- Return attributes if possible
add_attr() -- Add NEW attributes to dataset/group (no force overwrite)
get_data() -- Retrieve data in numpy.ndarray
add_data() -- Add dataset to H5 file
get_cmdlog() -- Return the command used to generate the data if possible
NOTE
----
1. As an interface class, it uses the lazy evaluation design
that reads the data only when it is absolutely necessary.
2. The command line used to generate each new feature is stored with
each dataset as dataset attribute.
"""
def __init__(self, h5f_path, new_file=False, dsXMLFile=None):
self.h5f_path = h5f_path
self.dsXMLFile = dsXMLFile
msg = 'Created by H5Talbe from DAMASK'
mode = 'w' if new_file else 'a'
with h5py.File(self.h5f_path, mode) as h5f:
h5f['/'].attrs['description'] = msg
def del_entry(self, feature_name):
"""Delete entry in HDF5 table"""
dataType, h5f_path = lables_to_path(feature_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
del h5f[h5f_path]
def get_attr(self, attr_name):
dataType, h5f_path = lables_to_path(attr_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
rst_attr = h5f[h5f_path].attrs[attr_name]
return rst_attr
def add_attr(self, attr_name, attr_data):
dataType, h5f_path = lables_to_path(attr_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
h5f[h5f_path].attrs[attr_name] = attr_data
h5f.flush()
def get_data(self, feature_name=None):
"""Extract dataset from HDF5 table and return it in a numpy array"""
dataType, h5f_path = lables_to_path(feature_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
h5f_dst = h5f[h5f_path] # get the handle for target dataset(table)
rst_data = np.zeros(h5f_dst.shape)
h5f_dst.read_direct(rst_data)
return rst_data
def add_data(self, feature_name, dataset, cmd_log=None):
"""Adding new feature into existing HDF5 file"""
dataType, h5f_path = lables_to_path(feature_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
# NOTE:
# --> If dataset exists, delete the old one so as to write
# a new one. For brand new dataset. For brand new one,
# record its state as fresh in the cmd log.
try:
del h5f[h5f_path]
print("***deleting old {} from {}".format(feature_name,self.h5f_path))
except:
# if no cmd log, None will used
cmd_log = str(cmd_log) + " [FRESH]"
h5f.create_dataset(h5f_path, data=dataset)
# store the cmd in log is possible
if cmd_log is not None:
h5f[h5f_path].attrs['log'] = str(cmd_log)
h5f.flush()
def get_cmdlog(self, feature_name):
"""Get cmd history used to generate the feature"""
dataType, h5f_path = lables_to_path(feature_name,
dsXMLPath=self.dsXMLFile)
with h5py.File(self.h5f_path, 'a') as h5f:
cmd_logs = h5f[h5f_path].attrs['log']
return cmd_logs

View File

@ -49,7 +49,8 @@ class Test():
self.dirBase = os.path.dirname(os.path.realpath(sys.modules[self.__class__.__module__].__file__))
self.parser = OptionParser(description = '{} (Test class version: {})'.format(self.description,damask.version),
self.parser = OptionParser(option_class=damask.extendableOption,
description = '{} (Test class version: {})'.format(self.description,damask.version),
usage = './test.py [options]')
self.parser.add_option("-k", "--keep",
action = "store_true",
@ -65,7 +66,8 @@ class Test():
help = "show all test variants without actual calculation")
self.parser.add_option("-s", "--select",
dest = "select",
help = "run test of given name only")
action = 'extend', metavar = '<string LIST>',
help = "run test(s) of given name only")
self.parser.set_defaults(keep = self.keep,
accept = self.accept,
update = self.updateRequest,
@ -90,7 +92,7 @@ class Test():
if self.options.show:
logging.critical('{}: {}'.format(variant+1,name))
elif self.options.select is not None \
and not (name == self.options.select or str(variant+1) == self.options.select):
and not (name in self.options.select or str(variant+1) in self.options.select):
pass
else:
try:
@ -106,7 +108,7 @@ class Test():
return variant+1 # return culprit
except Exception as e:
logging.critical('exception during variant execution: "{}"'.format(e.message))
logging.critical('exception during variant execution: "{}"'.format(str(e)))
return variant+1 # return culprit
return 0
@ -320,7 +322,9 @@ class Test():
cur1Name = self.fileInCurrent(cur1)
return self.compare_Array(cur0Name,cur1Name)
def compare_Table(self,headings0,file0,headings1,file1,normHeadings='',normType=None,
def compare_Table(self,headings0,file0,
headings1,file1,
normHeadings='',normType=None,
absoluteTolerance=False,perLine=False,skipLines=[]):
import numpy as np
@ -366,11 +370,11 @@ class Test():
key1 = ('1_' if length[i]>1 else '') + headings1[i]['label']
normKey = ('1_' if normLength[i]>1 else '') + normHeadings[i]['label']
if key0 not in table0.labels(raw = True):
raise Exception('column {} not found in 1. table...\n'.format(key0))
raise Exception('column "{}" not found in first table...\n'.format(key0))
elif key1 not in table1.labels(raw = True):
raise Exception('column {} not found in 2. table...\n'.format(key1))
raise Exception('column "{}" not found in second table...\n'.format(key1))
elif normKey not in table0.labels(raw = True):
raise Exception('column {} not found in 1. table...\n'.format(normKey))
raise Exception('column "{}" not found in first table...\n'.format(normKey))
else:
column[0][i] = table0.label_index(key0)
column[1][i] = table1.label_index(key1)
@ -398,9 +402,9 @@ class Test():
norm[i] = [1.0 for j in range(line0-len(skipLines))]
absTol[i] = True
if perLine:
logging.warning('At least one norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
logging.warning('At least one norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
else:
logging.warning('Maximum norm of {} in 1. table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
logging.warning('Maximum norm of "{}" in first table is 0.0, using absolute tolerance'.format(headings0[i]['label']))
line1 = 0
while table1.data_read(): # read next data line of ASCII table
@ -412,7 +416,7 @@ class Test():
norm[i][line1-len(skipLines)])
line1 +=1
if (line0 != line1): raise Exception('found {} lines in 1. table but {} in 2. table'.format(line0,line1))
if (line0 != line1): raise Exception('found {} lines in first table but {} in second table'.format(line0,line1))
logging.info(' ********')
for i in range(dataLength):
@ -559,25 +563,28 @@ class Test():
return allclose
def compare_TableRefCur(self,headingsRef,ref,headingsCur='',cur='',normHeadings='',normType=None,\
def compare_TableRefCur(self,headingsRef,ref,headingsCur='',cur='',
normHeadings='',normType=None,
absoluteTolerance=False,perLine=False,skipLines=[]):
if cur == '': cur = ref
if headingsCur == '': headingsCur = headingsRef
refName = self.fileInReference(ref)
curName = self.fileInCurrent(cur)
return self.compare_Table(headingsRef,refName,headingsCur,curName,normHeadings,normType,
return self.compare_Table(headingsRef,
self.fileInReference(ref),
headingsRef if headingsCur == '' else headingsCur,
self.fileInCurrent(ref if cur == '' else cur),
normHeadings,normType,
absoluteTolerance,perLine,skipLines)
def compare_TableCurCur(self,headingsCur0,Cur0,Cur1,headingsCur1='',normHeadings='',normType=None,\
def compare_TableCurCur(self,headingsCur0,Cur0,Cur1,
headingsCur1='',
normHeadings='',normType=None,
absoluteTolerance=False,perLine=False,skipLines=[]):
if headingsCur1 == '': headingsCur1 = headingsCur0
cur0Name = self.fileInCurrent(Cur0)
cur1Name = self.fileInCurrent(Cur1)
return self.compare_Table(headingsCur0,cur0Name,headingsCur1,cur1Name,normHeadings,normType,
absoluteTolerance,perLine,skipLines)
return self.compare_Table(headingsCur0,
self.fileInCurrent(Cur0),
headingsCur0 if headingsCur1 == '' else headingsCur1,
self.fileInCurrent(Cur1),
normHeadings,normType,absoluteTolerance,perLine,skipLines)
def report_Success(self,culprit):
@ -585,13 +592,13 @@ class Test():
ret = culprit
if culprit == 0:
msg = 'The test passed.' if (self.options.select is not None or len(self.variants) == 1) \
else 'All {} tests passed.'.format(len(self.variants))
count = len(self.variants) if self.options.select is None else len(self.options.select)
msg = 'Test passed.' if count == 1 else 'All {} tests passed.'.format(count)
elif culprit == -1:
msg = 'Warning: Could not start test...'
msg = 'Warning: could not start test...'
ret = 0
else:
msg = ' * Test "{}" failed.'.format(self.variants[culprit-1])
msg = 'Test "{}" failed.'.format(self.variantName(culprit-1))
logging.critical('\n'.join(['*'*40,msg,'*'*40]) + '\n')
return ret

View File

@ -100,6 +100,18 @@ def execute(cmd,
if process.returncode != 0: raise RuntimeError('{} failed with returncode {}'.format(cmd,process.returncode))
return out,error
def coordGridAndSize(coordinates):
"""Determines grid count and overall physical size along each dimension of an ordered array of coordinates"""
dim = coordinates.shape[1]
coords = [np.unique(coordinates[:,i]) for i in range(dim)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(dim,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
return grid,size
# -----------------------------
class extendableOption(Option):
"""
@ -130,7 +142,7 @@ class backgroundMessage(threading.Thread):
'hexagon': ['', ''],
'square': ['', '', '', ''],
'triangle': ['', '', '', '', '', ''],
'amoeba': ['', '', '', '', '', '', '', ''],
'amoeba': ['', '', '', '', '', '', '', ''],
'beat': ['', '', '', '', '', '', '', '', '', '', ''],
'prison': ['', '', '', '', '', '', '', ''],
'breath': ['', '', '', '', '', '', '', '', ''],

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@ -72,6 +72,7 @@ for name in filenames:
table.head_write()
# ------------------------------------------ process data ------------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
F = np.array(map(float,table.data[column[options.defgrad]:column[options.defgrad]+9]),'d').reshape(3,3)

View File

@ -73,22 +73,17 @@ for name in filenames:
table.head_write()
# ------------------------------------------ process data ------------------------------------------
table.data_readArray()
mask = []
for col,dim in zip(columns,dims): mask += range(col,col+dim) # isolate data columns to cumulate
cumulated = np.zeros(len(mask),dtype=float) # prepare output field
cumulated = np.zeros((len(table.data),len(mask))) # prepare output field
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table
for i,col in enumerate(mask):
cumulated[i] += float(table.data[col]) # cumulate values
table.data_append(cumulated)
for i,values in enumerate(table.data[:,mask]):
cumulated[i,:] = cumulated[max(0,i-1),:] + values # cumulate values
table.data = np.hstack((table.data,cumulated))
# ------------------------------------------ output result -----------------------------------------
table.data_writeArray()
outputAlive = table.data_write() # output processed line
# ------------------------------------------ output finalization -----------------------------------

View File

@ -9,25 +9,34 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def merge_dicts(*dict_args):
"""Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
result = {}
for dictionary in dict_args:
result.update(dictionary)
return result
def curlFFT(geomdim,field):
"""Calculate curl of a vector or tensor field by transforming into Fourier space."""
shapeFFT = np.array(np.shape(field))[0:3]
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: dataType = 'vector'
elif n == 9: dataType = 'tensor'
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
curl_fourier = np.empty(field_fourier.shape,'c16')
# differentiation in Fourier space
TWOPIIMG = 2.0j*math.pi
einsums = {
3:'slm,ijkl,ijkm->ijks', # vector, 3 -> 3
9:'slm,ijkl,ijknm->ijksn', # tensor, 3x3 -> 3x3
}
k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_si = np.arange(grid[0]//2+1)/geomdim[2]
@ -38,10 +47,7 @@ def curlFFT(geomdim,field):
e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = 1.0 # Levi-Civita symbols
e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
if dataType == 'tensor': # tensor, 3x3 -> 3x3
curl_fourier = np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*TWOPIIMG
elif dataType == 'vector': # vector, 3 -> 3
curl_fourier = np.einsum('slm,ijkl,ijkm->ijks',e,k_s,field_fourier)*TWOPIIMG
curl_fourier = np.einsum(einsums[n],e,k_s,field_fourier)*TWOPIIMG
return np.fft.irfftn(curl_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n])
@ -52,31 +58,37 @@ def curlFFT(geomdim,field):
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Add column(s) containing curl of requested column(s).
Operates on periodic ordered three-dimensional data sets.
Deals with both vector- and tensor fields.
Operates on periodic ordered three-dimensional data sets
of vector and tensor fields.
""", version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
parser.add_option('-l','--label',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values')
help = 'label(s) of field values')
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
if options.vector is None and options.tensor is None:
parser.error('no data column specified.')
if options.data is None: parser.error('no data column specified.')
# --- define possible data types -------------------------------------------------------------------
datatypes = {
3: {'name': 'vector',
'shape': [3],
},
9: {'name': 'tensor',
'shape': [3,3],
},
}
# --- loop over input files ------------------------------------------------------------------------
@ -87,30 +99,27 @@ for name in filenames:
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
items = {
'tensor': {'dim': 9, 'shape': [3,3], 'labels':options.tensor, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []
column = {}
errors = []
active = []
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
coordDim = table.label_dimension(options.pos)
if coordDim != 3:
errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
else: coordCol = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):
dim = table.label_dimension(what)
if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
for me in options.data:
dim = table.label_dimension(me)
if dim in datatypes:
active.append(merge_dicts({'label':me},datatypes[dim]))
remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
else:
items[type]['active'].append(what)
items[type]['column'].append(table.label_index(what))
remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
'"{}" not found...'.format(me) )
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -121,30 +130,24 @@ for name in filenames:
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for type, data in items.iteritems():
for label in data['active']:
table.labels_append(['{}_curlFFT({})'.format(i+1,label) for i in range(data['dim'])]) # extend ASCII header with new labels
for data in active:
table.labels_append(['{}_curlFFT({})'.format(i+1,data['label'])
for i in range(np.prod(np.array(data['shape'])))]) # extend ASCII header with new labels
table.head_write()
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
# ------------------------------------------ process value field -----------------------------------
stack = [table.data]
for type, data in items.iteritems():
for i,label in enumerate(data['active']):
for data in active:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(curlFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
table.data[:,table.label_indexrange(data['label'])].
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------

121
processing/post/addDerivative.py Executable file
View File

@ -0,0 +1,121 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys
import numpy as np
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def derivative(coordinates,what):
result = np.empty_like(what)
# use differentiation by interpolation
# as described in http://www2.math.umd.edu/~dlevy/classes/amsc466/lecture-notes/differentiation-chap.pdf
result[1:-1,:] = + what[1:-1,:] * (2.*coordinates[1:-1]-coordinates[:-2]-coordinates[2:]) / \
((coordinates[1:-1]-coordinates[:-2])*(coordinates[1:-1]-coordinates[2:])) \
+ what[2:,:] * (coordinates[1:-1]-coordinates[:-2]) / \
((coordinates[2:]-coordinates[1:-1])*(coordinates[2:]-coordinates[:-2])) \
+ what[:-2,:] * (coordinates[1:-1]-coordinates[2:]) / \
((coordinates[:-2]-coordinates[1:-1])*(coordinates[:-2]-coordinates[2:])) \
result[0,:] = (what[0,:] - what[1,:]) / \
(coordinates[0] - coordinates[1])
result[-1,:] = (what[-1,:] - what[-2,:]) / \
(coordinates[-1] - coordinates[-2])
return result
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Add column(s) containing numerical derivative of requested column(s) with respect to given coordinates.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'coordinates',
type = 'string', metavar='string',
help = 'heading of coordinate column')
parser.add_option('-l','--label',
dest = 'label',
action = 'extend', metavar = '<string LIST>',
help = 'heading of column(s) to differentiate')
(options,filenames) = parser.parse_args()
if options.coordinates is None:
parser.error('no coordinate column specified.')
if options.label is None:
parser.error('no data column specified.')
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
errors = []
remarks = []
columns = []
dims = []
if table.label_dimension(options.coordinates) != 1:
errors.append('coordinate column {} is not scalar.'.format(options.coordinates))
for what in options.label:
dim = table.label_dimension(what)
if dim < 0: remarks.append('column {} not found...'.format(what))
else:
dims.append(dim)
columns.append(table.label_index(what))
table.labels_append('d({})/d({})'.format(what,options.coordinates) if dim == 1 else
['{}_d({})/d({})'.format(i+1,what,options.coordinates) for i in range(dim)] ) # extend ASCII header with new labels
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data ------------------------------------------
table.data_readArray()
mask = []
for col,dim in zip(columns,dims): mask += range(col,col+dim) # isolate data columns to differentiate
differentiated = derivative(table.data[:,table.label_index(options.coordinates)].reshape((len(table.data),1)),
table.data[:,mask]) # calculate numerical derivative
table.data = np.hstack((table.data,differentiated))
# ------------------------------------------ output result -----------------------------------------
table.data_writeArray()
# ------------------------------------------ output finalization -----------------------------------
table.close() # close ASCII tables

