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DAMASK_EICMD
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Merge branch 'development' of git.damask.mpie.de:damask/DAMASK into typehints_orientation_rotation

This commit is contained in:
Daniel Otto de Mentock 2022-01-13 17:23:24 +01:00
parent 0a31ff0980 a000e477cf
commit 4ba9935ccc
57 changed files with 1374 additions and 877 deletions
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7
.github/workflows/Python.yml vendored
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@ -43,12 +43,13 @@ jobs:
pip install pytest
- name: Install dependencies
# https://github.com/actions/virtual-environments/issues/4790
run: >
sudo apt-get update &&
sudo apt-get install python3-pip python3-pytest python3-pandas python3-scipy
python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
sudo apt-get remove mysql* &&
sudo apt-get install python3-pandas python3-scipy python3-h5py python3-vtk7 python3-matplotlib python3-yaml -y
- name: Run unit tests
run: |
export PYTHONPATH=${PWD}/python
COLUMNS=256 python -m pytest python
COLUMNS=256 pytest python

48
.gitlab-ci.yml
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@ -36,14 +36,17 @@ variables:
# Names of module files to load
# ===============================================================================================
# ++++++++++++ Compiler +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
COMPILER_INTEL: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
COMPILER_GNU: "Compiler/GNU/10"
COMPILER_GNU: "Compiler/GNU/10"
COMPILER_INTELLLVM: "Compiler/oneAPI/2022.0.1 Libraries/IMKL/2022.0.1"
COMPILER_INTEL: "Compiler/Intel/2022.0.1 Libraries/IMKL/2022.0.1"
# ++++++++++++ MPI ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MPI_INTEL: "MPI/Intel/19.1.2/IntelMPI/2019"
MPI_GNU: "MPI/GNU/10/OpenMPI/4.1.1"
MPI_INTELLLVM: "MPI/oneAPI/2022.0.1/IntelMPI/2021.5.0"
MPI_INTEL: "MPI/Intel/2022.0.1/IntelMPI/2021.5.0"
# ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
PETSC_INTEL: "Libraries/PETSc/3.16.1/Intel-19.1.2-IntelMPI-2019"
PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
PETSC_INTEL: "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0"
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MSC: "FEM/MSC/2021.3.1"
IntelMarc: "Compiler/Intel/19.1.2 Libraries/IMKL/2020"
@ -76,20 +79,6 @@ mypy:
###################################################################################################
test_grid_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
test_mesh_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
test_grid_GNU:
stage: compile
script:
@ -104,6 +93,27 @@ test_mesh_GNU:
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_GNU
test_mesh_IntelLLVM:
stage: compile
script:
- module load ${COMPILER_INTELLLVM} ${MPI_INTELLLVM} ${PETSC_INTELLLVM}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_IntelLLVM
test_grid_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and grid' --basetemp ${TESTROOT}/compile_grid_Intel
test_mesh_Intel:
stage: compile
script:
- module load ${COMPILER_INTEL} ${MPI_INTEL} ${PETSC_INTEL}
- cd PRIVATE/testing/pytest
- pytest -k 'compile and mesh' --basetemp ${TESTROOT}/compile_mesh_Intel
test_Marc:
stage: compile
script:

14
CMakeLists.txt
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@ -82,20 +82,18 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
include(Compiler-Intel)
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
include(Compiler-GNU)
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "IntelLLVM")
include(Compiler-IntelLLVM)
else()
message(FATAL_ERROR "Compiler type(CMAKE_Fortran_COMPILER_ID) not recognized")
endif()
file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_EXTERNAL_LIB REGEX "PETSC_WITH_EXTERNAL_LIB = .*$?")
string(REGEX MATCHALL "-[lLW]([^\" ]+)" PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}")
list(REMOVE_DUPLICATES PETSC_EXTERNAL_LIB)
string(REPLACE ";" " " PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}")
file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_EXTERNAL_LIB REGEX "PETSC_EXTERNAL_LIB_BASIC = .*$?")
string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}")
message("PETSC_EXTERNAL_LIB:\n${PETSC_EXTERNAL_LIB}\n")
file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_INCLUDES REGEX "PETSC_FC_INCLUDES = .*$?")
string(REGEX MATCHALL "-I([^\" ]+)" PETSC_INCLUDES "${PETSC_INCLUDES}")
list(REMOVE_DUPLICATES PETSC_INCLUDES)
string(REPLACE ";" " " PETSC_INCLUDES "${PETSC_INCLUDES}")
string(REPLACE "PETSC_FC_INCLUDES = " "" PETSC_INCLUDES "${PETSC_INCLUDES}")
message("PETSC_INCLUDES:\n${PETSC_INCLUDES}\n")
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${BUILDCMD_PRE} ${OPENMP_FLAGS} ${STANDARD_CHECK} ${OPTIMIZATION_FLAGS} ${COMPILE_FLAGS} ${PRECISION_FLAGS}")
@ -107,7 +105,7 @@ if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
endif()
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> ${PETSC_EXTERNAL_LIB} -lz ${BUILDCMD_POST}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz ${BUILDCMD_POST}")
message("Fortran Compiler Flags:\n${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}}\n")
message("C Compiler Flags:\n${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}\n")