View File

@ -9,34 +9,41 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def merge_dicts(*dict_args):
"""Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
result = {}
for dictionary in dict_args:
result.update(dictionary)
return result
def divFFT(geomdim,field):
"""Calculate divergence of a vector or tensor field by transforming into Fourier space."""
shapeFFT = np.array(np.shape(field))[0:3]
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: dataType = 'vector'
elif n == 9: dataType = 'tensor'
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
div_fourier = np.empty(field_fourier.shape[0:len(np.shape(field))-1],'c16')
# differentiation in Fourier space
TWOPIIMG = 2.0j*math.pi
einsums = {
3:'ijkl,ijkl->ijk', # vector, 3 -> 1
9:'ijkm,ijklm->ijkl', # tensor, 3x3 -> 3
}
k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_si = np.arange(grid[0]//2+1)/geomdim[2]
kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')
if dataType == 'tensor': # tensor, 3x3 -> 3
div_fourier = np.einsum('ijklm,ijkm->ijkl',field_fourier,k_s)*TWOPIIMG
elif dataType == 'vector': # vector, 3 -> 1
div_fourier = np.einsum('ijkl,ijkl->ijk',field_fourier,k_s)*TWOPIIMG
div_fourier = np.einsum(einsums[n],k_s,field_fourier)*TWOPIIMG
return np.fft.irfftn(div_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,n/3])
@ -46,32 +53,38 @@ def divFFT(geomdim,field):
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Add column(s) containing divergence of requested column(s).
Operates on periodic ordered three-dimensional data sets.
Deals with both vector- and tensor-valued fields.
Add column(s) containing curl of requested column(s).
Operates on periodic ordered three-dimensional data sets
of vector and tensor fields.
""", version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
parser.add_option('-l','--label',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of vector field values')
parser.add_option('-t','--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values')
help = 'label(s) of field values')
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
if options.vector is None and options.tensor is None:
parser.error('no data column specified.')
if options.data is None: parser.error('no data column specified.')
# --- define possible data types -------------------------------------------------------------------
datatypes = {
3: {'name': 'vector',
'shape': [3],
},
9: {'name': 'tensor',
'shape': [3,3],
},
}
# --- loop over input files ------------------------------------------------------------------------
@ -82,30 +95,27 @@ for name in filenames:
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
items = {
'tensor': {'dim': 9, 'shape': [3,3], 'labels':options.tensor, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []
column = {}
errors = []
active = []
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
coordDim = table.label_dimension(options.pos)
if coordDim != 3:
errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
else: coordCol = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):
dim = table.label_dimension(what)
if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
for me in options.data:
dim = table.label_dimension(me)
if dim in datatypes:
active.append(merge_dicts({'label':me},datatypes[dim]))
remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
else:
items[type]['active'].append(what)
items[type]['column'].append(table.label_index(what))
remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
'"{}" not found...'.format(me) )
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -116,31 +126,25 @@ for name in filenames:
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for type, data in items.iteritems():
for label in data['active']:
table.labels_append(['divFFT({})'.format(label) if type == 'vector' else
'{}_divFFT({})'.format(i+1,label) for i in range(data['dim']//3)]) # extend ASCII header with new labels
for data in active:
table.labels_append(['divFFT({})'.format(data['label']) if data['shape'] == [3] \
else '{}_divFFT({})'.format(i+1,data['label'])
for i in range(np.prod(np.array(data['shape']))//3)]) # extend ASCII header with new labels
table.head_write()
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
# ------------------------------------------ process value field -----------------------------------
stack = [table.data]
for type, data in items.iteritems():
for i,label in enumerate(data['active']):
for data in active:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(divFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
table.data[:,table.label_indexrange(data['label'])].
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------

View File

@ -18,7 +18,7 @@ scriptID = ' '.join([scriptName,damask.version])
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Add column(s) containing Gaussian filtered values of requested column(s).
Operates on periodic and non-periodic ordered three-dimensional data sets.
For Details see scipy.ndimage documentation.
For details see scipy.ndimage documentation.
""", version = scriptID)
@ -43,15 +43,14 @@ parser.add_option('--sigma',
parser.add_option('--periodic',
dest = 'periodic',
action = 'store_true',
help = 'assume periodic grain structure'
)
help = 'assume periodic grain structure')
parser.set_defaults(pos = 'pos',
order = 0,
sigma = 1,
periodic = False
periodic = False,
)
(options,filenames) = parser.parse_args()
@ -110,12 +109,7 @@ for name in filenames:
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
# ------------------------------------------ process value field -----------------------------------

View File

@ -9,34 +9,41 @@ import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
def merge_dicts(*dict_args):
"""Given any number of dicts, shallow copy and merge into a new dict, with precedence going to key value pairs in latter dicts."""
result = {}
for dictionary in dict_args:
result.update(dictionary)
return result
def gradFFT(geomdim,field):
"""Calculate gradient of a vector or scalar field by transforming into Fourier space."""
shapeFFT = np.array(np.shape(field))[0:3]
grid = np.array(np.shape(field)[2::-1])
N = grid.prod() # field size
n = np.array(np.shape(field)[3:]).prod() # data size
if n == 3: dataType = 'vector'
elif n == 1: dataType = 'scalar'
field_fourier = np.fft.rfftn(field,axes=(0,1,2),s=shapeFFT)
grad_fourier = np.empty(field_fourier.shape+(3,),'c16')
# differentiation in Fourier space
TWOPIIMG = 2.0j*math.pi
einsums = {
1:'ijkl,ijkm->ijkm', # scalar, 1 -> 3
3:'ijkl,ijkm->ijklm', # vector, 3 -> 3x3
}
k_sk = np.where(np.arange(grid[2])>grid[2]//2,np.arange(grid[2])-grid[2],np.arange(grid[2]))/geomdim[0]
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[2]%2 == 0: k_sk[grid[2]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/geomdim[1]
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # for even grid, set Nyquist freq to 0 (Johnson, MIT, 2011)
if grid[1]%2 == 0: k_sj[grid[1]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
k_si = np.arange(grid[0]//2+1)/geomdim[2]
kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
k_s = np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3).astype('c16')
if dataType == 'vector': # vector, 3 -> 3x3
grad_fourier = np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*TWOPIIMG
elif dataType == 'scalar': # scalar, 1 -> 3
grad_fourier = np.einsum('ijkl,ijkl->ijkl',field_fourier,k_s)*TWOPIIMG
grad_fourier = np.einsum(einsums[n],field_fourier,k_s)*TWOPIIMG
return np.fft.irfftn(grad_fourier,axes=(0,1,2),s=shapeFFT).reshape([N,3*n])
@ -47,8 +54,8 @@ def gradFFT(geomdim,field):
parser = OptionParser(option_class=damask.extendableOption, usage='%prog option(s) [ASCIItable(s)]', description = """
Add column(s) containing gradient of requested column(s).
Operates on periodic ordered three-dimensional data sets.
Deals with both vector- and scalar fields.
Operates on periodic ordered three-dimensional data sets
of vector and scalar fields.
""", version = scriptID)
@ -56,22 +63,28 @@ parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
dest = 'vector',
parser.add_option('-l','--label',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of vector field values')
parser.add_option('-s','--scalar',
dest = 'scalar',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of scalar field values')
help = 'label(s) of field values')
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
if options.vector is None and options.scalar is None:
parser.error('no data column specified.')
if options.data is None: parser.error('no data column specified.')
# --- define possible data types -------------------------------------------------------------------
datatypes = {
1: {'name': 'scalar',
'shape': [1],
},
3: {'name': 'vector',
'shape': [3],
},
}
# --- loop over input files ------------------------------------------------------------------------
@ -82,30 +95,27 @@ for name in filenames:
except: continue
damask.util.report(scriptName,name)
# ------------------------------------------ read header ------------------------------------------
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
items = {
'scalar': {'dim': 1, 'shape': [1], 'labels':options.scalar, 'active':[], 'column': []},
'vector': {'dim': 3, 'shape': [3], 'labels':options.vector, 'active':[], 'column': []},
}
errors = []
remarks = []
column = {}
errors = []
active = []
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
coordDim = table.label_dimension(options.pos)
if coordDim != 3:
errors.append('coordinates "{}" must be three-dimensional.'.format(options.pos))
else: coordCol = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):
dim = table.label_dimension(what)
if dim != data['dim']: remarks.append('column {} is not a {}.'.format(what,type))
for me in options.data:
dim = table.label_dimension(me)
if dim in datatypes:
active.append(merge_dicts({'label':me},datatypes[dim]))
remarks.append('differentiating {} "{}"...'.format(datatypes[dim]['name'],me))
else:
items[type]['active'].append(what)
items[type]['column'].append(table.label_index(what))
remarks.append('skipping "{}" of dimension {}...'.format(me,dim) if dim != -1 else \
'"{}" not found...'.format(me) )
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -116,30 +126,24 @@ for name in filenames:
# ------------------------------------------ assemble header --------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
for type, data in items.iteritems():
for label in data['active']:
table.labels_append(['{}_gradFFT({})'.format(i+1,label) for i in range(3 * data['dim'])]) # extend ASCII header with new labels
for data in active:
table.labels_append(['{}_gradFFT({})'.format(i+1,data['label'])
for i in range(coordDim*np.prod(np.array(data['shape'])))]) # extend ASCII header with new labels
table.head_write()
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray()
coords = [np.unique(table.data[:,colCoord+i]) for i in range(3)]
mincorner = np.array(map(min,coords))
maxcorner = np.array(map(max,coords))
grid = np.array(map(len,coords),'i')
size = grid/np.maximum(np.ones(3,'d'), grid-1.0) * (maxcorner-mincorner) # size from edge to edge = dim * n/(n-1)
size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other ones
grid,size = damask.util.coordGridAndSize(table.data[:,table.label_indexrange(options.pos)])
# ------------------------------------------ process value field -----------------------------------
stack = [table.data]
for type, data in items.iteritems():
for i,label in enumerate(data['active']):
for data in active:
# we need to reverse order here, because x is fastest,ie rightmost, but leftmost in our x,y,z notation
stack.append(gradFFT(size[::-1],
table.data[:,data['column'][i]:data['column'][i]+data['dim']].
table.data[:,table.label_indexrange(data['label'])].
reshape(grid[::-1].tolist()+data['shape'])))
# ------------------------------------------ output result -----------------------------------------

View File

@ -49,7 +49,8 @@ for name in filenames:
table.head_read()
# ------------------------------------------ sanity checks ----------------------------------------
# ------------------------------------------ assemble header 1 ------------------------------------
items = {
'tensor': {'dim': 9, 'shape': [3,3], 'labels':options.tensor, 'column': []},
@ -74,12 +75,12 @@ for name in filenames:
table.close(dismiss = True)
continue
# ------------------------------------------ assemble header --------------------------------------
# ------------------------------------------ assemble header 2 ------------------------------------
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.head_write()
# ------------------------------------------ process data ------------------------------------------
# ------------------------------------------ process data -----------------------------------------
outputAlive = True
while outputAlive and table.data_read(): # read next data line of ASCII table

View File

@ -1,72 +0,0 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
# import re
# import sys
import collections
# import math
import damask
# import numpy as np
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# ----- Helper functions ----- #
def listify(x):
return x if isinstance(x, collections.Iterable) else [x]
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
usageEx = """
usage_in_details:
Column labels are tagged by '#label#' in formulas.
Use ';' for ',' in functions. Numpy is available as 'np'.
Special variables: #_row_# -- row index
Examples:
(1) magnitude of vector -- "np.linalg.norm(#vec#)"
(2) rounded root of row number -- "round(math.sqrt(#_row_#);3)"
"""
desp = "Add or alter column(s) with derived values according to "
desp += "user-defined arithmetic operation between column(s)."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]' + usageEx,
description=desp,
version=scriptID)
parser.add_option('-l', '--label',
dest='labels',
action='extend', metavar='<string LIST>',
help='(list of) new column labels')
parser.add_option('-f', '--formula',
dest='formulas',
action='extend', metavar='<string LIST>',
help='(list of) formulas corresponding to labels')
parser.add_option('-c', '--condition',
dest='condition', metavar='string',
help='condition to filter rows')
parser.set_defaults(condition=None)
(options, filenames) = parser.parse_args()
# ----- parse formulas ----- #
for i in range(len(options.formulas)):
options.formulas[i] = options.formulas[i].replace(';', ',')
# ----- loop over input files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
print("!!!Cannot process {}".format(name))
continue
damask.util.report(scriptName, name)
# Note:
# --> not immediately needed, come back later

View File

@ -1,61 +0,0 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
import damask
import numpy as np
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
def getCauchy(f, p):
"""Return Cauchy stress for given f and p"""
# [Cauchy] = (1/det(F)) * [P].[F_transpose]
f = f.reshape((3, 3))
p = p.reshape((3, 3))
return 1.0/np.linalg.det(f)*np.dot(p, f.T).reshape(9)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
desp = "Add column(s) containing Cauchy stress based on given column(s)"
desp += "of deformation gradient and first Piola--Kirchhoff stress."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=desp,
version=scriptID)
parser.add_option('-f', '--defgrad',
dest='defgrad',
type='string', metavar='string',
help='heading for deformation gradient [%default]')
parser.add_option('-p', '--stress',
dest='stress',
type='string', metavar='string',
help='heading for first Piola--Kirchhoff stress [%default]')
parser.set_defaults(defgrad='f',
stress='p')
(options, filenames) = parser.parse_args()
# ----- loop over input H5 files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
continue
damask.util.report(scriptName, name)
# ----- read in data ----- #
f = h5f.get_data("f")
p = h5f.get_data("p")
# ----- calculate Cauchy stress ----- #
cauchy = [getCauchy(f_i, p_i) for f_i, p_i in zip(f, p)]
# ----- write to HDF5 file ----- #
cmd_log = " ".join([scriptID, name])
h5f.add_data('Cauchy', np.array(cauchy), cmd_log=cmd_log)

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
import sys
import math
import damask
import numpy as np
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# TODO
# This implementation will have to iterate through the array one
# element at a time, maybe there are some other ways to make this
# faster.
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
desp = "Add RGB color value corresponding to TSL-OIM scheme for IPF."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=desp,
version=scriptID)
parser.add_option('-p', '--pole',
dest='pole',
type='float', nargs=3, metavar='float float float',
help='lab frame direction for IPF [%default]')
msg = ', '.join(damask.Symmetry.lattices[1:])
parser.add_option('-s', '--symmetry',
dest='symmetry',
type='choice', choices=damask.Symmetry.lattices[1:],
metavar='string',
help='crystal symmetry [%default] {{{}}} '.format(msg))
parser.add_option('-e', '--eulers',
dest='eulers',
type='string', metavar='string',
help='Euler angles label')
parser.add_option('-d', '--degrees',
dest='degrees',
action='store_true',
help='Euler angles are given in degrees [%default]')
parser.add_option('-m', '--matrix',
dest='matrix',
type='string', metavar='string',
help='orientation matrix label')
parser.add_option('-a',
dest='a',
type='string', metavar='string',
help='crystal frame a vector label')
parser.add_option('-b',
dest='b',
type='string', metavar='string',
help='crystal frame b vector label')
parser.add_option('-c',
dest='c',
type='string', metavar='string',
help='crystal frame c vector label')
parser.add_option('-q', '--quaternion',
dest='quaternion',
type='string', metavar='string',
help='quaternion label')
parser.set_defaults(pole=(0.0, 0.0, 1.0),
symmetry=damask.Symmetry.lattices[-1],
degrees=False)
(options, filenames) = parser.parse_args()
# safe guarding to have only one orientation representation
# use dynamic typing to group a,b,c into frame
options.frame = [options.a, options.b, options.c]
input = [options.eulers is not None,
all(options.frame),
options.matrix is not None,
options.quaternion is not None]
if np.sum(input) != 1:
parser.error('needs exactly one input format.')
# select input label that was requested (active)
label_active = np.where(input)[0][0]
(label, dim, inputtype) = [(options.eulers, 3, 'eulers'),
(options.frame, [3, 3, 3], 'frame'),
(options.matrix, 9, 'matrix'),
(options.quaternion, 4, 'quaternion')][label_active]
# rescale degrees to radians
toRadians = math.pi/180.0 if options.degrees else 1.0
# only use normalized pole
pole = np.array(options.pole)
pole /= np.linalg.norm(pole)
# ----- Loop over input files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
continue
damask.util.report(scriptName, name)
# extract data from HDF5 file
if inputtype == 'eulers':
orieData = h5f.get_data(label)
elif inputtype == 'matrix':
orieData = h5f.get_data(label)
orieData = orieData.reshape(orieData.shape[0], 3, 3)
elif inputtype == 'frame':
vctr_a = h5f.get_data(label[0])
vctr_b = h5f.get_data(label[1])
vctr_c = h5f.get_data(label[2])
frame = np.column_stack((vctr_a, vctr_b, vctr_c))
orieData = frame.reshape(frame.shape[0], 3, 3)
elif inputtype == 'quaternion':
orieData = h5f.get_data(label)
# calculate the IPF color
rgbArrays = np.zeros((orieData.shape[0], 3))
for ci in range(rgbArrays.shape[0]):
if inputtype == 'eulers':
o = damask.Orientation(Eulers=np.array(orieData[ci, :])*toRadians,
symmetry=options.symmetry).reduced()
elif inputtype == 'matrix':
o = damask.Orientation(matrix=orieData[ci, :, :].transpose(),
symmetry=options.symmetry).reduced()
elif inputtype == 'frame':
o = damask.Orientation(matrix=orieData[ci, :, :],
symmetry=options.symmetry).reduced()
elif inputtype == 'quaternion':
o = damask.Orientation(quaternion=orieData[ci, :],
symmetry=options.symmetry).reduced()
rgbArrays[ci, :] = o.IPFcolor(pole)
# compose labels/headers for IPF color (RGB)
labelIPF = 'IPF_{:g}{:g}{:g}_{sym}'.format(*options.pole,
sym=options.symmetry.lower())
# compose cmd history (go with dataset)
cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
# write data to HDF5 file
h5f.add_data(labelIPF, rgbArrays, cmd_log=cmd_log)

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
import sys
import math
import damask
import numpy as np
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# ----- Helper functions ----- #
def calcMises(what, tensor):
"""Calculate von Mises equivalent"""
dev = tensor - np.trace(tensor)/3.0*np.eye(3)
symdev = 0.5*(dev+dev.T)
return math.sqrt(np.sum(symdev*symdev.T) *
{
'stress': 3.0/2.0,
'strain': 2.0/3.0,
}[what.lower()])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
desp = "Add von Mises equivalent values for symmetric part of requested"
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=desp,
version=scriptID)
parser.add_option('-e', '--strain',
dest='strain',
metavar='string',
help='name of dataset containing strain tensors')
parser.add_option('-s', '--stress',
dest='stress',
metavar='string',
help='name of dataset containing stress tensors')
parser.set_defaults(strain=None, stress=None)
(options, filenames) = parser.parse_args()
# ----- Loop over input files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
continue
damask.util.report(scriptName, name)
# TODO:
# Could use some refactoring here
if options.stress is not None:
# extract stress tensor from HDF5
tnsr = h5f.get_data(options.stress)
# calculate von Mises equivalent row by row
vmStress = np.zeros(tnsr.shape[0])
for ri in range(tnsr.shape[0]):
stressTnsr = tnsr[ri, :].reshape(3, 3)
vmStress[ri] = calcMises('stress', stressTnsr)
# compose label
label = "Mises{}".format(options.stress)
# prepare log info
cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
# write data to HDF5 file
h5f.add_data(label, vmStress, cmd_log=cmd_log)
if options.strain is not None:
tnsr = h5f.get_data(options.strain)
vmStrain = np.zeros(tnsr.shape[0])
for ri in range(tnsr.shape[0]):
strainTnsr = tnsr[ri, :].reshape(3, 3)
vmStrain[ri] = calcMises('strain', strainTnsr)
label = "Mises{}".format(options.strain)
cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
h5f.add_data(label, vmStrain, cmd_log=cmd_log)

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
import sys
import damask
import numpy as np
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# ----- Helper functions ----- #
def operator(stretch, strain, eigenvalues):
# Albrecht Bertram: Elasticity and Plasticity of Large Deformations
# An Introduction (3rd Edition, 2012), p. 102
return {'V#ln': np.log(eigenvalues),
'U#ln': np.log(eigenvalues),
'V#Biot': (np.ones(3, 'd') - 1.0/eigenvalues),
'U#Biot': (eigenvalues - np.ones(3, 'd')),
'V#Green': (np.ones(3, 'd') - 1.0/eigenvalues/eigenvalues)*0.5,
'U#Green': (eigenvalues*eigenvalues - np.ones(3, 'd'))*0.5,
}[stretch+'#'+strain]
def calcEPS(defgrads, stretchType, strainType):
"""Calculate specific type of strain tensor"""
eps = np.zeros(defgrads.shape) # initialize container
# TODO:
# this loop can use some performance boost
# (multi-threading?)
for ri in range(defgrads.shape[0]):
f = defgrads[ri, :].reshape(3, 3)
U, S, Vh = np.linalg.svd(f)
R = np.dot(U, Vh) # rotation of polar decomposition
if stretchType == 'U':
stretch = np.dot(np.linalg.inv(R), f) # F = RU
elif stretchType == 'V':
stretch = np.dot(f, np.linalg.inv(R)) # F = VR
# kill nasty noisy data
stretch = np.where(abs(stretch) < 1e-12, 0, stretch)
(D, V) = np.linalg.eig(stretch)
# flip principal component with negative Eigen values
neg = np.where(D < 0.0)
D[neg] *= -1.
V[:, neg] *= -1.
# check each vector for orthogonality
# --> brutal force enforcing orthogonal base
# and re-normalize
for i, eigval in enumerate(D):
if np.dot(V[:, i], V[:, (i+1) % 3]) != 0.0:
V[:, (i+1) % 3] = np.cross(V[:, (i+2) % 3], V[:, i])
V[:, (i+1) % 3] /= np.sqrt(np.dot(V[:, (i+1) % 3],
V[:, (i+1) % 3].conj()))
# calculate requested version of strain tensor
d = operator(stretchType, strainType, D)
eps[ri] = (np.dot(V, np.dot(np.diag(d), V.T)).real).reshape(9)
return eps
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
desp = "Add column(s) containing given strains based on given stretches"
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=desp,
version=scriptID)
msg = 'material strains based on right Cauchy-Green deformation, i.e., C and U'
parser.add_option('-u', '--right',
dest='right',
action='store_true',
help=msg)
msg = 'spatial strains based on left Cauchy--Green deformation, i.e., B and V'
parser.add_option('-v', '--left',
dest='left',
action='store_true',
help=msg)
parser.add_option('-0', '--logarithmic',
dest='logarithmic',
action='store_true',
help='calculate logarithmic strain tensor')
parser.add_option('-1', '--biot',
dest='biot',
action='store_true',
help='calculate biot strain tensor')
parser.add_option('-2', '--green',
dest='green',
action='store_true',
help='calculate green strain tensor')
# NOTE:
# It might be easier to just calculate one type of deformation gradient
# at a time.
msg = 'heading(s) of columns containing deformation tensor values'
parser.add_option('-f', '--defgrad',
dest='defgrad',
action='extend',
metavar='<string LIST>',
help=msg)
parser.set_defaults(right=False, left=False,
logarithmic=False, biot=False, green=False,
defgrad='f')
(options, filenames) = parser.parse_args()
stretches = []
strains = []
if options.right:
stretches.append('U')
if options.left:
stretches.append('V')
if options.logarithmic:
strains.append('ln')
if options.biot:
strains.append('Biot')
if options.green:
strains.append('Green')
if options.defgrad is None:
parser.error('no data column specified.')
# ----- Loop over input files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
continue
damask.util.report(scriptName, name)
# extract defgrads from HDF5 storage
F = h5f.get_data(options.defgrad)
# allow calculate multiple types of strain within the
# same cmd call
for stretchType in stretches:
for strainType in strains:
# calculate strain tensor for this type
eps = calcEPS(F, stretchType, strainType)
# compose labels/headers for this strain tensor
labelsStrain = strainType + stretchType
# prepare log info
cmd_log = scriptID + '\t' + ' '.join(sys.argv[1:])
# write data to HDF5 file
h5f.add_data(labelsStrain, eps, cmd_log=cmd_log)

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
# ------------------------------------------------------------------- #
# NOTE: #
# 1. Current Xdmf rendering in Paraview has some memory issue where #
# large number of polyvertices will cause segmentation fault. By #
# default, paraview output a cell based xdmf description, which #
# is working for small and medium mesh (<10,000) points. Hence a #
# rectangular mesh is used as the de facto Geometry description #
# here. #
# 2. Due to the unstable state Xdmf, it is safer to use port data #
# to VTR rather than using xdmf as interpretive layer for data #
# visualization. #
# ------------------------------------------------------------------- #
import os
import damask
import h5py
import xml.etree.cElementTree as ET
from optparse import OptionParser
from xml.dom import minidom
from damask.h5table import lables_to_path
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# ----- HELPER FUNCTIONS -----#
def addTopLvlCmt(xmlstr, topLevelCmt):
"""Add top level comment to string from ET"""
# a quick hack to add the top level comment to XML file
# --> somehow Elementtree does not provide this functionality
# --> by default
strList = xmlstr.split("\n")
strList[0] += "\n"+topLevelCmt
return "\n".join(strList)
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
msg = 'Generate Xdmf wrapper for HDF5 file.'
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description = msg,
version = scriptID)
(options, filenames) = parser.parse_args()
h5f = filenames[0]
h5f_base = h5f.split("/")[-1]
# ----- parse HDF5 file ----- #
h5f_dataDim = {}
h5f_dataPath = {}
h5f_dataType = {}
with h5py.File(h5f, 'a') as f:
labels = f.keys()
labels += f['/Constitutive'].keys()
labels += f['/Crystallite'].keys()
labels += ['Vx', 'Vy', "Vz"]
# remove group names as they do not contain real data
# TODO: use h5py/H5table API to detect dataset name to
# avoid necessary name space pruning.
labels.remove('Constitutive')
labels.remove('Crystallite')
labels.remove('Geometry')
# loop through remaining labels
for label in labels:
dataType, h5Path = lables_to_path(label)
h5f_dataType[label] = dataType
h5f_dataDim[label] = " ".join(map(str,f[h5Path].shape))
h5f_dataPath[label] = h5Path
# ----- constructing xdmf elements ----- #
root = ET.Element("Xdmf", version='3.3')
root.set('xmlns:xi', "http://www.w3.org/2001/XInclude")
root.append(ET.Comment('Generated Xdmf wapper for DAMASH H5 output'))
# usually there should only be ONE domain
domain = ET.SubElement(root, 'Domain',
Name=h5f_base.split(".")[0])
# use global topology through reference
grid = ET.SubElement(domain, 'Grid', GridType="Uniform")
# geometry section
geometry = ET.SubElement(grid, 'Geometry', GeometryType="VXVYVZ")
for vector in ["Vz", "Vy", "Vx"]:
dataitem = ET.SubElement(geometry, "DataItem",
DataType="Float",
Dimensions=h5f_dataDim[vector],
Name=vector,
Format="HDF")
dataitem.text = h5f_base.split("/")[-1] + ":{}".format(h5f_dataPath[vector])
# topology section
# TODO: support for other format based on given option
meshDim = [h5f_dataDim["Vz"], h5f_dataDim["Vy"], h5f_dataDim["Vx"]]
topology = ET.SubElement(grid, 'Topology',
TopologyType="3DRectMesh",
Dimensions=" ".join(map(str, meshDim)))
# attributes section
# Question: how to properly handle data mapping for multiphase situations
labelsProcessed = ['Vx', 'Vy', 'Vz']
# walk through each attributes
for label in labels:
if label in labelsProcessed: continue
print("adding {}...".format(label))
attr = ET.SubElement(grid, 'Attribute',
Name=label,
Type="None",
Center="Cell")
dataitem = ET.SubElement(attr, 'DataItem',
Name=label,
Format='HDF',
Dimensions=h5f_dataDim[label])
dataitem.text = h5f_base + ":" + h5f_dataPath[label]
# update progress list
labelsProcessed.append(label)
# pretty print the xdmf(xml) file content
xmlstr = minidom.parseString(ET.tostring(root)).toprettyxml(indent="\t")
xmlstr = addTopLvlCmt(xmlstr, '<!DOCTYPE Xdmf SYSTEM "Xdmf.dtd" []>')
# write str to file through native python API
with open(h5f.replace(".h5", ".xmf"), 'w') as f:
f.write(xmlstr)

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#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os
import vtk
import damask
from vtk.util import numpy_support
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
msg = "Add scalars, vectors, and/or an RGB tuple from"
msg += "an HDF5 to existing VTK rectilinear grid (.vtr/.vtk)."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=msg,
version=scriptID)
parser.add_option('--vtk',
dest='vtk',
type='string', metavar='string',
help='VTK file name')
parser.add_option('--inplace',
dest='inplace',
action='store_true',
help='modify VTK file in-place')
parser.add_option('-r', '--render',
dest='render',
action='store_true',
help='open output in VTK render window')
parser.add_option('-d', '--data',
dest='data',
action='extend', metavar='<string LIST>',
help='scalar/vector value(s) label(s)')
parser.add_option('-t', '--tensor',
dest='tensor',
action='extend', metavar='<string LIST>',
help='tensor (3x3) value label(s)')
parser.add_option('-c', '--color',
dest='color',
action='extend', metavar='<string LIST>',
help='RGB color tuple label')
parser.add_option('-m',
'--mode',
dest='mode',
metavar='string',
type='choice', choices=['cell', 'point'],
help='cell-centered or point-centered coordinates')
parser.set_defaults(data=[],
tensor=[],
color=[],
mode='cell',
inplace=False,
render=False)
(options, filenames) = parser.parse_args()
# ----- Legacy VTK format support ----- #
if os.path.splitext(options.vtk)[1] == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
reader.SetFileName(options.vtk)
reader.Update()
rGrid = reader.GetOutput()
elif os.path.splitext(options.vtk)[1] == '.vtk':
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(options.vtk)
reader.Update()
rGrid = reader.GetRectilinearGridOutput()
else:
parser.error('Unsupported VTK file type extension.')
Npoints = rGrid.GetNumberOfPoints()
Ncells = rGrid.GetNumberOfCells()
# ----- Summary output (Sanity Check) ----- #
msg = '{}: {} points and {} cells...'.format(options.vtk,
Npoints,
Ncells)
damask.util.croak(msg)
# ----- Read HDF5 file ----- #
# NOTE:
# --> It is possible in the future we are trying to add data
# from different increment into the same VTK file, but
# this feature is not supported for the moment.
# --> Let it fail, if the HDF5 is invalid, python interpretor
# --> should be able to catch this error.
h5f = damask.H5Table(filenames[0], new_file=False)
# ----- Process data ----- #
featureToAdd = {'data': options.data,
'tensor': options.tensor,
'color': options.color}
VTKarray = {} # store all vtkData in dict, then ship them to file
for dataType in featureToAdd.keys():
featureNames = featureToAdd[dataType]
for featureName in featureNames:
VTKtype = vtk.VTK_DOUBLE
VTKdata = h5f.get_data(featureName)
if dataType == 'color':
VTKtype = vtk.VTK_UNSIGNED_CHAR
VTKdata = (VTKdata*255).astype(int)
elif dataType == 'tensor':
# Force symmetries tensor type data
VTKdata[:, 1] = VTKdata[:, 3] = 0.5*(VTKdata[:, 1]+VTKdata[:, 3])
VTKdata[:, 2] = VTKdata[:, 6] = 0.5*(VTKdata[:, 2]+VTKdata[:, 6])
VTKdata[:, 5] = VTKdata[:, 7] = 0.5*(VTKdata[:, 5]+VTKdata[:, 7])
# use vtk build-in numpy support to add data (much faster)
# NOTE:
# --> deep copy is necessary here, otherwise memory leak could occur
VTKarray[featureName] = numpy_support.numpy_to_vtk(num_array=VTKdata,
deep=True,
array_type=VTKtype)
VTKarray[featureName].SetName(featureName)
# ----- ship data to vtkGrid ----- #
mode = options.mode
damask.util.croak('{} mode...'.format(mode))
# NOTE:
# --> For unknown reason, Paraview only recognize one
# tensor attributes per cell, thus it would be safe
# to only add one attributes as tensor.
for dataType in featureToAdd.keys():
featureNames = featureToAdd[dataType]
for featureName in featureNames:
if dataType == 'color':
if mode == 'cell':
rGrid.GetCellData().SetScalars(VTKarray[featureName])
elif mode == 'point':
rGrid.GetPointData().SetScalars(VTKarray[featureName])
elif dataType == 'tensor':
if mode == 'cell':
rGrid.GetCellData().SetTensors(VTKarray[featureName])
elif mode == 'point':
rGrid.GetPointData().SetTensors(VTKarray[featureName])
else:
if mode == 'cell':
rGrid.GetCellData().AddArray(VTKarray[featureName])
elif mode == 'point':
rGrid.GetPointData().AddArray(VTKarray[featureName])
rGrid.Modified()
if vtk.VTK_MAJOR_VERSION <= 5:
rGrid.Update()
# ----- write Grid to VTK file ----- #
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
vtkFileN = os.path.splitext(options.vtk)[0]
vtkExtsn = '.vtr' if options.inplace else '_added.vtr'
writer.SetFileName(vtkFileN+vtkExtsn)
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(rGrid)
else:
writer.SetInputData(rGrid)
writer.Write()
# ----- render results from script ----- #
if options.render:
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(rGrid)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create the graphics structure. The renderer renders into the
# render window. The render window interactor captures mouse events
# and will perform appropriate camera or actor manipulation
# depending on the nature of the events.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
ren.AddActor(actor)
ren.SetBackground(1, 1, 1)
renWin.SetSize(200, 200)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.Initialize()
renWin.Render()
iren.Start()