6
Makefile
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@ -10,14 +10,12 @@ all: grid mesh
.PHONY: grid
grid:
@cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
@cmake --build build/grid --parallel
@cmake --install build/grid
@cmake --build build/grid --parallel --target install
.PHONY: mesh
mesh:
@cmake -B build/mesh -DDAMASK_SOLVER=mesh -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
@cmake --build build/mesh --parallel
@cmake --install build/mesh
@cmake --build build/mesh --parallel --target install
.PHONY: clean
clean:

2
PRIVATE

@ -1 +1 @@
Subproject commit e6e1f93a36d63348359a81d7c373083a39977694
Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53

3
cmake/Compiler-Intel.cmake
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@ -106,8 +106,9 @@ set (DEBUG_FLAGS "${DEBUG_FLAGS} -fpe-all=0")
#set (DEBUG_FLAGS "${DEBUG_FLAGS},stderrors")
# ... warnings about Fortran standard violations are changed to errors
set (DEBUG_FLAGS "${DEBUG_FLAGS} -debug-parameters all")
#set (DEBUG_FLAGS "${DEBUG_FLAGS} -debug-parameters all")
# generate debug information for parameters
# Disabled due to ICE when compiling phase_damage.f90 (not understandable, there is no parameter in there)
# Additional options
# -heap-arrays: Should not be done for OpenMP, but set "ulimit -s unlimited" on shell. Probably it helps also to unlimit other limits

121
cmake/Compiler-IntelLLVM.cmake Normal file
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@ -0,0 +1,121 @@
###################################################################################################
# Intel Compiler
###################################################################################################
if (CMAKE_Fortran_COMPILER_VERSION VERSION_LESS 18.0)
message (FATAL_ERROR "Intel Compiler version: ${CMAKE_Fortran_COMPILER_VERSION} not supported")
endif ()
if (OPENMP)
set (OPENMP_FLAGS "-qopenmp")
endif ()
if (OPTIMIZATION STREQUAL "OFF")
set (OPTIMIZATION_FLAGS "-O0")
elseif (OPTIMIZATION STREQUAL "DEFENSIVE")
set (OPTIMIZATION_FLAGS "-O2")
elseif (OPTIMIZATION STREQUAL "AGGRESSIVE")
set (OPTIMIZATION_FLAGS "-ipo -O3 -fp-model fast=2 -xHost")
# -fast = -ipo, -O3, -no-prec-div, -static, -fp-model fast=2, and -xHost"
endif ()
# -assume std_mod_proc_name (included in -standard-semantics) causes problems if other modules
# (PETSc, HDF5) are not compiled with this option (https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/62172)
set (STANDARD_CHECK "-stand f18 -assume nostd_mod_proc_name")
set (LINKER_FLAGS "${LINKER_FLAGS} -shared-intel")
# Link against shared Intel libraries instead of static ones
#------------------------------------------------------------------------------------------------
# Fine tuning compilation options
set (COMPILE_FLAGS "${COMPILE_FLAGS} -fpp")
# preprocessor
set (COMPILE_FLAGS "${COMPILE_FLAGS} -ftz")
# flush underflow to zero, automatically set if -O[1,2,3]
set (COMPILE_FLAGS "${COMPILE_FLAGS} -diag-disable")
# disables warnings ...
set (COMPILE_FLAGS "${COMPILE_FLAGS} 5268")
# ... the text exceeds right hand column allowed on the line (we have only comments there)
set (COMPILE_FLAGS "${COMPILE_FLAGS},7624")
# ... about deprecated forall (has nice syntax and most likely a performance advantage)
set (COMPILE_FLAGS "${COMPILE_FLAGS} -warn")
# enables warnings ...
set (COMPILE_FLAGS "${COMPILE_FLAGS} declarations")
# ... any undeclared names (alternative name: -implicitnone)
set (COMPILE_FLAGS "${COMPILE_FLAGS},general")
# ... warning messages and informational messages are issued by the compiler
set (COMPILE_FLAGS "${COMPILE_FLAGS},usage")
# ... questionable programming practices
set (COMPILE_FLAGS "${COMPILE_FLAGS},interfaces")
# ... checks the interfaces of all SUBROUTINEs called and FUNCTIONs invoked in your compilation against an external set of interface blocks
set (COMPILE_FLAGS "${COMPILE_FLAGS},ignore_loc")
# ... %LOC is stripped from an actual argument
set (COMPILE_FLAGS "${COMPILE_FLAGS},alignments")
# ... data that is not naturally aligned
set (COMPILE_FLAGS "${COMPILE_FLAGS},unused")
# ... declared variables that are never used
# Additional options
# -warn: enables warnings, where
# truncated_source: Determines whether warnings occur when source exceeds the maximum column width in fixed-format files.
# (too many warnings because we have comments beyond character 132)
# uncalled: Determines whether warnings occur when a statement function is never called
# all:
# -name as_is: case sensitive Fortran!
#------------------------------------------------------------------------------------------------
# Runtime debugging
set (DEBUG_FLAGS "${DEBUG_FLAGS} -g")
# Generate symbolic debugging information in the object file
set (DEBUG_FLAGS "${DEBUG_FLAGS} -traceback")
# Generate extra information in the object file to provide source file traceback information when a severe error occurs at run time
set (DEBUG_FLAGS "${DEBUG_FLAGS} -gen-interfaces")
# Generate an interface block for each routine. http://software.intel.com/en-us/blogs/2012/01/05/doctor-fortran-gets-explicit-again/
set (DEBUG_FLAGS "${DEBUG_FLAGS} -fp-stack-check")
# Generate extra code after every function call to ensure that the floating-point (FP) stack is in the expected state
set (DEBUG_FLAGS "${DEBUG_FLAGS} -fp-model strict")
# Trap uninitalized variables
set (DEBUG_FLAGS "${DEBUG_FLAGS} -check" )
# Checks at runtime ...
set (DEBUG_FLAGS "${DEBUG_FLAGS} bounds")
# ... if an array index is too small (<1) or too large!
set (DEBUG_FLAGS "${DEBUG_FLAGS},format")
# ... for the data type of an item being formatted for output.
set (DEBUG_FLAGS "${DEBUG_FLAGS},output_conversion")
# ... for the fit of data items within a designated format descriptor field.
set (DEBUG_FLAGS "${DEBUG_FLAGS},pointers")
# ... for certain disassociated or uninitialized pointers or unallocated allocatable objects.
set (DEBUG_FLAGS "${DEBUG_FLAGS},uninit")
# ... for uninitialized variables.
set (DEBUG_FLAGS "${DEBUG_FLAGS} -ftrapuv")
# ... initializes stack local variables to an unusual value to aid error detection
set (DEBUG_FLAGS "${DEBUG_FLAGS} -fpe-all=0")
# ... capture all floating-point exceptions, sets -ftz automatically
# disable due to compiler bug https://community.intel.com/t5/Intel-Fortran-Compiler/false-positive-stand-f18-and-IEEE-SELECTED-REAL-KIND/m-p/1227336
#set (DEBUG_FLAGS "${DEBUG_FLAGS} -warn")
# enables warnings ...
#set (DEBUG_FLAGS "${DEBUG_FLAGS} errors")
# ... warnings are changed to errors
#set (DEBUG_FLAGS "${DEBUG_FLAGS},stderrors")
# ... warnings about Fortran standard violations are changed to errors
set (DEBUG_FLAGS "${DEBUG_FLAGS} -debug-parameters all")
# generate debug information for parameters
# Additional options
# -heap-arrays: Should not be done for OpenMP, but set "ulimit -s unlimited" on shell. Probably it helps also to unlimit other limits
# -check: Checks at runtime, where
# arg_temp_created: will cause a lot of warnings because we create a bunch of temporary arrays (performance?)
# stack:
#------------------------------------------------------------------------------------------------
# precision settings
set (PRECISION_FLAGS "${PRECISION_FLAGS} -real-size 64")
# set precision for standard real to 32 | 64 | 128 (= 4 | 8 | 16 bytes, type pReal is always 8 bytes)

23
examples/config/Phase_Phenopowerlaw_BCC-Martensite.yaml
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@ -1,17 +1,12 @@
# Tasan et.al. 2015 Acta Materalia
# Tasan et.al. 2015 International Journal of Plasticity
# Diehl et.al. 2015 Meccanica
Martensite:
lattice: cI
mechanical:
elastic: {C_11: 417.4e+9, C_12: 242.4e+9, C_44: 211.1e+9, type: Hooke}
plastic:
N_sl: [12, 12]
a_sl: 2.0
dot_gamma_0_sl: 0.001
h_0_sl-sl: 563.0e+9
h_sl-sl: [1, 1.4, 1, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
type: phenopowerlaw
xi_0_sl: [405.8e+6, 456.7e+6]
xi_inf_sl: [872.9e+6, 971.2e+6]
N_sl: [12, 12]
a_sl: 2.0
dot_gamma_0_sl: 0.001
h_0_sl-sl: 563.0e+9
h_sl-sl: [1, 1.4, 1, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4, 1.4]
n_sl: 20
type: phenopowerlaw
xi_0_sl: [405.8e+6, 456.7e+6]
xi_inf_sl: [872.9e+6, 971.2e+6]

6
examples/config/phase/AISI304.yaml Normal file
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@ -0,0 +1,6 @@
references:
- H.M. Ledbetter
physica status solidi (a) 85(1):89-96, 1984
https://doi.org/10.1002/pssa.2210850111
lattice: cF
rho: 7937.0

4
examples/config/phase/Ag.yaml Normal file
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@ -0,0 +1,4 @@
references:
- https://en.wikipedia.org/wiki/Silver
lattice: cF
rho: 10490.0

7
examples/config/phase/mechanical/eigen/thermalexpansion_AISI304.yaml Normal file
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@ -0,0 +1,7 @@
type: thermalexpansion
references:
- R.H. Bogaard et al.
Thermochimica Acta 218:373-393, 1993
https://doi.org/10.1016/0040-6031(93)80437-F
A_11: 15.0e-6
T_ref: 300.0

8
examples/config/phase/mechanical/elastic/Hooke_AISI304.yaml Normal file
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@ -0,0 +1,8 @@
type: Hooke
references:
- H.M. Ledbetter
physica status solidi (a) 85(1):89-96, 1984
https://doi.org/10.1002/pssa.2210850111
C_11: 204.6e+9
C_12: 137.7e+9
C_44: 126.2e+9