View File

@ -1,135 +0,0 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
# ------------------------------------------------------------------ #
# NOTE: #
# 1. It might be a good idea to separate IO and calculation. #
# 2. Some of the calculation could be useful in other situations, #
# why not build a math_util, or math_sup module that contains #
# all the useful functions. #
# ------------------------------------------------------------------ #
import os
import vtk
import numpy as np
import damask
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
# ----- HELPER FUNCTION ----- #
def getMeshFromXYZ(xyzArray, mode):
"""Calc Vx,Vy,Vz vectors for vtk rectangular mesh"""
# NOTE:
# --> np.unique will automatically sort the list
# --> although not exactly n(1), but since mesh dimension should
# small anyway, so this is still light weight.
dim = xyzArray.shape[1] # 2D:2, 3D:3
coords = [np.unique(xyzArray[:, i]) for i in range(dim)]
if mode == 'cell':
# since x, y, z might now have the same number of elements,
# we have to deal with them individually
for ri in range(dim):
vctr_pt = coords[ri]
vctr_cell = np.empty(len(vctr_pt)+1)
# calculate first and last end point
vctr_cell[0] = vctr_pt[0] - 0.5*abs(vctr_pt[1] - vctr_pt[0])
vctr_cell[-1] = vctr_pt[-1] + 0.5*abs(vctr_pt[-2] - vctr_pt[-1])
for cj in range(1, len(vctr_cell)-1):
vctr_cell[cj] = 0.5*(vctr_pt[cj-1] + vctr_pt[cj])
# update the coords
coords[ri] = vctr_cell
if dim < 3:
coords.append([0]) # expand to a 3D with 0 for z
# auxiliary description
grid = np.array(map(len, coords), 'i')
N = grid.prod() if mode == 'point' else (grid-1).prod()
return coords, grid, N
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
msg = "Create regular voxel grid from points in an ASCIItable."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description=msg,
version=scriptID)
parser.add_option('-m',
'--mode',
dest='mode',
metavar='string',
type='choice', choices=['cell', 'point'],
help='cell-centered or point-centered coordinates')
parser.add_option('-p',
'--pos', '--position',
dest='pos',
type='string', metavar='string',
help='label of coordinates [%default]')
parser.set_defaults(mode='cell',
pos='pos')
(options, filenames) = parser.parse_args()
# ----- loop over input files ----- #
for name in filenames:
try:
h5f = damask.H5Table(name, new_file=False)
except:
continue
damask.util.report(scriptName, name)
# ----- read xyzArray from HDF5 file ----- #
xyzArray = h5f.get_data(options.pos)
# ----- figure out size and grid ----- #
coords, grid, N = getMeshFromXYZ(xyzArray, options.mode)
# ----- process data ----- #
rGrid = vtk.vtkRectilinearGrid()
# WARNING: list expansion does not work here as these are
# just pointers for a vtk instance. Simply put,
# DON't USE
# [<VTK_CONSTRUCTOR>] * <NUM_OF_ELEMENTS>
coordArray = [vtk.vtkDoubleArray(),
vtk.vtkDoubleArray(),
vtk.vtkDoubleArray()]
rGrid.SetDimensions(*grid)
for i, points in enumerate(coords):
for point in points:
coordArray[i].InsertNextValue(point)
rGrid.SetXCoordinates(coordArray[0])
rGrid.SetYCoordinates(coordArray[1])
rGrid.SetZCoordinates(coordArray[2])
# ----- output result ----- #
dirPath = os.path.split(name)[0]
if name:
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetCompressorTypeToZLib()
writer.SetDataModeToBinary()
# getting the name is a little bit tricky
vtkFileName = os.path.splitext(os.path.split(name)[1])[0]
vtkFileName += '_{}({})'.format(options.pos, options.mode)
vtkFileName += '.' + writer.GetDefaultFileExtension()
writer.SetFileName(os.path.join(dirPath, vtkFileName))
else:
writer = vtk.vtkDataSetWriter()
writer.SetHeader('# powered by '+scriptID)
writer.WriteToOutputStringOn()
if vtk.VTK_MAJOR_VERSION <= 5:
writer.SetInput(rGrid)
else:
writer.SetInputData(rGrid)
writer.Write()

199
processing/post/marc_to_vtk.py Executable file
View File

@ -0,0 +1,199 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,sys,re
import argparse
import damask
import vtk, numpy as np
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName, damask.version])
parser = argparse.ArgumentParser(description='Convert from Marc input file format (.dat) to VTK format (.vtu)', version = scriptID)
parser.add_argument('filename', type=str, help='file to convert')
parser.add_argument('-t', '--table', type=str, help='ASCIItable file containing nodal data to subdivide and interpolate')
args = parser.parse_args()
with open(args.filename, 'r') as marcfile:
marctext = marcfile.read();
# Load table (if any)
if args.table is not None:
try:
table = damask.ASCIItable(
name=args.table,
outname='subdivided_{}'.format(args.table),
buffered=True
)
table.head_read()
table.data_readArray()
# Python list is faster for appending
nodal_data = list(table.data)
except: args.table = None
# Extract connectivity chunk from file...
connectivity_text = re.findall(r'connectivity[\n\r]+(.*?)[\n\r]+[a-zA-Z]', marctext, flags=(re.MULTILINE | re.DOTALL))[0]
connectivity_lines = re.split(r'[\n\r]+', connectivity_text, flags=(re.MULTILINE | re.DOTALL))
connectivity_header = connectivity_lines[0]
connectivity_lines = connectivity_lines[1:]
# Construct element map
elements = dict(map(lambda line:
(
int(line[0:10]), # index
{
'type': int(line[10:20]),
'verts': list(map(int, re.split(r' +', line[20:].strip())))
}
), connectivity_lines))
# Extract coordinate chunk from file
coordinates_text = re.findall(r'coordinates[\n\r]+(.*?)[\n\r]+[a-zA-Z]', marctext, flags=(re.MULTILINE | re.DOTALL))[0]
coordinates_lines = re.split(r'[\n\r]+', coordinates_text, flags=(re.MULTILINE | re.DOTALL))
coordinates_header = coordinates_lines[0]
coordinates_lines = coordinates_lines[1:]
# marc input file does not use "e" in scientific notation, this adds it and converts
fl_format = lambda string: float(re.sub(r'(\d)([\+\-])', r'\1e\2', string))
# Construct coordinate map
coordinates = dict(map(lambda line:
(
int(line[0:10]),
np.array([
fl_format(line[10:30]),
fl_format(line[30:50]),
fl_format(line[50:70])
])
), coordinates_lines))
# Subdivide volumes
grid = vtk.vtkUnstructuredGrid()
vertex_count = len(coordinates)
edge_to_vert = dict() # when edges are subdivided, a new vertex in the middle is produced and placed in here
ordered_pair = lambda a, b: (a, b) if a < b else (b, a) # edges are bidirectional
def subdivide_edge(vert1, vert2):
edge = ordered_pair(vert1, vert2)
if edge in edge_to_vert:
return edge_to_vert[edge]
# Vertex does not exist, create it
newvert = len(coordinates) + 1
coordinates[newvert] = 0.5 * (coordinates[vert1] + coordinates[vert2]) # Average
edge_to_vert[edge] = newvert;
# Interpolate nodal data
if args.table is not None:
nodal_data.append(0.5 * (nodal_data[vert1 - 1] + nodal_data[vert2 - 1]))
return newvert;
for el_id in range(1, len(elements) + 1): # Marc starts counting at 1
el = elements[el_id]
if el['type'] == 7:
# Hexahedron, subdivided
# There may be a better way to iterate over these, but this is consistent
# with the ordering scheme provided at https://damask.mpie.de/pub/Documentation/ElementType
subverts = np.zeros((3,3,3), dtype=int)
# Get corners
subverts[0, 0, 0] = el['verts'][0]
subverts[2, 0, 0] = el['verts'][1]
subverts[2, 2, 0] = el['verts'][2]
subverts[0, 2, 0] = el['verts'][3]
subverts[0, 0, 2] = el['verts'][4]
subverts[2, 0, 2] = el['verts'][5]
subverts[2, 2, 2] = el['verts'][6]
subverts[0, 2, 2] = el['verts'][7]
# lower edges
subverts[1, 0, 0] = subdivide_edge(subverts[0, 0, 0], subverts[2, 0, 0])
subverts[2, 1, 0] = subdivide_edge(subverts[2, 0, 0], subverts[2, 2, 0])
subverts[1, 2, 0] = subdivide_edge(subverts[2, 2, 0], subverts[0, 2, 0])
subverts[0, 1, 0] = subdivide_edge(subverts[0, 2, 0], subverts[0, 0, 0])
# middle edges
subverts[0, 0, 1] = subdivide_edge(subverts[0, 0, 0], subverts[0, 0, 2])
subverts[2, 0, 1] = subdivide_edge(subverts[2, 0, 0], subverts[2, 0, 2])
subverts[2, 2, 1] = subdivide_edge(subverts[2, 2, 0], subverts[2, 2, 2])
subverts[0, 2, 1] = subdivide_edge(subverts[0, 2, 0], subverts[0, 2, 2])
# top edges
subverts[1, 0, 2] = subdivide_edge(subverts[0, 0, 2], subverts[2, 0, 2])
subverts[2, 1, 2] = subdivide_edge(subverts[2, 0, 2], subverts[2, 2, 2])
subverts[1, 2, 2] = subdivide_edge(subverts[2, 2, 2], subverts[0, 2, 2])
subverts[0, 1, 2] = subdivide_edge(subverts[0, 2, 2], subverts[0, 0, 2])
# then faces... The edge_to_vert addition is due to there being two ways
# to calculate a face vertex, depending on which opposite vertices are used to subdivide.
# This way, we avoid creating duplicate vertices.
subverts[1, 1, 0] = subdivide_edge(subverts[1, 0, 0], subverts[1, 2, 0])
edge_to_vert[ordered_pair(subverts[0, 1, 0], subverts[2, 1, 0])] = subverts[1, 1, 0]
subverts[1, 0, 1] = subdivide_edge(subverts[1, 0, 0], subverts[1, 0, 2])
edge_to_vert[ordered_pair(subverts[0, 0, 1], subverts[2, 0, 1])] = subverts[1, 0, 1]
subverts[2, 1, 1] = subdivide_edge(subverts[2, 1, 0], subverts[2, 1, 2])
edge_to_vert[ordered_pair(subverts[2, 0, 1], subverts[2, 2, 1])] = subverts[2, 1, 1]
subverts[1, 2, 1] = subdivide_edge(subverts[1, 2, 0], subverts[1, 2, 2])
edge_to_vert[ordered_pair(subverts[0, 2, 1], subverts[2, 2, 1])] = subverts[1, 2, 1]
subverts[0, 1, 1] = subdivide_edge(subverts[0, 1, 0], subverts[0, 1, 2])
edge_to_vert[ordered_pair(subverts[0, 0, 1], subverts[0, 2, 1])] = subverts[0, 1, 1]
subverts[1, 1, 2] = subdivide_edge(subverts[1, 0, 2], subverts[1, 2, 2])
edge_to_vert[ordered_pair(subverts[0, 1, 2], subverts[2, 1, 2])] = subverts[1, 1, 2]
# and finally the center. There are three ways to calculate, but elements should
# not intersect, so the edge_to_vert part isn't needed here.
subverts[1, 1, 1] = subdivide_edge(subverts[1, 1, 0], subverts[1, 1, 2])
# Now make the hexahedron subelements
# order in which vtk expects vertices for a hexahedron
order = np.array([(0,0,0),(1,0,0),(1,1,0),(0,1,0),(0,0,1),(1,0,1),(1,1,1),(0,1,1)])
for z in range(2):
for y in range(2):
for x in range(2):
hex_ = vtk.vtkHexahedron()
for vert_id in range(8):
coord = order[vert_id] + (x, y, z)
# minus one, since vtk starts at zero but marc starts at one
hex_.GetPointIds().SetId(vert_id, subverts[coord[0], coord[1], coord[2]] - 1)
grid.InsertNextCell(hex_.GetCellType(), hex_.GetPointIds())
else:
damask.util.croak('Unsupported Marc element type: {} (skipping)'.format(el['type']))
# Load all points
points = vtk.vtkPoints()
for point in range(1, len(coordinates) + 1): # marc indices start at 1
points.InsertNextPoint(coordinates[point].tolist())
grid.SetPoints(points)
# grid now contains the elements from the given marc file
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetFileName(re.sub(r'\..+', ".vtu", args.filename)) # *.vtk extension does not work in paraview
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
else: writer.SetInputData(grid)
writer.Write()
if args.table is not None:
table.info_append([
scriptID + ' ' + ' '.join(sys.argv[1:]),
])
table.head_write()
table.output_flush()
table.data = np.array(nodal_data)
table.data_writeArray()
table.close()

View File

@ -0,0 +1,206 @@
#!/usr/bin/env python2.7
# -*- coding: UTF-8 no BOM -*-
import os,vtk
import damask
from vtk.util import numpy_support
from collections import defaultdict
from optparse import OptionParser
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
msg = "Add scalars, vectors, and/or an RGB tuple from"
msg += "an ASCIItable to existing VTK grid (.vtr/.vtk/.vtu)."
parser = OptionParser(option_class=damask.extendableOption,
usage='%prog options [file[s]]',
description = msg,
version = scriptID)
parser.add_option( '--vtk',
dest = 'vtk',
type = 'string', metavar = 'string',
help = 'VTK file name')
parser.add_option( '--inplace',
dest = 'inplace',
action = 'store_true',
help = 'modify VTK file in-place')
parser.add_option('-r', '--render',
dest = 'render',
action = 'store_true',
help = 'open output in VTK render window')
parser.add_option('-d', '--data',
dest = 'data',
action = 'extend', metavar = '<string LIST>',
help = 'scalar/vector value(s) label(s)')
parser.add_option('-t', '--tensor',
dest = 'tensor',
action = 'extend', metavar = '<string LIST>',
help = 'tensor (3x3) value label(s)')
parser.add_option('-c', '--color',
dest = 'color',
action = 'extend', metavar = '<string LIST>',
help = 'RGB color tuple label')
parser.set_defaults(data = [],
tensor = [],
color = [],
inplace = False,
render = False,
)
(options, filenames) = parser.parse_args()
if not options.vtk: parser.error('No VTK file specified.')
if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
if os.path.splitext(options.vtk)[1] == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
reader.SetFileName(options.vtk)
reader.Update()
rGrid = reader.GetOutput()
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
elif os.path.splitext(options.vtk)[1] == '.vtk':
reader = vtk.vtkGenericDataObjectReader()
reader.SetFileName(options.vtk)
reader.Update()
rGrid = reader.GetRectilinearGridOutput()
writer = vtk.vtkXMLRectilinearGridWriter()
writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
elif os.path.splitext(options.vtk)[1] == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
reader.SetFileName(options.vtk)
reader.Update()
rGrid = reader.GetOutput()
writer = vtk.vtkXMLUnstructuredGridWriter()
writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtu' if options.inplace else '_added.vtu'))
else:
parser.error('Unsupported VTK file type extension.')
Npoints = rGrid.GetNumberOfPoints()
Ncells = rGrid.GetNumberOfCells()
damask.util.croak('{}: {} points and {} cells...'.format(options.vtk,Npoints,Ncells))
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
buffered = False,
readonly = True)
except: continue
damask.util.report(scriptName, name)
# --- interpret header ----------------------------------------------------------------------------
table.head_read()
remarks = []
errors = []
VTKarray = {}
active = defaultdict(list)
for datatype,dimension,label in [['data',99,options.data],
['tensor',9,options.tensor],
['color' ,3,options.color],
]:
for i,dim in enumerate(table.label_dimension(label)):
me = label[i]
if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
else:
remarks.append('adding {} "{}"...'.format(datatype,me))
active[datatype].append(me)
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
continue
# ------------------------------------------ process data ---------------------------------------
table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
for datatype,labels in active.items(): # loop over scalar,color
for me in labels: # loop over all requested items
VTKtype = vtk.VTK_DOUBLE
VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
if datatype == 'color':
VTKtype = vtk.VTK_UNSIGNED_CHAR
VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
elif datatype == 'tensor':
VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,deep=True,array_type=VTKtype)
VTKarray[me].SetName(me)
table.close() # close input ASCII table
# ------------------------------------------ add data ---------------------------------------
if len(table.data) == Npoints: mode = 'point'
elif len(table.data) == Ncells: mode = 'cell'
else:
damask.util.croak('Data count is incompatible with grid...')
continue
damask.util.croak('{} mode...'.format(mode))
for datatype,labels in active.items(): # loop over scalar,color
if datatype == 'color':
if mode == 'cell': rGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
elif mode == 'point': rGrid.GetPointData().SetScalars(VTKarray[active['color'][0]])
for me in labels: # loop over all requested items
if mode == 'cell': rGrid.GetCellData().AddArray(VTKarray[me])
elif mode == 'point': rGrid.GetPointData().AddArray(VTKarray[me])
rGrid.Modified()
if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update()
# ------------------------------------------ output result ---------------------------------------
writer.SetDataModeToBinary()
writer.SetCompressorTypeToZLib()
if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
else: writer.SetInputData(rGrid)
writer.Write()
# ------------------------------------------ render result ---------------------------------------
if options.render:
mapper = vtk.vtkDataSetMapper()
mapper.SetInputData(rGrid)
actor = vtk.vtkActor()
actor.SetMapper(mapper)
# Create the graphics structure. The renderer renders into the
# render window. The render window interactor captures mouse events
# and will perform appropriate camera or actor manipulation
# depending on the nature of the events.
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
ren.AddActor(actor)
ren.SetBackground(1, 1, 1)
renWin.SetSize(200, 200)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
iren.Initialize()
renWin.Render()
iren.Start()

0
processing/pre/3DRVEfrom2Dang.py Normal file → Executable file
View File

View File

@ -74,10 +74,8 @@ add_library (PLASTIC OBJECT
"plastic_disloUCLA.f90"
"plastic_isotropic.f90"
"plastic_phenopowerlaw.f90"
"plastic_titanmod.f90"
"plastic_nonlocal.f90"
"plastic_none.f90"
"plastic_phenoplus.f90")
"plastic_none.f90")
add_dependencies(PLASTIC DAMASK_HELPERS)
list(APPEND OBJECTFILES $<TARGET_OBJECTS:PLASTIC>)

View File

@ -485,8 +485,8 @@ program DAMASK_spectral
min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
call MPI_file_write(resUnit, &
reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)), &
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults, &
[(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), &
(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt), &
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if (ierr /= 0_pInt) call IO_error(error_ID=894_pInt, ext_msg='MPI_file_write')
enddo
@ -683,8 +683,8 @@ program DAMASK_spectral
outputIndex=int([(i-1_pInt)*((maxRealOut)/materialpoint_sizeResults)+1_pInt, &
min(i*((maxRealOut)/materialpoint_sizeResults),size(materialpoint_results,3))],pLongInt)
call MPI_file_write(resUnit,reshape(materialpoint_results(:,:,outputIndex(1):outputIndex(2)),&
[(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults]), &
(outputIndex(2)-outputIndex(1)+1)*materialpoint_sizeResults,&
[(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt)]), &
(outputIndex(2)-outputIndex(1)+1)*int(materialpoint_sizeResults,pLongInt),&
MPI_DOUBLE, MPI_STATUS_IGNORE, ierr)
if(ierr /=0_pInt) call IO_error(894_pInt, ext_msg='MPI_file_write')
enddo