22
examples/config/phase/mechanical/elastic/Hooke_Ag.yaml Normal file
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@ -0,0 +1,22 @@
type: Hooke
references:
- J.R. Neighbours and G.A. Alers,
Physical Review 111:707-712, 1958,
https://doi.org/10.1103/PhysRev.111.707
- Y.A. Chang and L. Himmel,
Journal of Applied Physics 37:3567-3572, 1966,
https://doi.org/10.1063/1.1708903
T_ref: 300
C_11: 122.9e+9
C_11,T: -313.5e+5
C_11,T^2: -107.3e+2
C_12: 91.55e+9
C_12,T: -164.1e+5
C_12,T^2: -681.6e+1
C_44: 42.63e+9
C_44,T: -180.5e+5
C_44,T^2: -353.8e+1

26
examples/config/phase/mechanical/elastic/Hooke_Al.yaml
View File

@ -1,8 +1,22 @@
type: Hooke
references:
- J. Vallin et al.,
Journal of Applied Physics 35(6):1825-1826, 1964,
https://doi.org/10.1063/1.1713749
C_11: 107.3e+9
C_12: 60.8e+9
C_44: 28.3e+9
- G.N. Kamm and G.A. Alers,
Journal of Applied Physics 35:327-330, 1964,
https://doi.org/10.1063/1.1713309
- D. Gerlich and E.S. Fisher,
Journal of Physics and Chemistry of Solids 30:1197-1205, 1969
https://doi.org/10.1016/0022-3697(69)90377-1
T_ref: 300
C_11: 106.1e+9
C_11,T: -359.3e+5
C_11,T^2: -152.7e+2
C_12: 57.83e+9
C_12,T: -781.6e+4
C_12,T^2: -551.3e+1
C_44: 24.31e+9
C_44,T: -142.9e+5
C_44,T^2: -404.6e+1

24
examples/config/phase/mechanical/elastic/Hooke_Fe.yaml
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@ -1,9 +1,19 @@
type: Hooke
references:
- J.P. Hirth and J. Lothe,
Theory of Dislocations, 1982,
John Wiley & Sons,
page 837
C_11: 242.e9
C_12: 146.5e+9
C_44: 112.e9
- D.J. Dever,
Journal of Applied Physics 43(8):3293-3301, 1972,
https://doi.org/10.1063/1.1661710
T_ref: 300
C_11: 231.7e+9
C_11,T: -47.6e+6
C_11,T^2: -54.4e+3
C_12: 135.8e+9
C_12,T: -12.9e+6
C_12,T^2: -7.3e+3
C_44: 116.8e+9
C_44,T: -19.4e+6
C_44,T^2: -2.5e+3

8
examples/config/phase/mechanical/elastic/Hooke_SAE1050-martensite.yaml Normal file
View File

@ -0,0 +1,8 @@
type: Hooke
references:
- S.A. Kim and W.L. Johnson,
Materials Science & Engineering A 452-453:633-639, 2007,
https://doi.org/10.1016/j.msea.2006.11.147
C_11: 268.1e+9
C_12: 111.2e+9
C_44: 79.06e+9

3
examples/config/phase/mechanical/plastic/dislotwin_IF-steel.yaml
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@ -4,7 +4,8 @@ references:
International Journal of Plasticity 134:102779, 2020,
https://doi.org/10.1016/j.ijplas.2020.102779
- K. Sedighiani et al.,
Mechanics of Materials, submitted
Mechanics of Materials, 164:104117, 2022,
https://doi.org/10.1016/j.mechmat.2021.104117
output: [rho_dip, rho_mob]
N_sl: [12, 12]
b_sl: [2.49e-10, 2.49e-10]

9
examples/config/phase/thermal/AISI304.yaml Normal file
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@ -0,0 +1,9 @@
references:
- B.F. Blackwell et al.
Proceedings of 34th National Heat Transfer Conference 2000
https://www.osti.gov/servlets/purl/760791
- R.H. Bogaard et al.
Thermochimica Acta 218:373-393, 1993
https://doi.org/10.1016/0040-6031(93)80437-F
C_p: 470.0
K_11: 14.34

0
examples/config/phase/thermal/Steel-0.5C.yaml → examples/config/phase/thermal/steel-0.5C.yaml
View File

8
install/MarcMentat/apply_DAMASK_modifications.py
View File

@ -67,9 +67,7 @@ os.system(f'xvfb-run -a {executable} -compile {menu_file}')
print('setting file access rights...')
files = (glob.glob(str(marc_root/f'marc{marc_version}/tools/*_damask*')) +
glob.glob(str(marc_root/f'mentat{marc_version}/bin/kill[4-6]')) +
glob.glob(str(marc_root/f'mentat{marc_version}/bin/submit[4-6]')))
for file in files:
for file in (glob.glob(str(marc_root/f'marc{marc_version}/tools/*_damask*')) +
glob.glob(str(marc_root/f'mentat{marc_version}/bin/kill[4-6]')) +
glob.glob(str(marc_root/f'mentat{marc_version}/bin/submit[4-6]'))):
os.chmod(file , 0o755)

71
processing/legacy/addDisplacement.py vendored
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@ -1,71 +0,0 @@
#!/usr/bin/env python3
import os
import sys
from io import StringIO
from optparse import OptionParser
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
# MAIN
# --------------------------------------------------------------------
parser = OptionParser(usage='%prog options [ASCIItable(s)]', description = """
Add displacments resulting from deformation gradient field.
Operates on periodic three-dimensional x,y,z-ordered data sets.
Outputs at cell centers or cell nodes (into separate file).
""", version = scriptID)
parser.add_option('-f',
'--defgrad',
dest = 'f',
metavar = 'string',
help = 'label of deformation gradient [%default]')
parser.add_option('-p',
'--pos', '--position',
dest = 'pos',
metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('--nodal',
dest = 'nodal',
action = 'store_true',
help = 'output nodal (instead of cell-centered) displacements')
parser.set_defaults(f = 'f',
pos = 'pos',
)
(options,filenames) = parser.parse_args()
for name in filenames:
damask.util.report(scriptName,name)
table = damask.Table.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
F = table.get(options.f).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
if options.nodal:
damask.Table(damask.grid_filters.coordinates0_node(grid,size).reshape(-1,3,order='F'),
{'pos':(3,)})\
.add('avg({}).{}'.format(options.f,options.pos),
damask.grid_filters.displacement_avg_node(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))\
.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.displacement_fluct_node(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))\
.save((sys.stdout if name is None else os.path.splitext(name)[0]+'_nodal.txt'))
else:
table.add('avg({}).{}'.format(options.f,options.pos),
damask.grid_filters.displacement_avg_point(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))\
.add('fluct({}).{}'.format(options.f,options.pos),
damask.grid_filters.displacement_fluct_point(size,F).reshape(-1,3,order='F'),
scriptID+' '+' '.join(sys.argv[1:]))\
.save((sys.stdout if name is None else name))

2
python/damask/VERSION
View File

@ -1 +1 @@
v3.0.0-alpha5-272-g3192a31e1
v3.0.0-alpha5-379-g731222d09

1
python/damask/__init__.py
View File

@ -8,6 +8,7 @@ with open(_Path(__file__).parent/_Path('VERSION')) as _f:
version = _re.sub(r'^v','',_f.readline().strip())
__version__ = version
from . import _typehints # noqa
from . import util # noqa
from . import seeds # noqa
from . import tensor # noqa