View File

@ -50,6 +50,7 @@ module IO
IO_skipChunks, &
IO_extractValue, &
IO_countDataLines, &
IO_countNumericalDataLines, &
IO_countContinuousIntValues, &
IO_continuousIntValues, &
IO_error, &
@ -1247,6 +1248,37 @@ integer(pInt) function IO_countDataLines(fileUnit)
end function IO_countDataLines
!--------------------------------------------------------------------------------------------------
!> @brief count lines containig data up to next *keyword
!--------------------------------------------------------------------------------------------------
integer(pInt) function IO_countNumericalDataLines(fileUnit)
implicit none
integer(pInt), intent(in) :: fileUnit !< file handle
integer(pInt), allocatable, dimension(:) :: chunkPos
character(len=65536) :: line, &
tmp
IO_countNumericalDataLines = 0_pInt
line = ''
do while (trim(line) /= IO_EOF)
line = IO_read(fileUnit)
chunkPos = IO_stringPos(line)
tmp = IO_lc(IO_stringValue(line,chunkPos,1_pInt))
if (verify(trim(tmp) ,"0123456789")/=0) then ! found keyword
line = IO_read(fileUnit, .true.) ! reset IO_read
exit
else
IO_countNumericalDataLines = IO_countNumericalDataLines + 1_pInt
endif
enddo
backspace(fileUnit)
end function IO_countNumericalDataLines
!--------------------------------------------------------------------------------------------------
!> @brief count items in consecutive lines depending on lines
!> @details Marc: ints concatenated by "c" as last char or range of values a "to" b
@ -1313,7 +1345,7 @@ end function IO_countContinuousIntValues
!--------------------------------------------------------------------------------------------------
!> @brief return integer list corrsponding to items in consecutive lines.
!> @brief return integer list corresponding to items in consecutive lines.
!! First integer in array is counter
!> @details Marc: ints concatenated by "c" as last char, range of a "to" b, or named set
!! Abaqus: triplet of start,stop,inc or named set
@ -1807,12 +1839,12 @@ integer(pInt) function IO_verifyIntValue (string,validChars,myName)
invalidWhere = verify(string,validChars)
if (invalidWhere == 0_pInt) then
read(UNIT=string,iostat=readStatus,FMT=*) IO_verifyIntValue ! no offending chars found
if (readStatus /= 0_pInt) & ! error during string to float conversion
if (readStatus /= 0_pInt) & ! error during string to integer conversion
call IO_warning(203_pInt,ext_msg=myName//'"'//string//'"')
else
call IO_warning(202_pInt,ext_msg=myName//'"'//string//'"') ! complain about offending characters
read(UNIT=string(1_pInt:invalidWhere-1_pInt),iostat=readStatus,FMT=*) IO_verifyIntValue ! interpret remaining string
if (readStatus /= 0_pInt) & ! error during string to float conversion
if (readStatus /= 0_pInt) & ! error during string to integer conversion
call IO_warning(203_pInt,ext_msg=myName//'"'//string(1_pInt:invalidWhere-1_pInt)//'"')
endif

View File

@ -28,8 +28,6 @@
#include "plastic_none.f90"
#include "plastic_isotropic.f90"
#include "plastic_phenopowerlaw.f90"
#include "plastic_phenoplus.f90"
#include "plastic_titanmod.f90"
#include "plastic_dislotwin.f90"
#include "plastic_disloUCLA.f90"
#include "plastic_nonlocal.f90"

View File

@ -74,10 +74,8 @@ subroutine constitutive_init()
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
PLASTICITY_disloucla_ID, &
PLASTICITY_titanmod_ID, &
PLASTICITY_nonlocal_ID ,&
SOURCE_thermal_dissipation_ID, &
SOURCE_thermal_externalheat_ID, &
@ -97,10 +95,8 @@ subroutine constitutive_init()
PLASTICITY_NONE_label, &
PLASTICITY_ISOTROPIC_label, &
PLASTICITY_PHENOPOWERLAW_label, &
PLASTICITY_PHENOPLUS_label, &
PLASTICITY_DISLOTWIN_label, &
PLASTICITY_DISLOUCLA_label, &
PLASTICITY_TITANMOD_label, &
PLASTICITY_NONLOCAL_label, &
SOURCE_thermal_dissipation_label, &
SOURCE_thermal_externalheat_label, &
@ -117,10 +113,8 @@ subroutine constitutive_init()
use plastic_none
use plastic_isotropic
use plastic_phenopowerlaw
use plastic_phenoplus
use plastic_dislotwin
use plastic_disloucla
use plastic_titanmod
use plastic_nonlocal
use source_thermal_dissipation
use source_thermal_externalheat
@ -162,10 +156,8 @@ subroutine constitutive_init()
if (any(phase_plasticity == PLASTICITY_NONE_ID)) call plastic_none_init
if (any(phase_plasticity == PLASTICITY_ISOTROPIC_ID)) call plastic_isotropic_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_PHENOPOWERLAW_ID)) call plastic_phenopowerlaw_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_PHENOPLUS_ID)) call plastic_phenoplus_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_DISLOTWIN_ID)) call plastic_dislotwin_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_DISLOUCLA_ID)) call plastic_disloucla_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_TITANMOD_ID)) call plastic_titanmod_init(FILEUNIT)
if (any(phase_plasticity == PLASTICITY_NONLOCAL_ID)) then
call plastic_nonlocal_init(FILEUNIT)
call plastic_nonlocal_stateInit()
@ -194,11 +186,11 @@ subroutine constitutive_init()
if (any(phase_kinematics == KINEMATICS_hydrogen_strain_ID)) call kinematics_hydrogen_strain_init(FILEUNIT)
close(FILEUNIT)
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- constitutive init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
mainProcess: if (worldrank == 0) then
!--------------------------------------------------------------------------------------------------
! write description file for constitutive output
call IO_write_jobFile(FILEUNIT,'outputConstitutive')
@ -222,11 +214,6 @@ subroutine constitutive_init()
thisNoutput => plastic_phenopowerlaw_Noutput
thisOutput => plastic_phenopowerlaw_output
thisSize => plastic_phenopowerlaw_sizePostResult
case (PLASTICITY_PHENOPLUS_ID) plasticityType
outputName = PLASTICITY_PHENOPLUS_label
thisNoutput => plastic_phenoplus_Noutput
thisOutput => plastic_phenoplus_output
thisSize => plastic_phenoplus_sizePostResult
case (PLASTICITY_DISLOTWIN_ID) plasticityType
outputName = PLASTICITY_DISLOTWIN_label
thisNoutput => plastic_dislotwin_Noutput
@ -237,11 +224,6 @@ subroutine constitutive_init()
thisNoutput => plastic_disloucla_Noutput
thisOutput => plastic_disloucla_output
thisSize => plastic_disloucla_sizePostResult
case (PLASTICITY_TITANMOD_ID) plasticityType
outputName = PLASTICITY_TITANMOD_label
thisNoutput => plastic_titanmod_Noutput
thisOutput => plastic_titanmod_output
thisSize => plastic_titanmod_sizePostResult
case (PLASTICITY_NONLOCAL_ID) plasticityType
outputName = PLASTICITY_NONLOCAL_label
thisNoutput => plastic_nonlocal_Noutput
@ -396,11 +378,8 @@ function constitutive_homogenizedC(ipc,ip,el)
use material, only: &
phase_plasticity, &
material_phase, &
PLASTICITY_TITANMOD_ID, &
PLASTICITY_DISLOTWIN_ID, &
PLASTICITY_DISLOUCLA_ID
use plastic_titanmod, only: &
plastic_titanmod_homogenizedC
use plastic_dislotwin, only: &
plastic_dislotwin_homogenizedC
use lattice, only: &
@ -416,8 +395,6 @@ function constitutive_homogenizedC(ipc,ip,el)
plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
case (PLASTICITY_DISLOTWIN_ID) plasticityType
constitutive_homogenizedC = plastic_dislotwin_homogenizedC(ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
constitutive_homogenizedC = plastic_titanmod_homogenizedC (ipc,ip,el)
case default plasticityType
constitutive_homogenizedC = lattice_C66(1:6,1:6,material_phase (ipc,ip,el))
end select plasticityType
@ -438,19 +415,13 @@ subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
thermalMapping, &
PLASTICITY_dislotwin_ID, &
PLASTICITY_disloucla_ID, &
PLASTICITY_titanmod_ID, &
PLASTICITY_nonlocal_ID, &
PLASTICITY_phenoplus_ID
use plastic_titanmod, only: &
plastic_titanmod_microstructure
PLASTICITY_nonlocal_ID
use plastic_nonlocal, only: &
plastic_nonlocal_microstructure
use plastic_dislotwin, only: &
plastic_dislotwin_microstructure
use plastic_disloucla, only: &
plastic_disloucla_microstructure
use plastic_phenoplus, only: &
plastic_phenoplus_microstructure
implicit none
integer(pInt), intent(in) :: &
@ -474,12 +445,8 @@ subroutine constitutive_microstructure(orientations, Fe, Fp, ipc, ip, el)
call plastic_dislotwin_microstructure(temperature(ho)%p(tme),ipc,ip,el)
case (PLASTICITY_DISLOUCLA_ID) plasticityType
call plastic_disloucla_microstructure(temperature(ho)%p(tme),ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
call plastic_titanmod_microstructure (temperature(ho)%p(tme),ipc,ip,el)
case (PLASTICITY_NONLOCAL_ID) plasticityType
call plastic_nonlocal_microstructure (Fe,Fp,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
call plastic_phenoplus_microstructure(orientations,ipc,ip,el)
end select plasticityType
end subroutine constitutive_microstructure
@ -505,23 +472,17 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
PLASTICITY_NONE_ID, &
PLASTICITY_ISOTROPIC_ID, &
PLASTICITY_PHENOPOWERLAW_ID, &
PLASTICITY_PHENOPLUS_ID, &
PLASTICITY_DISLOTWIN_ID, &
PLASTICITY_DISLOUCLA_ID, &
PLASTICITY_TITANMOD_ID, &
PLASTICITY_NONLOCAL_ID
use plastic_isotropic, only: &
plastic_isotropic_LpAndItsTangent
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_LpAndItsTangent
use plastic_phenoplus, only: &
plastic_phenoplus_LpAndItsTangent
use plastic_dislotwin, only: &
plastic_dislotwin_LpAndItsTangent
use plastic_disloucla, only: &
plastic_disloucla_LpAndItsTangent
use plastic_titanmod, only: &
plastic_titanmod_LpAndItsTangent
use plastic_nonlocal, only: &
plastic_nonlocal_LpAndItsTangent
@ -564,8 +525,6 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
call plastic_isotropic_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
call plastic_phenopowerlaw_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
call plastic_phenoplus_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v,ipc,ip,el)
case (PLASTICITY_NONLOCAL_ID) plasticityType
call plastic_nonlocal_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v, &
temperature(ho)%p(tme),ip,el)
@ -575,9 +534,6 @@ subroutine constitutive_LpAndItsTangent(Lp, dLp_dTstar3333, dLp_dFi3333, Tstar_v
case (PLASTICITY_DISLOUCLA_ID) plasticityType
call plastic_disloucla_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v, &
temperature(ho)%p(tme), ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
call plastic_titanmod_LpAndItsTangent(Lp,dLp_dMstar,Mstar_v, &
temperature(ho)%p(tme), ipc,ip,el)
end select plasticityType
dLp_dTstar3333 = math_Plain99to3333(dLp_dMstar)
@ -888,10 +844,8 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
PLASTICITY_disloucla_ID, &
PLASTICITY_titanmod_ID, &
PLASTICITY_nonlocal_ID, &
SOURCE_damage_isoDuctile_ID, &
SOURCE_damage_anisoBrittle_ID, &
@ -901,14 +855,10 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
plastic_isotropic_dotState
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_dotState
use plastic_phenoplus, only: &
plastic_phenoplus_dotState
use plastic_dislotwin, only: &
plastic_dislotwin_dotState
use plastic_disloucla, only: &
plastic_disloucla_dotState
use plastic_titanmod, only: &
plastic_titanmod_dotState
use plastic_nonlocal, only: &
plastic_nonlocal_dotState
use source_damage_isoDuctile, only: &
@ -954,17 +904,12 @@ subroutine constitutive_collectDotState(Tstar_v, FeArray, FpArray, subdt, subfra
call plastic_isotropic_dotState (Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
call plastic_phenopowerlaw_dotState(Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
call plastic_phenoplus_dotState (Tstar_v,ipc,ip,el)
case (PLASTICITY_DISLOTWIN_ID) plasticityType
call plastic_dislotwin_dotState (Tstar_v,temperature(ho)%p(tme), &
ipc,ip,el)
case (PLASTICITY_DISLOUCLA_ID) plasticityType
call plastic_disloucla_dotState (Tstar_v,temperature(ho)%p(tme), &
ipc,ip,el)
case (PLASTICITY_TITANMOD_ID) plasticityType
call plastic_titanmod_dotState (Tstar_v,temperature(ho)%p(tme), &
ipc,ip,el)
case (PLASTICITY_NONLOCAL_ID) plasticityType
call plastic_nonlocal_dotState (Tstar_v,FeArray,FpArray,temperature(ho)%p(tme), &
subdt,subfracArray,ip,el)
@ -1097,10 +1042,8 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
PLASTICITY_NONE_ID, &
PLASTICITY_ISOTROPIC_ID, &
PLASTICITY_PHENOPOWERLAW_ID, &
PLASTICITY_PHENOPLUS_ID, &
PLASTICITY_DISLOTWIN_ID, &
PLASTICITY_DISLOUCLA_ID, &
PLASTICITY_TITANMOD_ID, &
PLASTICITY_NONLOCAL_ID, &
SOURCE_damage_isoBrittle_ID, &
SOURCE_damage_isoDuctile_ID, &
@ -1110,14 +1053,10 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
plastic_isotropic_postResults
use plastic_phenopowerlaw, only: &
plastic_phenopowerlaw_postResults
use plastic_phenoplus, only: &
plastic_phenoplus_postResults
use plastic_dislotwin, only: &
plastic_dislotwin_postResults
use plastic_disloucla, only: &
plastic_disloucla_postResults
use plastic_titanmod, only: &
plastic_titanmod_postResults
use plastic_nonlocal, only: &
plastic_nonlocal_postResults
use source_damage_isoBrittle, only: &
@ -1157,16 +1096,11 @@ function constitutive_postResults(Tstar_v, FeArray, ipc, ip, el)
endPos = plasticState(material_phase(ipc,ip,el))%sizePostResults
plasticityType: select case (phase_plasticity(material_phase(ipc,ip,el)))
case (PLASTICITY_TITANMOD_ID) plasticityType
constitutive_postResults(startPos:endPos) = plastic_titanmod_postResults(ipc,ip,el)
case (PLASTICITY_ISOTROPIC_ID) plasticityType
constitutive_postResults(startPos:endPos) = plastic_isotropic_postResults(Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPOWERLAW_ID) plasticityType
constitutive_postResults(startPos:endPos) = &
plastic_phenopowerlaw_postResults(Tstar_v,ipc,ip,el)
case (PLASTICITY_PHENOPLUS_ID) plasticityType
constitutive_postResults(startPos:endPos) = &
plastic_phenoplus_postResults(Tstar_v,ipc,ip,el)
case (PLASTICITY_DISLOTWIN_ID) plasticityType
constitutive_postResults(startPos:endPos) = &
plastic_dislotwin_postResults(Tstar_v,temperature(ho)%p(tme),ipc,ip,el)