87
python/damask/_colormap.py
View File

@ -3,9 +3,10 @@ import json
import functools
import colorsys
from pathlib import Path
from typing import Sequence, Union, TextIO
from typing import Union, TextIO
import numpy as np
import scipy.interpolate as interp
import matplotlib as mpl
if os.name == 'posix' and 'DISPLAY' not in os.environ:
mpl.use('Agg')
@ -13,6 +14,7 @@ import matplotlib.pyplot as plt
from matplotlib import cm
from PIL import Image
from ._typehints import FloatSequence, FileHandle
from . import util
from . import Table
@ -41,7 +43,7 @@ class Colormap(mpl.colors.ListedColormap):
https://doi.org/10.1016/j.ijplas.2012.09.012
Matplotlib colormaps overview
https://matplotlib.org/tutorials/colors/colormaps.html
https://matplotlib.org/stable/tutorials/colors/colormaps.html
"""
@ -77,8 +79,8 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def from_range(low: Sequence[float],
high: Sequence[float],
def from_range(low: FloatSequence,
high: FloatSequence,
name: str = 'DAMASK colormap',
N: int = 256,
model: str = 'rgb') -> 'Colormap':
@ -128,7 +130,7 @@ class Colormap(mpl.colors.ListedColormap):
if model.lower() not in toMsh:
raise ValueError(f'Invalid color model: {model}.')
low_high = np.vstack((low,high))
low_high = np.vstack((low,high)).astype(float)
out_of_bounds = np.bool_(False)
if model.lower() == 'rgb':
@ -141,7 +143,7 @@ class Colormap(mpl.colors.ListedColormap):
out_of_bounds = np.any(low_high[:,0]<0)
if out_of_bounds:
raise ValueError(f'{model.upper()} colors {low} | {high} are out of bounds.')
raise ValueError(f'{model.upper()} colors {low_high[0]} | {low_high[1]} are out of bounds.')
low_,high_ = map(toMsh[model.lower()],low_high)
msh = map(functools.partial(Colormap._interpolate_msh,low=low_,high=high_),np.linspace(0,1,N))
@ -191,19 +193,50 @@ class Colormap(mpl.colors.ListedColormap):
return Colormap.from_range(definition['low'],definition['high'],name,N)
def at(self,
fraction : Union[float,FloatSequence]) -> np.ndarray:
"""
Interpolate color at fraction.
Parameters
----------
fraction : float or sequence of float
Fractional coordinate(s) to evaluate Colormap at.
Returns
-------
color : numpy.ndarray, shape(...,4)
RGBA values of interpolated color(s).
Examples
--------
>>> import damask
>>> cmap = damask.Colormap.from_predefined('gray')
>>> cmap.at(0.5)
array([0.5, 0.5, 0.5, 1. ])
>>> 'rgb({},{},{})'.format(*cmap.at(0.5))
'rgb(0.5,0.5,0.5)'
"""
return interp.interp1d(np.linspace(0,1,self.N),
self.colors,
axis=0,
assume_sorted=True)(fraction)
def shade(self,
field: np.ndarray,
bounds: Sequence[float] = None,
bounds: FloatSequence = None,
gap: float = None) -> Image:
"""
Generate PIL image of 2D field using colormap.
Parameters
----------
field : numpy.array, shape (:,:)
field : numpy.ndarray, shape (:,:)
Data to be shaded.
bounds : sequence of float, len (2), optional
Value range (low,high) spanned by colormap.
Value range (left,right) spanned by colormap.
gap : field.dtype, optional
Transparent value. NaN will always be rendered transparent.
@ -213,21 +246,20 @@ class Colormap(mpl.colors.ListedColormap):
RGBA image of shaded data.
"""
N = len(self.colors)
mask = np.logical_not(np.isnan(field) if gap is None else \
np.logical_or (np.isnan(field), field == gap)) # mask NaN (and gap if present)
lo,hi = (field[mask].min(),field[mask].max()) if bounds is None else \
(min(bounds[:2]),max(bounds[:2]))
l,r = (field[mask].min(),field[mask].max()) if bounds is None else \
np.array(bounds,float)[:2]
delta,avg = hi-lo,0.5*(hi+lo)
delta,avg = r-l,0.5*abs(r+l)
if delta * 1e8 <= avg: # delta is similar to numerical noise
hi,lo = hi+0.5*avg,lo-0.5*avg # extend range to have actual data centered within
if abs(delta) * 1e8 <= avg: # delta is similar to numerical noise
l,r = l-0.5*avg*np.sign(delta),r+0.5*avg*np.sign(delta), # extend range to have actual data centered within
return Image.fromarray(
(np.dstack((
self.colors[(np.round(np.clip((field-lo)/(hi-lo),0.0,1.0)*(N-1))).astype(np.uint16),:3],
self.colors[(np.round(np.clip((field-l)/delta,0.0,1.0)*(self.N-1))).astype(np.uint16),:3],
mask.astype(float)
)
)*255
@ -261,7 +293,7 @@ class Colormap(mpl.colors.ListedColormap):
def _get_file_handle(self,
fname: Union[TextIO, str, Path, None],
fname: Union[FileHandle, None],
suffix: str = '') -> TextIO:
"""
Provide file handle.
@ -288,7 +320,7 @@ class Colormap(mpl.colors.ListedColormap):
return fname
def save_paraview(self, fname: Union[TextIO, str, Path] = None):
def save_paraview(self, fname: FileHandle = None):
"""
Save as JSON file for use in Paraview.
@ -315,7 +347,7 @@ class Colormap(mpl.colors.ListedColormap):
fhandle.write('\n')
def save_ASCII(self, fname: Union[TextIO, str, Path] = None):
def save_ASCII(self, fname: FileHandle = None):
"""
Save as ASCII file.
@ -330,7 +362,7 @@ class Colormap(mpl.colors.ListedColormap):
t.save(self._get_file_handle(fname,'.txt'))
def save_GOM(self, fname: Union[TextIO, str, Path] = None):
def save_GOM(self, fname: FileHandle = None):
"""
Save as ASCII file for use in GOM Aramis.
@ -343,14 +375,14 @@ class Colormap(mpl.colors.ListedColormap):
# ToDo: test in GOM
GOM_str = '1 1 {name} 9 {name} '.format(name=self.name.replace(" ","_")) \
+ '0 1 0 3 0 0 -1 9 \\ 0 0 0 255 255 255 0 0 255 ' \
+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {len(self.colors)}' \
+ f'30 NO_UNIT 1 1 64 64 64 255 1 0 0 0 0 0 0 3 0 {self.N}' \
+ ' '.join([f' 0 {c[0]} {c[1]} {c[2]} 255 1' for c in reversed((self.colors*255).astype(int))]) \
+ '\n'
self._get_file_handle(fname,'.legend').write(GOM_str)
def save_gmsh(self, fname: Union[TextIO, str, Path] = None):
def save_gmsh(self, fname: FileHandle = None):
"""
Save as ASCII file for use in gmsh.
@ -581,7 +613,7 @@ class Colormap(mpl.colors.ListedColormap):
@staticmethod
def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
def _lab2xyz(lab: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Lab to CIE Xyz.
@ -589,6 +621,8 @@ class Colormap(mpl.colors.ListedColormap):
----------
lab : numpy.ndarray, shape (3)
CIE lab values.
ref_white : numpy.ndarray, shape (3)
Reference white, default value is the standard 2° observer for D65.
Returns
-------
@ -607,10 +641,10 @@ class Colormap(mpl.colors.ListedColormap):
f_x**3. if f_x**3. > _EPS else (116.*f_x-16.)/_KAPPA,
((lab[0]+16.)/116.)**3 if lab[0]>_KAPPA*_EPS else lab[0]/_KAPPA,
f_z**3. if f_z**3. > _EPS else (116.*f_z-16.)/_KAPPA
])*(ref_white if ref_white is not None else _REF_WHITE)
])*ref_white
@staticmethod
def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = None) -> np.ndarray:
def _xyz2lab(xyz: np.ndarray, ref_white: np.ndarray = _REF_WHITE) -> np.ndarray:
"""
CIE Xyz to CIE Lab.
@ -618,6 +652,8 @@ class Colormap(mpl.colors.ListedColormap):
----------
xyz : numpy.ndarray, shape (3)
CIE Xyz values.
ref_white : numpy.ndarray, shape (3)
Reference white, default value is the standard 2° observer for D65.
Returns
-------
@ -629,7 +665,6 @@ class Colormap(mpl.colors.ListedColormap):
http://www.brucelindbloom.com/index.html?Eqn_Lab_to_XYZ.html
"""
ref_white = ref_white if ref_white is not None else _REF_WHITE
f = np.where(xyz/ref_white > _EPS,(xyz/ref_white)**(1./3.),(_KAPPA*xyz/ref_white+16.)/116.)
return np.array([

94
python/damask/_crystal.py
View File

@ -114,12 +114,13 @@ class Crystal():
def __repr__(self):
"""Represent."""
return '\n'.join([f'Crystal family {self.family}']
+ ([] if self.lattice is None else [f'Bravais lattice {self.lattice}']+
list(map(lambda x:f'{x[0]}: {x[1]:.5g}',
zip(['a','b','c','α','β','γ',],
self.parameters))))
)
family = f'Crystal family: {self.family}'
return family if self.lattice is None else \
'\n'.join([family,
f'Bravais lattice: {self.lattice}',
'a={:.5g}m, b={:.5g}m, c={:.5g}m'.format(*self.parameters[:3]),
'α={:.5g}°, β={:.5g}°, γ={:.5g}°'.format(*np.degrees(self.parameters[3:]))])
def __eq__(self,other):
"""
@ -378,7 +379,7 @@ class Crystal():
"""
_kinematics = {
'cF': {
'slip' :[np.array([
'slip': [np.array([
[+0,+1,-1, +1,+1,+1],
[-1,+0,+1, +1,+1,+1],
[+1,-1,+0, +1,+1,+1],
@ -398,7 +399,7 @@ class Crystal():
[+1,+0,-1, +1,+0,+1],
[+0,+1,+1, +0,+1,-1],
[+0,+1,-1, +0,+1,+1]])],
'twin' :[np.array([
'twin': [np.array([
[-2, 1, 1, 1, 1, 1],
[ 1,-2, 1, 1, 1, 1],
[ 1, 1,-2, 1, 1, 1],
@ -413,7 +414,7 @@ class Crystal():
[-1, 1, 2, -1, 1,-1]])]
},
'cI': {
'slip' :[np.array([
'slip': [np.array([
[+1,-1,+1, +0,+1,+1],
[-1,-1,+1, +0,+1,+1],
[+1,+1,+1, +0,-1,+1],
@ -464,7 +465,7 @@ class Crystal():
[+1,+1,+1, -3,+2,+1],
[+1,+1,-1, +3,-2,+1],
[+1,-1,+1, +3,+2,-1]])],
'twin' :[np.array([
'twin': [np.array([
[-1, 1, 1, 2, 1, 1],
[ 1, 1, 1, -2, 1, 1],
[ 1, 1,-1, 2,-1, 1],
@ -479,7 +480,7 @@ class Crystal():
[ 1, 1, 1, 1, 1,-2]])]
},
'hP': {
'slip' :[np.array([
'slip': [np.array([
[+2,-1,-1,+0, +0,+0,+0,+1],
[-1,+2,-1,+0, +0,+0,+0,+1],
[-1,-1,+2,+0, +0,+0,+0,+1]]),
@ -514,7 +515,7 @@ class Crystal():
[+1,+1,-2,+3, -1,-1,+2,+2],
[-1,+2,-1,+3, +1,-2,+1,+2],
[-2,+1,+1,+3, +2,-1,-1,+2]])],
'twin' :[np.array([
'twin': [np.array([
[-1, 0, 1, 1, 1, 0,-1, 2], # shear = (3-(c/a)^2)/(sqrt(3) c/a) <-10.1>{10.2}
[ 0,-1, 1, 1, 0, 1,-1, 2],
[ 1,-1, 0, 1, -1, 1, 0, 2],
@ -542,7 +543,74 @@ class Crystal():
[-1,-1, 2,-3, -1,-1, 2, 2],
[ 1,-2, 1,-3, 1,-2, 1, 2],
[ 2,-1,-1,-3, 2,-1,-1, 2]])]
},
},
'tI': {
'slip': [np.array([
[+0,+0,+1, +1,+0,+0],
[+0,+0,+1, +0,+1,+0]]),
np.array([
[+0,+0,+1, +1,+1,+0],
[+0,+0,+1, -1,+1,+0]]),
np.array([
[+0,+1,+0, +1,+0,+0],
[+1,+0,+0, +0,+1,+0]]),
np.array([
[+1,-1,+1, +1,+1,+0],
[+1,-1,-1, +1,+1,+0],
[-1,-1,-1, -1,+1,+0],
[-1,-1,+1, -1,+1,+0]]),
np.array([
[+1,-1,+0, +1,+1,+0],
[+1,+1,+0, +1,-1,+0]]),
np.array([
[+0,+1,+1, +1,+0,+0],
[+0,-1,+1, +1,+0,+0],
[-1,+0,+1, +0,+1,+0],
[+1,+0,+1, +0,+1,+0]]),
np.array([
[+0,+1,+0, +0,+0,+1],
[+1,+0,+0, +0,+0,+1]]),
np.array([
[+1,+1,+0, +0,+0,+1],
[-1,+1,+0, +0,+0,+1]]),
np.array([
[+0,+1,-1, +0,+1,+1],
[+0,-1,-1, +0,-1,+1],
[-1,+0,-1, -1,+0,+1],
[+1,+0,-1, +1,+0,+1]]),
np.array([
[+1,-1,+1, +0,+1,+1],
[+1,+1,-1, +0,+1,+1],
[+1,+1,+1, +0,+1,-1],
[-1,+1,+1, +0,+1,-1],
[+1,-1,-1, +1,+0,+1],
[-1,-1,+1, +1,+0,+1],
[+1,+1,+1, +1,+0,-1],
[+1,-1,+1, +1,+0,-1]]),
np.array([
[+1,+0,+0, +0,+1,+1],
[+1,+0,+0, +0,+1,-1],
[+0,+1,+0, +1,+0,+1],
[+0,+1,+0, +1,+0,-1]]),
np.array([
[+0,+1,-1, +2,+1,+1],
[+0,-1,-1, +2,-1,+1],
[+1,+0,-1, +1,+2,+1],
[-1,+0,-1, -1,+2,+1],
[+0,+1,-1, -2,+1,+1],
[+0,-1,-1, -2,-1,+1],
[-1,+0,-1, -1,-2,+1],
[+1,+0,-1, +1,-2,+1]]),
np.array([
[-1,+1,+1, +2,+1,+1],
[-1,-1,+1, +2,-1,+1],
[+1,-1,+1, +1,+2,+1],
[-1,-1,+1, -1,+2,+1],
[+1,+1,+1, -2,+1,+1],
[+1,-1,+1, -2,-1,+1],
[-1,+1,+1, -1,-2,+1],
[+1,+1,+1, +1,-2,+1]])]
}
}
master = _kinematics[self.lattice][mode]
if self.lattice == 'hP':