View File

@ -554,7 +554,6 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
FEsolving_execIP
use mesh, only: &
mesh_element, &
mesh_NcpElems, &
mesh_maxNips, &
mesh_ipNeighborhood, &
FE_NipNeighbors, &
@ -565,8 +564,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
plasticState, &
sourceState, &
phase_Nsources, &
phaseAt, phasememberAt, &
homogenization_maxNgrains
phaseAt, phasememberAt
use constitutive, only: &
constitutive_TandItsTangent, &
constitutive_LpAndItsTangent, &
@ -794,7 +792,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
if (.not. crystallite_localPlasticity(1,neighboring_i,neighboring_e) &
.and. .not. crystallite_converged(1,neighboring_i,neighboring_e)) then
crystallite_neighborEnforcedCutback(i,e) = .true.
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt) &
write(6,'(a12,i5,1x,i2,a,i5,1x,i2)') '<< CRYST >> ', neighboring_e,neighboring_i, &
' enforced cutback at ',e,i
@ -829,7 +827,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
if (.not. crystallite_localPlasticity(1,neighboring_i,neighboring_e) &
.and. .not. crystallite_converged(1,neighboring_i,neighboring_e)) then
crystallite_syncSubFrac(i,e) = .true.
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt) &
write(6,'(a12,i5,1x,i2,a,i5,1x,i2)') '<< CRYST >> ',neighboring_e,neighboring_i, &
' enforced time synchronization at ',e,i
@ -937,7 +935,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
crystallite_todo(c,i,e) = .true.
endif
!$OMP FLUSH(crystallite_todo)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite),debug_levelBasic) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i .and. c == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) &
@ -987,7 +985,7 @@ subroutine crystallite_stressAndItsTangent(updateJaco)
! cant restore dotState here, since not yet calculated in first cutback after initialization
crystallite_todo(c,i,e) = crystallite_subStep(c,i,e) > subStepMinCryst ! still on track or already done (beyond repair)
!$OMP FLUSH(crystallite_todo)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite),debug_levelBasic) /= 0_pInt) then
if (crystallite_todo(c,i,e)) then
write(6,'(a,f12.8,a,i8,1x,i2,1x,i3,/)') '<< CRYST >> cutback step in crystallite_stressAndItsTangent &
@ -1393,7 +1391,7 @@ subroutine crystallite_integrateStateRK4()
* crystallite_subdt(g,i,e) * timeStepFraction(n)
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (n == 4 &
.and. iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i .and. g == debug_g) &
@ -1784,7 +1782,7 @@ subroutine crystallite_integrateStateRKCK45()
! --- dot state and RK dot state---
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt) &
write(6,'(a,1x,i1)') '<< CRYST >> Runge--Kutta step',stage+1_pInt
#endif
@ -1933,7 +1931,7 @@ subroutine crystallite_integrateStateRKCK45()
sourceState(p)%p(mySource)%aTolState(1:mySizeSourceDotState))
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt&
.and. ((e == debug_e .and. i == debug_i .and. g == debug_g)&
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -2317,7 +2315,7 @@ subroutine crystallite_integrateStateAdaptiveEuler()
!$OMP FLUSH(relPlasticStateResiduum)
!$OMP FLUSH(relSourceStateResiduum)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i .and. g == debug_g)&
@ -2513,7 +2511,7 @@ eIter = FEsolving_execElem(1:2)
* crystallite_subdt(g,i,e)
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i .and. g == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -2962,7 +2960,7 @@ subroutine crystallite_integrateStateFPI()
* (1.0_pReal - sourceStateDamper)
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i .and. g == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -3134,7 +3132,7 @@ logical function crystallite_stateJump(ipc,ip,el)
sourceState(p)%p(mySource)%deltaState(1:mySizeSourceDeltaState,c)
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (any(dNeq0(plasticState(p)%deltaState(1:mySizePlasticDeltaState,c))) &
.and. iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
@ -3309,7 +3307,7 @@ logical function crystallite_integrateStress(&
!* be pessimistic
crystallite_integrateStress = .false.
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) &
@ -3342,9 +3340,9 @@ logical function crystallite_integrateStress(&
invFp_current = math_inv33(Fp_current)
failedInversionFp: if (all(dEq0(invFp_current))) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) then
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3)') '<< CRYST >> integrateStress failed on inversion of Fp_current at el (elFE) ip g ',&
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3)') '<< CRYST >> integrateStress failed on inversion of Fp_current at el (elFE) ip ipc ',&
el,'(',mesh_element(1,el),')',ip,ipc
if (iand(debug_level(debug_crystallite), debug_levelExtensive) > 0_pInt) &
write(6,'(/,a,/,3(12x,3(f12.7,1x)/))') '<< CRYST >> Fp_current',math_transpose33(Fp_current(1:3,1:3))
@ -3358,7 +3356,7 @@ logical function crystallite_integrateStress(&
invFi_current = math_inv33(Fi_current)
failedInversionFi: if (all(dEq0(invFi_current))) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) then
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3)') '<< CRYST >> integrateStress failed on inversion of Fi_current at el (elFE) ip ipc ',&
el,'(',mesh_element(1,el),')',ip,ipc
@ -3379,10 +3377,10 @@ logical function crystallite_integrateStress(&
LiLoop: do
NiterationStressLi = NiterationStressLi + 1_pInt
IloopsExeced: if (NiterationStressLi > nStress) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) &
write(6,'(a,i3,a,i8,1x,a,i8,a,1x,i2,1x,i3,/)') '<< CRYST >> integrateStress reached inelastic loop limit',nStress, &
' at el (elFE) ip ipc ', el,mesh_element(1,el),ip,ipc
' at el (elFE) ip ipc ', el,'(',mesh_element(1,el),')',ip,ipc
#endif
return
endif IloopsExeced
@ -3400,7 +3398,7 @@ logical function crystallite_integrateStress(&
LpLoop: do ! inner stress integration loop for consistency with Fi
NiterationStressLp = NiterationStressLp + 1_pInt
loopsExeced: if (NiterationStressLp > nStress) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) &
write(6,'(a,i3,a,i8,1x,a,i8,a,1x,i2,1x,i3,/)') '<< CRYST >> integrateStress reached loop limit',nStress, &
' at el (elFE) ip ipc ', el,mesh_element(1,el),ip,ipc
@ -3433,7 +3431,7 @@ logical function crystallite_integrateStress(&
!$OMP END CRITICAL (debugTimingLpTangent)
endif
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -3451,10 +3449,10 @@ logical function crystallite_integrateStress(&
residuumLp = Lpguess - Lp_constitutive
if (any(IEEE_is_NaN(residuumLp))) then ! NaN in residuum...
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) &
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,a,i3,a)') '<< CRYST >> integrateStress encountered NaN at el (elFE) ip ipc ', &
el,mesh_element(1,el),ip,ipc, &
el,'(',mesh_element(1,el),')',ip,ipc, &
' ; iteration ', NiterationStressLp,&
' >> returning..!'
#endif
@ -3486,10 +3484,10 @@ logical function crystallite_integrateStress(&
work = math_plain33to9(residuumLp)
call dgesv(9,1,dRLp_dLp2,9,ipiv,work,9,ierr) ! solve dRLp/dLp * delta Lp = -res for delta Lp
if (ierr /= 0_pInt) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) then
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,a,i3)') '<< CRYST >> integrateStress failed on dR/dLp inversion at el ip ipc ', &
el,mesh_element(1,el),ip,ipc
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3)') '<< CRYST >> integrateStress failed on dR/dLp inversion at el (elFE) ip ipc ', &
el,'(',mesh_element(1,el),')',ip,ipc
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g)&
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -3527,7 +3525,7 @@ logical function crystallite_integrateStress(&
call constitutive_LiAndItsTangent(Li_constitutive, dLi_dT3333, dLi_dFi3333, &
Tstar_v, Fi_new, ipc, ip, el)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -3575,10 +3573,10 @@ logical function crystallite_integrateStress(&
work = math_plain33to9(residuumLi)
call dgesv(9,1,dRLi_dLi,9,ipiv,work,9,ierr) ! solve dRLi/dLp * delta Li = -res for delta Li
if (ierr /= 0_pInt) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) then
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,a,i3)') '<< CRYST >> integrateStress failed on dR/dLi inversion at el ip ipc ', &
el,mesh_element(1,el),ip,ipc
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3)') '<< CRYST >> integrateStress failed on dR/dLi inversion at el (elFE) ip ipc ', &
el,'(',mesh_element(1,el),')',ip,ipc
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g)&
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then
@ -3615,10 +3613,10 @@ logical function crystallite_integrateStress(&
invFp_new = invFp_new / math_det33(invFp_new)**(1.0_pReal/3.0_pReal) ! regularize by det
Fp_new = math_inv33(invFp_new)
failedInversionInvFp: if (all(dEq0(Fp_new))) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite), debug_levelBasic) /= 0_pInt) then
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,a,i3)') '<< CRYST >> integrateStress failed on invFp_new inversion at el ip ipc ',&
el,mesh_element(1,el),ip,ipc, ' ; iteration ', NiterationStressLp
write(6,'(a,i8,1x,a,i8,a,1x,i2,1x,i3,a,i3)') '<< CRYST >> integrateStress failed on invFp_new inversion at el (elFE) ip ipc ',&
el,'(',mesh_element(1,el),')',ip,ipc, ' ; iteration ', NiterationStressLp
if (iand(debug_level(debug_crystallite), debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) &
@ -3649,7 +3647,7 @@ logical function crystallite_integrateStress(&
!* set return flag to true
crystallite_integrateStress = .true.
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_crystallite),debug_levelExtensive) /= 0_pInt &
.and. ((el == debug_e .and. ip == debug_i .and. ipc == debug_g) &
.or. .not. iand(debug_level(debug_crystallite), debug_levelSelective) /= 0_pInt)) then

View File

@ -72,8 +72,6 @@ subroutine damage_local_init(fileUnit)
damage, &
damage_initialPhi, &
material_partHomogenization
use numerics,only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -86,11 +84,9 @@ subroutine damage_local_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- damage_'//DAMAGE_local_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(damage_type == DAMAGE_local_ID),pInt)
if (maxNinstance == 0_pInt) return

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@ -26,19 +26,15 @@ subroutine damage_none_init()
use IO, only: &
IO_timeStamp
use material
use numerics, only: &
worldrank
implicit none
integer(pInt) :: &
homog, &
NofMyHomog
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- damage_'//DAMAGE_none_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
initializeInstances: do homog = 1_pInt, material_Nhomogenization

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@ -77,8 +77,6 @@ subroutine damage_nonlocal_init(fileUnit)
damage, &
damage_initialPhi, &
material_partHomogenization
use numerics,only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -91,11 +89,9 @@ subroutine damage_nonlocal_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- damage_'//DAMAGE_nonlocal_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(damage_type == DAMAGE_nonlocal_ID),pInt)
if (maxNinstance == 0_pInt) return

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@ -542,6 +542,7 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
debug_level, &
debug_homogenization, &
debug_levelBasic, &
debug_levelExtensive, &
debug_levelSelective, &
debug_e, &
debug_i, &
@ -638,8 +639,8 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
IpLooping1: do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e)
converged: if ( materialpoint_converged(i,e) ) then
#ifndef _OPENMP
if (iand(debug_level(debug_homogenization), debug_levelBasic) /= 0_pInt &
#ifdef DEBUG
if (iand(debug_level(debug_homogenization), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i) &
.or. .not. iand(debug_level(debug_homogenization),debug_levelSelective) /= 0_pInt)) then
write(6,'(a,1x,f12.8,1x,a,1x,f12.8,1x,a,i8,1x,i2/)') '<< HOMOG >> winding forward from', &
@ -741,8 +742,8 @@ subroutine materialpoint_stressAndItsTangent(updateJaco,dt)
materialpoint_subStep(i,e) = subStepSizeHomog * materialpoint_subStep(i,e) ! crystallite had severe trouble, so do a significant cutback
!$OMP FLUSH(materialpoint_subStep)
#ifndef _OPENMP
if (iand(debug_level(debug_homogenization), debug_levelBasic) /= 0_pInt &
#ifdef DEBUG
if (iand(debug_level(debug_homogenization), debug_levelExtensive) /= 0_pInt &
.and. ((e == debug_e .and. i == debug_i) &
.or. .not. iand(debug_level(debug_homogenization), debug_levelSelective) /= 0_pInt)) then
write(6,'(a,1x,f12.8,a,i8,1x,i2/)') &

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@ -100,8 +100,6 @@ subroutine homogenization_RGC_init(fileUnit)
FE_geomtype
use IO
use material
use numerics, only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit !< file pointer to material configuration
@ -117,11 +115,9 @@ subroutine homogenization_RGC_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- homogenization_'//HOMOGENIZATION_RGC_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(homogenization_type == HOMOGENIZATION_RGC_ID),pInt)
if (maxNinstance == 0_pInt) return

View File

@ -62,8 +62,6 @@ subroutine homogenization_isostrain_init(fileUnit)
debug_levelBasic
use IO
use material
use numerics, only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -80,11 +78,9 @@ subroutine homogenization_isostrain_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- homogenization_'//HOMOGENIZATION_ISOSTRAIN_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = count(homogenization_type == HOMOGENIZATION_ISOSTRAIN_ID)
if (maxNinstance == 0) return

View File

@ -29,19 +29,15 @@ subroutine homogenization_none_init()
use IO, only: &
IO_timeStamp
use material
use numerics, only: &
worldrank
implicit none
integer(pInt) :: &
homog, &
NofMyHomog
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- homogenization_'//HOMOGENIZATION_NONE_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
initializeInstances: do homog = 1_pInt, material_Nhomogenization

View File

@ -84,8 +84,6 @@ subroutine hydrogenflux_cahnhilliard_init(fileUnit)
hydrogenflux_initialCh, &
material_partHomogenization, &
material_partPhase
use numerics,only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -98,11 +96,9 @@ subroutine hydrogenflux_cahnhilliard_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- hydrogenflux_'//HYDROGENFLUX_cahnhilliard_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(hydrogenflux_type == HYDROGENFLUX_cahnhilliard_ID),pInt)
if (maxNinstance == 0_pInt) return

View File

@ -27,19 +27,15 @@ subroutine hydrogenflux_isoconc_init()
use IO, only: &
IO_timeStamp
use material
use numerics, only: &
worldrank
implicit none
integer(pInt) :: &
homog, &
NofMyHomog
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- hydrogenflux_'//HYDROGENFLUX_isoconc_label//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
initializeInstances: do homog = 1_pInt, material_Nhomogenization

View File

@ -81,8 +81,6 @@ subroutine kinematics_cleavage_opening_init(fileUnit)
KINEMATICS_cleavage_opening_ID, &
material_Nphase, &
MATERIAL_partPhase
use numerics,only: &
worldrank
use lattice, only: &
lattice_maxNcleavageFamily, &
lattice_NcleavageSystem
@ -97,11 +95,9 @@ subroutine kinematics_cleavage_opening_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- kinematics_'//KINEMATICS_cleavage_opening_LABEL//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(phase_kinematics == KINEMATICS_cleavage_opening_ID),pInt)
if (maxNinstance == 0_pInt) return

View File

@ -81,8 +81,6 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
KINEMATICS_slipplane_opening_ID, &
material_Nphase, &
MATERIAL_partPhase
use numerics,only: &
worldrank
use lattice, only: &
lattice_maxNslipFamily, &
lattice_NslipSystem
@ -97,11 +95,9 @@ subroutine kinematics_slipplane_opening_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- kinematics_'//KINEMATICS_slipplane_opening_LABEL//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(phase_kinematics == KINEMATICS_slipplane_opening_ID),pInt)
if (maxNinstance == 0_pInt) return

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@ -71,8 +71,6 @@ subroutine kinematics_thermal_expansion_init(fileUnit)
KINEMATICS_thermal_expansion_ID, &
material_Nphase, &
MATERIAL_partPhase
use numerics,only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -83,11 +81,9 @@ subroutine kinematics_thermal_expansion_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- kinematics_'//KINEMATICS_thermal_expansion_LABEL//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(phase_kinematics == KINEMATICS_thermal_expansion_ID),pInt)
if (maxNinstance == 0_pInt) return

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@ -71,8 +71,6 @@ subroutine kinematics_vacancy_strain_init(fileUnit)
KINEMATICS_vacancy_strain_ID, &
material_Nphase, &
MATERIAL_partPhase
use numerics,only: &
worldrank
implicit none
integer(pInt), intent(in) :: fileUnit
@ -83,11 +81,9 @@ subroutine kinematics_vacancy_strain_init(fileUnit)
tag = '', &
line = ''
mainProcess: if (worldrank == 0) then
write(6,'(/,a)') ' <<<+- kinematics_'//KINEMATICS_vacancy_strain_LABEL//' init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
endif mainProcess
maxNinstance = int(count(phase_kinematics == KINEMATICS_vacancy_strain_ID),pInt)
if (maxNinstance == 0_pInt) return

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@ -96,19 +96,19 @@ module lattice
real(pReal), dimension(3+3,LATTICE_fcc_Nslip), parameter, private :: &
LATTICE_fcc_systemSlip = reshape(real([&
! Slip direction Plane normal
0, 1,-1, 1, 1, 1, &
-1, 0, 1, 1, 1, 1, &
1,-1, 0, 1, 1, 1, &
0,-1,-1, -1,-1, 1, &
1, 0, 1, -1,-1, 1, &
-1, 1, 0, -1,-1, 1, &
0,-1, 1, 1,-1,-1, &
-1, 0,-1, 1,-1,-1, &
1, 1, 0, 1,-1,-1, &
0, 1, 1, -1, 1,-1, &
1, 0,-1, -1, 1,-1, &
-1,-1, 0, -1, 1,-1 &
! Slip direction Plane normal ! SCHMID-BOAS notation
0, 1,-1, 1, 1, 1, & ! B2
-1, 0, 1, 1, 1, 1, & ! B4
1,-1, 0, 1, 1, 1, & ! B5
0,-1,-1, -1,-1, 1, & ! C1
1, 0, 1, -1,-1, 1, & ! C3
-1, 1, 0, -1,-1, 1, & ! C5
0,-1, 1, 1,-1,-1, & ! A2
-1, 0,-1, 1,-1,-1, & ! A3
1, 1, 0, 1,-1,-1, & ! A6
0, 1, 1, -1, 1,-1, & ! D1
1, 0,-1, -1, 1,-1, & ! D4
-1,-1, 0, -1, 1,-1 & ! D6
],pReal),[ 3_pInt + 3_pInt,LATTICE_fcc_Nslip]) !< Slip system <110>{111} directions. Sorted according to Eisenlohr & Hantcherli
real(pReal), dimension(3+3,LATTICE_fcc_Ntwin), parameter, private :: &

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@ -25,10 +25,8 @@ module material
PLASTICITY_none_label = 'none', &
PLASTICITY_isotropic_label = 'isotropic', &
PLASTICITY_phenopowerlaw_label = 'phenopowerlaw', &
PLASTICITY_phenoplus_label = 'phenoplus', &
PLASTICITY_dislotwin_label = 'dislotwin', &
PLASTICITY_disloucla_label = 'disloucla', &
PLASTICITY_titanmod_label = 'titanmod', &
PLASTICITY_nonlocal_label = 'nonlocal', &
SOURCE_thermal_dissipation_label = 'thermal_dissipation', &
SOURCE_thermal_externalheat_label = 'thermal_externalheat', &
@ -74,10 +72,8 @@ module material
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
PLASTICITY_disloucla_ID, &
PLASTICITY_titanmod_ID, &
PLASTICITY_nonlocal_ID
end enum
@ -312,10 +308,8 @@ module material
PLASTICITY_none_ID, &
PLASTICITY_isotropic_ID, &
PLASTICITY_phenopowerlaw_ID, &
PLASTICITY_phenoplus_ID, &
PLASTICITY_dislotwin_ID, &
PLASTICITY_disloucla_ID, &
PLASTICITY_titanmod_ID, &
PLASTICITY_nonlocal_ID, &
SOURCE_thermal_dissipation_ID, &
SOURCE_thermal_externalheat_ID, &
@ -989,14 +983,10 @@ subroutine material_parsePhase(fileUnit,myPart)
phase_plasticity(section) = PLASTICITY_ISOTROPIC_ID
case (PLASTICITY_PHENOPOWERLAW_label)
phase_plasticity(section) = PLASTICITY_PHENOPOWERLAW_ID
case (PLASTICITY_PHENOPLUS_label)
phase_plasticity(section) = PLASTICITY_PHENOPLUS_ID
case (PLASTICITY_DISLOTWIN_label)
phase_plasticity(section) = PLASTICITY_DISLOTWIN_ID
case (PLASTICITY_DISLOUCLA_label)
phase_plasticity(section) = PLASTICITY_DISLOUCLA_ID
case (PLASTICITY_TITANMOD_label)
phase_plasticity(section) = PLASTICITY_TITANMOD_ID
case (PLASTICITY_NONLOCAL_label)
phase_plasticity(section) = PLASTICITY_NONLOCAL_ID
case default

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@ -178,7 +178,7 @@ subroutine math_init
compiler_version, &
compiler_options
#endif
use numerics, only: fixedSeed
use numerics, only: randomSeed
use IO, only: IO_timeStamp
implicit none
@ -195,8 +195,8 @@ subroutine math_init
call random_seed(size=randSize)
if (allocated(randInit)) deallocate(randInit)
allocate(randInit(randSize))
if (fixedSeed > 0_pInt) then
randInit(1:randSize) = int(fixedSeed) ! fixedSeed is of type pInt, randInit not
if (randomSeed > 0_pInt) then
randInit(1:randSize) = int(randomSeed) ! randomSeed is of type pInt, randInit not
call random_seed(put=randInit)
else
call random_seed()
@ -1440,34 +1440,36 @@ end function math_RtoQ
!--------------------------------------------------------------------------------------------------
!> @brief rotation matrix from Euler angles (in radians)
!> @details rotation matrix is meant to represent a PASSIVE rotation,
!> @details composed of INTRINSIC rotations around the axes of the
!> @details rotating reference frame
!> @details (see http://en.wikipedia.org/wiki/Euler_angles for definitions)
!> @brief rotation matrix from Bunge-Euler (3-1-3) angles (in radians)
!> @details rotation matrix is meant to represent a PASSIVE rotation, composed of INTRINSIC
!> @details rotations around the axes of the details rotating reference frame.
!> @details similar to eu2om from "D Rowenhorst et al. Consistent representations of and conversions
!> @details between 3D rotations, Model. Simul. Mater. Sci. Eng. 23-8 (2015)", but R is transposed
!--------------------------------------------------------------------------------------------------
pure function math_EulerToR(Euler)
implicit none
real(pReal), dimension(3), intent(in) :: Euler
real(pReal), dimension(3,3) :: math_EulerToR
real(pReal) c1, c, c2, s1, s, s2
real(pReal) :: c1, C, c2, s1, S, s2
C1 = cos(Euler(1))
c1 = cos(Euler(1))
C = cos(Euler(2))
C2 = cos(Euler(3))
S1 = sin(Euler(1))
c2 = cos(Euler(3))
s1 = sin(Euler(1))
S = sin(Euler(2))
S2 = sin(Euler(3))
s2 = sin(Euler(3))
math_EulerToR(1,1)=C1*C2-S1*S2*C
math_EulerToR(1,2)=-C1*S2-S1*C2*C
math_EulerToR(1,3)=S1*S
math_EulerToR(2,1)=S1*C2+C1*S2*C
math_EulerToR(2,2)=-S1*S2+C1*C2*C
math_EulerToR(2,3)=-C1*S
math_EulerToR(3,1)=S2*S
math_EulerToR(3,2)=C2*S
math_EulerToR(1,1) = c1*c2 -s1*C*s2
math_EulerToR(1,2) = -c1*s2 -s1*C*c2
math_EulerToR(1,3) = s1*S
math_EulerToR(2,1) = s1*c2 +c1*C*s2
math_EulerToR(2,2) = -s1*s2 +c1*C*c2
math_EulerToR(2,3) = -c1*S
math_EulerToR(3,1) = S*s2
math_EulerToR(3,2) = S*c2
math_EulerToR(3,3) = C
math_EulerToR = transpose(math_EulerToR) ! convert to passive rotation
@ -1476,29 +1478,29 @@ end function math_EulerToR
!--------------------------------------------------------------------------------------------------
!> @brief quaternion (w+ix+jy+kz) from 3-1-3 Euler angles (in radians)
!> @details quaternion is meant to represent a PASSIVE rotation,
!> @details composed of INTRINSIC rotations around the axes of the
!> @details rotating reference frame
!> @details (see http://en.wikipedia.org/wiki/Euler_angles for definitions)
!> @brief quaternion (w+ix+jy+kz) from Bunge-Euler (3-1-3) angles (in radians)
!> @details rotation matrix is meant to represent a PASSIVE rotation, composed of INTRINSIC
!> @details rotations around the axes of the details rotating reference frame.
!> @details similar to eu2qu from "D Rowenhorst et al. Consistent representations of and
!> @details conversions between 3D rotations, Model. Simul. Mater. Sci. Eng. 23-8 (2015)", but
!> @details Q is conjucated and Q is not reversed for Q(0) < 0.
!--------------------------------------------------------------------------------------------------
pure function math_EulerToQ(eulerangles)
implicit none
real(pReal), dimension(3), intent(in) :: eulerangles
real(pReal), dimension(4) :: math_EulerToQ
real(pReal), dimension(3) :: halfangles
real(pReal) :: c, s
real(pReal) :: c, s, sigma, delta
halfangles = 0.5_pReal * eulerangles
c = cos(0.5_pReal * eulerangles(2))
s = sin(0.5_pReal * eulerangles(2))
sigma = 0.5_pReal * (eulerangles(1)+eulerangles(3))
delta = 0.5_pReal * (eulerangles(1)-eulerangles(3))
c = cos(halfangles(2))
s = sin(halfangles(2))
math_EulerToQ= [cos(halfangles(1)+halfangles(3)) * c, &
cos(halfangles(1)-halfangles(3)) * s, &
sin(halfangles(1)-halfangles(3)) * s, &
sin(halfangles(1)+halfangles(3)) * c ]
math_EulerToQ= [c * cos(sigma), &
s * cos(delta), &
s * sin(delta), &
c * sin(sigma) ]
math_EulerToQ = math_qConj(math_EulerToQ) ! convert to passive rotation
end function math_EulerToQ
@ -1509,6 +1511,8 @@ end function math_EulerToQ
!> @details rotation matrix is meant to represent a ACTIVE rotation
!> @details (see http://en.wikipedia.org/wiki/Euler_angles for definitions)
!> @details formula for active rotation taken from http://mathworld.wolfram.com/RodriguesRotationFormula.html
!> @details equivalent to eu2om (P=-1) from "D Rowenhorst et al. Consistent representations of and
!> @details conversions between 3D rotations, Model. Simul. Mater. Sci. Eng. 23-8 (2015)"
!--------------------------------------------------------------------------------------------------
pure function math_axisAngleToR(axis,omega)
@ -1516,31 +1520,31 @@ pure function math_axisAngleToR(axis,omega)
real(pReal), dimension(3,3) :: math_axisAngleToR
real(pReal), dimension(3), intent(in) :: axis
real(pReal), intent(in) :: omega
real(pReal), dimension(3) :: axisNrm
real(pReal), dimension(3) :: n
real(pReal) :: norm,s,c,c1
norm = norm2(axis)
if (norm > 1.0e-8_pReal) then ! non-zero rotation
axisNrm = axis/norm ! normalize axis to be sure
wellDefined: if (norm > 1.0e-8_pReal) then
n = axis/norm ! normalize axis to be sure
s = sin(omega)
c = cos(omega)
c1 = 1.0_pReal - c
math_axisAngleToR(1,1) = c + c1*axisNrm(1)**2.0_pReal
math_axisAngleToR(1,2) = -s*axisNrm(3) + c1*axisNrm(1)*axisNrm(2)
math_axisAngleToR(1,3) = s*axisNrm(2) + c1*axisNrm(1)*axisNrm(3)
math_axisAngleToR(1,1) = c + c1*n(1)**2.0_pReal
math_axisAngleToR(1,2) = c1*n(1)*n(2) - s*n(3)
math_axisAngleToR(1,3) = c1*n(1)*n(3) + s*n(2)
math_axisAngleToR(2,1) = s*axisNrm(3) + c1*axisNrm(2)*axisNrm(1)
math_axisAngleToR(2,2) = c + c1*axisNrm(2)**2.0_pReal
math_axisAngleToR(2,3) = -s*axisNrm(1) + c1*axisNrm(2)*axisNrm(3)
math_axisAngleToR(2,1) = c1*n(1)*n(2) + s*n(3)
math_axisAngleToR(2,2) = c + c1*n(2)**2.0_pReal
math_axisAngleToR(2,3) = c1*n(2)*n(3) - s*n(1)
math_axisAngleToR(3,1) = -s*axisNrm(2) + c1*axisNrm(3)*axisNrm(1)
math_axisAngleToR(3,2) = s*axisNrm(1) + c1*axisNrm(3)*axisNrm(2)
math_axisAngleToR(3,3) = c + c1*axisNrm(3)**2.0_pReal
else
math_axisAngleToR(3,1) = c1*n(1)*n(3) - s*n(2)
math_axisAngleToR(3,2) = c1*n(2)*n(3) + s*n(1)
math_axisAngleToR(3,3) = c + c1*n(3)**2.0_pReal
else wellDefined
math_axisAngleToR = math_I3
endif
endif wellDefined
end function math_axisAngleToR
@ -1549,6 +1553,8 @@ end function math_axisAngleToR
!> @brief rotation matrix from axis and angle (in radians)
!> @details rotation matrix is meant to represent a PASSIVE rotation
!> @details (see http://en.wikipedia.org/wiki/Euler_angles for definitions)
!> @details eq-uivalent to eu2qu (P=+1) from "D Rowenhorst et al. Consistent representations of and
!> @details conversions between 3D rotations, Model. Simul. Mater. Sci. Eng. 23-8 (2015)"
!--------------------------------------------------------------------------------------------------
pure function math_EulerAxisAngleToR(axis,omega)
@ -1587,6 +1593,8 @@ end function math_EulerAxisAngleToQ
!> @details (see http://en.wikipedia.org/wiki/Euler_angles for definitions)
!> @details formula for active rotation taken from
!> @details http://en.wikipedia.org/wiki/Rotation_representation_%28mathematics%29#Rodrigues_parameters
!> @details equivalent to eu2qu (P=+1) from "D Rowenhorst et al. Consistent representations of and
!> @details conversions between 3D rotations, Model. Simul. Mater. Sci. Eng. 23-8 (2015)"
!--------------------------------------------------------------------------------------------------
pure function math_axisAngleToQ(axis,omega)
@ -1597,13 +1605,13 @@ pure function math_axisAngleToQ(axis,omega)
real(pReal), dimension(3) :: axisNrm
real(pReal) :: norm
norm = sqrt(math_mul3x3(axis,axis))
rotation: if (norm > 1.0e-8_pReal) then
norm = norm2(axis)
wellDefined: if (norm > 1.0e-8_pReal) then
axisNrm = axis/norm ! normalize axis to be sure
math_axisAngleToQ = [cos(0.5_pReal*omega), sin(0.5_pReal*omega) * axisNrm(1:3)]
else rotation
else wellDefined
math_axisAngleToQ = [1.0_pReal,0.0_pReal,0.0_pReal,0.0_pReal]
endif rotation
endif wellDefined
end function math_axisAngleToQ

View File

@ -73,8 +73,11 @@ module mesh
#ifdef Marc4DAMASK
integer(pInt), private :: &
MarcVersion, & !< Version of input file format (Marc only)
hypoelasticTableStyle, & !< Table style (Marc only)
initialcondTableStyle !< Table style (Marc only)
integer(pInt), dimension(:), allocatable, private :: &
Marc_matNumber !< array of material numbers for hypoelastic material (Marc only)
#endif
integer(pInt), dimension(2), private :: &
@ -428,7 +431,9 @@ module mesh
mesh_spectral_build_elements, &
mesh_spectral_build_ipNeighborhood, &
#elif defined Marc4DAMASK
mesh_marc_get_fileFormat, &
mesh_marc_get_tableStyles, &
mesh_marc_get_matNumber, &
mesh_marc_count_nodesAndElements, &
mesh_marc_count_elementSets, &
mesh_marc_map_elementSets, &
@ -519,6 +524,8 @@ subroutine mesh_init(ip,el)
integer(pInt) :: j
logical :: myDebug
external :: MPI_comm_size
write(6,'(/,a)') ' <<<+- mesh init -+>>>'
write(6,'(a15,a)') ' Current time: ',IO_timeStamp()
#include "compilation_info.f90"
@ -577,8 +584,14 @@ subroutine mesh_init(ip,el)
#elif defined Marc4DAMASK
call IO_open_inputFile(FILEUNIT,modelName) ! parse info from input file...
if (myDebug) write(6,'(a)') ' Opened input file'; flush(6)
call mesh_marc_get_fileFormat(FILEUNIT)
if (myDebug) write(6,'(a)') ' Got input file format'; flush(6)
call mesh_marc_get_tableStyles(FILEUNIT)
if (myDebug) write(6,'(a)') ' Got table styles'; flush(6)
if (MarcVersion > 12) then
call mesh_marc_get_matNumber(FILEUNIT)
if (myDebug) write(6,'(a)') ' Got hypoleastic material number'; flush(6)
endif
call mesh_marc_count_nodesAndElements(FILEUNIT)
if (myDebug) write(6,'(a)') ' Counted nodes/elements'; flush(6)
call mesh_marc_count_elementSets(FILEUNIT)
@ -1532,6 +1545,37 @@ end function mesh_nodesAroundCentres
#endif
#ifdef Marc4DAMASK
!--------------------------------------------------------------------------------------------------
!> @brief Figures out version of Marc input file format and stores ist as MarcVersion
!--------------------------------------------------------------------------------------------------
subroutine mesh_marc_get_fileFormat(fileUnit)
use IO, only: &
IO_lc, &
IO_intValue, &
IO_stringValue, &
IO_stringPos
implicit none
integer(pInt), intent(in) :: fileUnit
integer(pInt), allocatable, dimension(:) :: chunkPos
character(len=300) line
610 FORMAT(A300)
rewind(fileUnit)
do
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
if ( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'version') then
MarcVersion = IO_intValue(line,chunkPos,2_pInt)
exit
endif
enddo
620 end subroutine mesh_marc_get_fileFormat
!--------------------------------------------------------------------------------------------------
!> @brief Figures out table styles (Marc only) and stores to 'initialcondTableStyle' and
!! 'hypoelasticTableStyle'
@ -1568,6 +1612,52 @@ subroutine mesh_marc_get_tableStyles(fileUnit)
620 end subroutine mesh_marc_get_tableStyles
!--------------------------------------------------------------------------------------------------
!> @brief Figures out material number of hypoelastic material and stores it in Marc_matNumber array
!--------------------------------------------------------------------------------------------------
subroutine mesh_marc_get_matNumber(fileUnit)
use IO, only: &
IO_lc, &
IO_intValue, &
IO_stringValue, &
IO_stringPos
implicit none
integer(pInt), intent(in) :: fileUnit
integer(pInt), allocatable, dimension(:) :: chunkPos
integer(pInt) :: i, j, data_blocks
character(len=300) line
610 FORMAT(A300)
rewind(fileUnit)
data_blocks = 1_pInt
do
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
if ( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'hypoelastic') then
read (fileUnit,610,END=620) line
if (len(trim(line))/=0_pInt) then
chunkPos = IO_stringPos(line)
data_blocks = IO_intValue(line,chunkPos,1_pInt)
endif
allocate(Marc_matNumber(data_blocks))
do i=1_pInt,data_blocks ! read all data blocks
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
Marc_matNumber(i) = IO_intValue(line,chunkPos,1_pInt)
do j=1_pint,2_pInt + hypoelasticTableStyle ! read 2 or 3 remaining lines of data block
read (fileUnit,610,END=620) line
enddo
enddo
exit
endif
enddo
620 end subroutine mesh_marc_get_matNumber
!--------------------------------------------------------------------------------------------------
!> @brief Count overall number of nodes and elements in mesh and stores the numbers in
@ -1697,13 +1787,14 @@ subroutine mesh_marc_count_cpElements(fileUnit)
IO_stringPos, &
IO_countContinuousIntValues, &
IO_error, &
IO_intValue
IO_intValue, &
IO_countNumericalDataLines
implicit none
integer(pInt), intent(in) :: fileUnit
integer(pInt), allocatable, dimension(:) :: chunkPos
integer(pInt) :: i, version
integer(pInt) :: i
character(len=300):: line
mesh_NcpElems = 0_pInt
@ -1711,13 +1802,7 @@ subroutine mesh_marc_count_cpElements(fileUnit)
610 FORMAT(A300)
rewind(fileUnit)
do
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
if ( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'version') then
version = IO_intValue(line,chunkPos,2_pInt)
if (version < 13) then ! Marc 2016 or earlier
rewind(fileUnit)
if (MarcVersion < 13) then ! Marc 2016 or earlier
do
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
@ -1725,15 +1810,23 @@ subroutine mesh_marc_count_cpElements(fileUnit)
do i=1_pInt,3_pInt+hypoelasticTableStyle ! Skip 3 or 4 lines
read (fileUnit,610,END=620) line
enddo
mesh_NcpElems = mesh_NcpElems + IO_countContinuousIntValues(fileUnit) ! why not simply mesh_NcpElems = IO_countContinuousIntValues(fileUnit)? keyword hypoelastic might appear several times
mesh_NcpElems = mesh_NcpElems + IO_countContinuousIntValues(fileUnit) ! why not simply mesh_NcpElems = IO_countContinuousIntValues(fileUnit)? not fully correct as hypoelastic can have multiple data fields, needs update
exit
endif
enddo
else ! Marc2017 and later
call IO_error(error_ID=701_pInt)
do
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
if ( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'connectivity') then
read (fileUnit,610,END=620) line
chunkPos = IO_stringPos(line)
if (any(Marc_matNumber==IO_intValue(line,chunkPos,6_pInt))) then
mesh_NcpElems = mesh_NcpElems + IO_countNumericalDataLines(fileUnit)
endif
endif
enddo
end if
620 end subroutine mesh_marc_count_cpElements
@ -1746,6 +1839,7 @@ subroutine mesh_marc_map_elements(fileUnit)
use math, only: math_qsort
use IO, only: IO_lc, &
IO_intValue, &
IO_stringValue, &
IO_stringPos, &
IO_continuousIntValues
@ -1754,7 +1848,8 @@ subroutine mesh_marc_map_elements(fileUnit)
integer(pInt), intent(in) :: fileUnit
integer(pInt), allocatable, dimension(:) :: chunkPos
character(len=300) :: line
character(len=300) :: line, &
tmp
integer(pInt), dimension (1_pInt+mesh_NcpElems) :: contInts
integer(pInt) :: i,cpElem = 0_pInt
@ -1763,25 +1858,47 @@ subroutine mesh_marc_map_elements(fileUnit)
610 FORMAT(A300)
contInts = 0_pInt
rewind(fileUnit)
do
read (fileUnit,610,END=660) line
chunkPos = IO_stringPos(line)
if (MarcVersion < 13) then ! Marc 2016 or earlier
if( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'hypoelastic' ) then
do i=1_pInt,3_pInt+hypoelasticTableStyle ! skip three (or four if new table style!) lines
read (fileUnit,610,END=660) line
enddo
contInts = IO_continuousIntValues(fileUnit,mesh_NcpElems,mesh_nameElemSet,&
mesh_mapElemSet,mesh_NelemSets)
do i = 1_pInt,contInts(1)
exit
endif
else ! Marc2017 and later
if ( IO_lc(IO_stringValue(line,chunkPos,1_pInt)) == 'connectivity') then
read (fileUnit,610,END=660) line
chunkPos = IO_stringPos(line)
if(any(Marc_matNumber==IO_intValue(line,chunkPos,6_pInt))) then
do
read (fileUnit,610,END=660) line
chunkPos = IO_stringPos(line)
tmp = IO_lc(IO_stringValue(line,chunkPos,1_pInt))
if (verify(trim(tmp),"0123456789")/=0) then ! found keyword
exit
else
contInts(1) = contInts(1) + 1_pInt
read (tmp,*) contInts(contInts(1)+1)
endif
enddo
endif
endif
endif
enddo
660 do i = 1_pInt,contInts(1)
cpElem = cpElem+1_pInt
mesh_mapFEtoCPelem(1,cpElem) = contInts(1_pInt+i)
mesh_mapFEtoCPelem(2,cpElem) = cpElem
enddo
endif
enddo
660 call math_qsort(mesh_mapFEtoCPelem,1_pInt,int(size(mesh_mapFEtoCPelem,2_pInt),pInt)) ! should be mesh_NcpElems
call math_qsort(mesh_mapFEtoCPelem,1_pInt,int(size(mesh_mapFEtoCPelem,2_pInt),pInt)) ! should be mesh_NcpElems
end subroutine mesh_marc_map_elements
@ -2936,7 +3053,6 @@ subroutine mesh_build_sharedElems
allocate(node_seen(maxval(FE_NmatchingNodes)))
node_count = 0_pInt
do e = 1_pInt,mesh_NcpElems

View File

@ -25,7 +25,7 @@ module numerics
nState = 10_pInt, & !< state loop limit
nStress = 40_pInt, & !< stress loop limit
pert_method = 1_pInt, & !< method used in perturbation technique for tangent
fixedSeed = 0_pInt, & !< fixed seeding for pseudo-random number generator, Default 0: use random seed
randomSeed = 0_pInt, & !< fixed seeding for pseudo-random number generator, Default 0: use random seed
worldrank = 0_pInt, & !< MPI worldrank (/=0 for MPI simulations only)
worldsize = 0_pInt !< MPI worldsize (/=0 for MPI simulations only)
integer(4), protected, public :: &
@ -359,8 +359,8 @@ subroutine numerics_init
!--------------------------------------------------------------------------------------------------
! random seeding parameter
case ('fixed_seed')
fixedSeed = IO_intValue(line,chunkPos,2_pInt)
case ('random_seed','fixed_seed')
randomSeed = IO_intValue(line,chunkPos,2_pInt)
!--------------------------------------------------------------------------------------------------
! gradient parameter
@ -560,9 +560,9 @@ subroutine numerics_init
!--------------------------------------------------------------------------------------------------
! Random seeding parameter
write(6,'(a24,1x,i16,/)') ' fixed_seed: ',fixedSeed
if (fixedSeed <= 0_pInt) &
write(6,'(a,/)') ' No fixed Seed: Random is random!'
write(6,'(a24,1x,i16,/)') ' random_seed: ',randomSeed
if (randomSeed <= 0_pInt) &
write(6,'(a,/)') ' random seed will be generated!'
!--------------------------------------------------------------------------------------------------
! gradient parameter

View File

@ -1178,7 +1178,7 @@ end subroutine plastic_disloUCLA_dotState
function plastic_disloUCLA_postResults(Tstar_v,Temperature,ipc,ip,el)
use prec, only: &
tol_math_check, &
dEq
dEq, dNeq0
use math, only: &
pi
use material, only: &
@ -1445,9 +1445,13 @@ function plastic_disloUCLA_postResults(Tstar_v,Temperature,ipc,ip,el)
index_myFamily = sum(lattice_NslipSystem(1:f-1_pInt,ph)) ! at which index starts my family
slipSystems2: do i = 1_pInt,plastic_disloUCLA_Nslip(f,instance)
j = j + 1_pInt
if (dNeq0(abs(dot_product(Tstar_v,lattice_Sslip_v(:,1,index_myFamily+i,ph))))) then
plastic_disloUCLA_postResults(c+j) = &
(3.0_pReal*lattice_mu(ph)*plastic_disloUCLA_burgersPerSlipSystem(j,instance))/&
(16.0_pReal*pi*abs(dot_product(Tstar_v,lattice_Sslip_v(:,1,index_myFamily+i,ph))))
else
plastic_disloUCLA_postResults(c+j) = huge(1.0_pReal)
endif
plastic_disloUCLA_postResults(c+j)=min(plastic_disloUCLA_postResults(c+j),&
state(instance)%mfp_slip(j,of))
enddo slipSystems2; enddo slipFamilies2

View File

@ -1029,7 +1029,7 @@ subroutine plastic_dislotwin_init(fileUnit)
do p = 1_pInt,3_pInt; do q = 1_pInt,3_pInt; do r = 1_pInt,3_pInt; do s = 1_pInt,3_pInt
plastic_dislotwin_Ctwin3333(l,m,n,o,index_myFamily+j,instance) = &
plastic_dislotwin_Ctwin3333(l,m,n,o,index_myFamily+j,instance) + &
lattice_C3333(p,q,r,s,instance) * &
lattice_C3333(p,q,r,s,phase) * &
lattice_Qtwin(l,p,index_otherFamily+j,phase) * &
lattice_Qtwin(m,q,index_otherFamily+j,phase) * &
lattice_Qtwin(n,r,index_otherFamily+j,phase) * &
@ -1087,7 +1087,7 @@ subroutine plastic_dislotwin_init(fileUnit)
do p = 1_pInt,3_pInt; do q = 1_pInt,3_pInt; do r = 1_pInt,3_pInt; do s = 1_pInt,3_pInt
plastic_dislotwin_Ctrans3333(l,m,n,o,index_myFamily+j,instance) = &
plastic_dislotwin_Ctrans3333(l,m,n,o,index_myFamily+j,instance) + &
lattice_trans_C3333(p,q,r,s,instance) * &
lattice_trans_C3333(p,q,r,s,phase) * &
lattice_Qtrans(l,p,index_otherFamily+j,phase) * &
lattice_Qtrans(m,q,index_otherFamily+j,phase) * &
lattice_Qtrans(n,r,index_otherFamily+j,phase) * &

View File

@ -1823,14 +1823,14 @@ plasticState(ph)%state(iRhoF(1:ns,instance),of) = rhoForest
plasticState(ph)%state(iTauF(1:ns,instance),of) = tauThreshold
plasticState(ph)%state(iTauB(1:ns,instance),of) = tauBack
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt)) then
write(6,'(/,a,i8,1x,i2,1x,i1,/)') '<< CONST >> nonlocal_microstructure at el ip ',el,ip
write(6,'(a,/,12x,12(e10.3,1x))') '<< CONST >> rhoForest', rhoForest
write(6,'(a,/,12x,12(f10.5,1x))') '<< CONST >> tauThreshold / MPa', tauThreshold/1e6
write(6,'(a,/,12x,12(f10.5,1x),/)') '<< CONST >> tauBack / MPa', tauBack/1e6
write(6,'(a,/,12x,12(f10.5,1x))') '<< CONST >> tauThreshold / MPa', tauThreshold*1e-6
write(6,'(a,/,12x,12(f10.5,1x),/)') '<< CONST >> tauBack / MPa', tauBack*1e-6
endif
#endif
@ -1978,15 +1978,15 @@ if (Temperature > 0.0_pReal) then
endif
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt)) then
write(6,'(/,a,i8,1x,i2,1x,i1,/)') '<< CONST >> nonlocal_kinetics at el ip',el,ip
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tauThreshold / MPa', tauThreshold / 1e6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tau / MPa', tau / 1e6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tauNS / MPa', tauNS / 1e6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> v / 1e-3m/s', v * 1e3
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tauThreshold / MPa', tauThreshold * 1e-6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tau / MPa', tau * 1e-6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> tauNS / MPa', tauNS * 1e-6_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> v / mm/s', v * 1e3
write(6,'(a,/,12x,12(e12.5,1x))') '<< CONST >> dv_dtau', dv_dtau
write(6,'(a,/,12x,12(e12.5,1x))') '<< CONST >> dv_dtauNS', dv_dtauNS
endif
@ -2176,12 +2176,12 @@ enddo
dLp_dTstar99 = math_Plain3333to99(dLp_dTstar3333)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt )) then
write(6,'(/,a,i8,1x,i2,1x,i1,/)') '<< CONST >> nonlocal_LpandItsTangent at el ip',el,ip
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> gdot total / 1e-3',gdotTotal*1e3_pReal
write(6,'(a,/,12x,12(f12.5,1x))') '<< CONST >> gdot total',gdotTotal
write(6,'(a,/,3(12x,3(f12.7,1x),/))') '<< CONST >> Lp',transpose(Lp)
endif
#endif
@ -2248,7 +2248,7 @@ real(pReal), dimension(totalNslip(phase_plasticityInstance(material_phase(1,ip,e
dUpperOld, & ! old maximum stable dipole distance for edges and screws
deltaDUpper ! change in maximum stable dipole distance for edges and screws
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt)) &
@ -2361,7 +2361,7 @@ forall (s = 1:ns, c = 1_pInt:2_pInt) &
plasticState(ph)%deltaState(iRhoD(s,c,instance),of) = deltaRho(s,c+8_pInt)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt )) then
@ -2522,11 +2522,11 @@ logical considerEnteringFlux, &
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt)) &
write(6,'(/,a,i8,1x,i2,1x,i1,/)') '<< CONST >> nonlocal_dotState at el ip ',el,ip
write(6,'(/,a,i8,1x,i2,/)') '<< CONST >> nonlocal_dotState at el ip ',el,ip
#endif
ph = material_phase(1_pInt,ip,el)
@ -2589,7 +2589,7 @@ endif
forall (t = 1_pInt:4_pInt) &
gdot(1_pInt:ns,t) = rhoSgl(1_pInt:ns,t) * burgers(1:ns,instance) * v(1:ns,t)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelBasic) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt )) then
@ -2663,7 +2663,7 @@ else
/ burgers(s,instance) * sqrt(rhoForest(s)) / lambda0(s,instance)
endif
enddo
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt )) &
@ -2690,7 +2690,7 @@ if (.not. phase_localPlasticity(material_phase(1_pInt,ip,el))) then
if (any( abs(gdot) > 0.0_pReal & ! any active slip system ...
.and. CFLfactor(instance) * abs(v) * timestep &
> mesh_ipVolume(ip,el) / maxval(mesh_ipArea(:,ip,el)))) then ! ...with velocity above critical value (we use the reference volume and area for simplicity here)
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt) then
write(6,'(a,i5,a,i2)') '<< CONST >> CFL condition not fullfilled at el ',el,' ip ',ip
write(6,'(a,e10.3,a,e10.3)') '<< CONST >> velocity is at ', &
@ -2952,7 +2952,7 @@ if (numerics_integrationMode == 1_pInt) then
endif
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt &
.and. ((debug_e == el .and. debug_i == ip .and. debug_g == 1_pInt)&
.or. .not. iand(debug_level(debug_constitutive),debug_levelSelective) /= 0_pInt )) then
@ -2978,7 +2978,7 @@ endif
if ( any(rhoSglOriginal(1:ns,1:4) + rhoDot(1:ns,1:4) * timestep < -aTolRho(instance)) &
.or. any(rhoDipOriginal(1:ns,1:2) + rhoDot(1:ns,9:10) * timestep < -aTolRho(instance))) then
#ifndef _OPENMP
#ifdef DEBUG
if (iand(debug_level(debug_constitutive),debug_levelExtensive) /= 0_pInt) then
write(6,'(a,i5,a,i2)') '<< CONST >> evolution rate leads to negative density at el ',el,' ip ',ip
write(6,'(a)') '<< CONST >> enforcing cutback !!!'

File diff suppressed because it is too large Load Diff

File diff suppressed because it is too large Load Diff

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@ -137,6 +137,7 @@ end subroutine prec_init
!> @brief equality comparison for float with double precision
! replaces "==" but for certain (relative) tolerance. Counterpart to dNeq
! https://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
! AlmostEqualRelative
!--------------------------------------------------------------------------------------------------
logical elemental pure function dEq(a,b,tol)
@ -153,6 +154,7 @@ end function dEq
!> @brief inequality comparison for float with double precision
! replaces "!=" but for certain (relative) tolerance. Counterpart to dEq
! https://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
! AlmostEqualRelative NOT
!--------------------------------------------------------------------------------------------------
logical elemental pure function dNeq(a,b,tol)
@ -167,33 +169,35 @@ end function dNeq
!--------------------------------------------------------------------------------------------------
!> @brief equality to 0 comparison for float with double precision
! replaces "==0" but for certain (absolute) tolerance. Counterpart to dNeq0
! https://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
! replaces "==0" but everything not representable as a normal number is treated as 0. Counterpart to dNeq0
! https://de.mathworks.com/help/matlab/ref/realmin.html
! https://docs.oracle.com/cd/E19957-01/806-3568/ncg_math.html
!--------------------------------------------------------------------------------------------------
logical elemental pure function dEq0(a,tol)
implicit none
real(pReal), intent(in) :: a
real(pReal), intent(in), optional :: tol
real(pReal), parameter :: eps = 2.220446049250313E-16 ! DBL_EPSILON in C
real(pReal), parameter :: eps = 2.2250738585072014E-308 ! smallest non-denormalized number
dEq0 = merge(.True., .False.,abs(a) <= merge(tol,eps,present(tol))*10.0_pReal)
dEq0 = merge(.True., .False.,abs(a) <= merge(tol,eps,present(tol)))
end function dEq0
!--------------------------------------------------------------------------------------------------
!> @brief inequality to 0 comparison for float with double precision
! replaces "!=0" but for certain (absolute) tolerance. Counterpart to dEq0
! https://randomascii.wordpress.com/2012/02/25/comparing-floating-point-numbers-2012-edition/
! replaces "!=0" but everything not representable as a normal number is treated as 0. Counterpart to dEq0
! https://de.mathworks.com/help/matlab/ref/realmin.html
! https://docs.oracle.com/cd/E19957-01/806-3568/ncg_math.html
!--------------------------------------------------------------------------------------------------
logical elemental pure function dNeq0(a,tol)
implicit none
real(pReal), intent(in) :: a
real(pReal), intent(in), optional :: tol
real(pReal), parameter :: eps = 2.220446049250313E-16 ! DBL_EPSILON in C
real(pReal), parameter :: eps = 2.2250738585072014E-308 ! smallest non-denormalized number
dNeq0 = merge(.False., .True.,abs(a) <= merge(tol,eps,present(tol))*10.0_pReal)
dNeq0 = merge(.False., .True.,abs(a) <= merge(tol,eps,present(tol)))
end function dNeq0

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@ -310,7 +310,6 @@ subroutine BasicPETSC_formResidual(in,x_scal,f_scal,dummy,ierr)
debug_spectral, &
debug_spectralRotation
use spectral_utilities, only: &
wgt, &
tensorField_real, &
utilities_FFTtensorForward, &
utilities_fourierGammaConvolution, &

View File

@ -971,6 +971,9 @@ subroutine utilities_constitutiveResponse(F_lastInc,F,timeinc, &
real(pReal), dimension(3,3,3,3) :: max_dPdF, min_dPdF
real(pReal) :: max_dPdF_norm, min_dPdF_norm, defgradDetMin, defgradDetMax, defgradDet
external :: &
MPI_Allreduce
write(6,'(/,a)') ' ... evaluating constitutive response ......................................'
flush(6)
age = .False.