355
python/damask/_grid.py
View File

@ -3,6 +3,9 @@ import copy
import warnings
import multiprocessing as mp
from functools import partial
import typing
from typing import Union, Optional, TextIO, List, Sequence
from pathlib import Path
import numpy as np
import pandas as pd
@ -13,7 +16,8 @@ from . import VTK
from . import util
from . import grid_filters
from . import Rotation
from . import Table
from ._typehints import FloatSequence, IntSequence
class Grid:
"""
@ -25,30 +29,34 @@ class Grid:
the physical size.
"""
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
def __init__(self,
material: np.ndarray,
size: FloatSequence,
origin: FloatSequence = np.zeros(3),
comments: Union[str, Sequence[str]] = []):
"""
New geometry definition for grid solvers.
Parameters
----------
material : numpy.ndarray of shape (:,:,:)
material : numpy.ndarray, shape (:,:,:)
Material indices. The shape of the material array defines
the number of cells.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of grid in meter.
origin : list or numpy.ndarray of shape (3), optional
Coordinates of grid origin in meter.
comments : list of str, optional
origin : sequence of float, len (3), optional
Coordinates of grid origin in meter. Defaults to [0.0,0.0,0.0].
comments : (list of) str, optional
Comments, e.g. history of operations.
"""
self.material = material
self.size = size
self.origin = origin
self.comments = comments
self.size = size # type: ignore
self.origin = origin # type: ignore
self.comments = comments # type: ignore
def __repr__(self):
def __repr__(self) -> str:
"""Basic information on grid definition."""
mat_min = np.nanmin(self.material)
mat_max = np.nanmax(self.material)
@ -62,14 +70,14 @@ class Grid:
])
def __copy__(self):
def __copy__(self) -> "Grid":
"""Create deep copy."""
return copy.deepcopy(self)
copy = __copy__
def __eq__(self,other):
def __eq__(self, other: object) -> bool:
"""
Test equality of other.
@ -79,22 +87,24 @@ class Grid:
Grid to compare self against.
"""
return (np.allclose(other.size,self.size)
if not isinstance(other, Grid):
return NotImplemented
return bool(np.allclose(other.size,self.size)
and np.allclose(other.origin,self.origin)
and np.all(other.cells == self.cells)
and np.all(other.material == self.material))
@property
def material(self):
def material(self) -> np.ndarray:
"""Material indices."""
return self._material
@material.setter
def material(self,material):
def material(self, material: np.ndarray):
if len(material.shape) != 3:
raise ValueError(f'invalid material shape {material.shape}')
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
elif material.dtype not in np.sctypes['float'] and material.dtype not in np.sctypes['int']:
raise TypeError(f'invalid material data type {material.dtype}')
else:
self._material = np.copy(material)
@ -105,59 +115,59 @@ class Grid:
@property
def size(self):
def size(self) -> np.ndarray:
"""Physical size of grid in meter."""
return self._size
@size.setter
def size(self,size):
def size(self, size: FloatSequence):
if len(size) != 3 or any(np.array(size) < 0):
raise ValueError(f'invalid size {size}')
else:
self._size = np.array(size)
@property
def origin(self):
def origin(self) -> np.ndarray:
"""Coordinates of grid origin in meter."""
return self._origin
@origin.setter
def origin(self,origin):
def origin(self, origin: FloatSequence):
if len(origin) != 3:
raise ValueError(f'invalid origin {origin}')
else:
self._origin = np.array(origin)
@property
def comments(self):
def comments(self) -> List[str]:
"""Comments, e.g. history of operations."""
return self._comments
@comments.setter
def comments(self,comments):
def comments(self, comments: Union[str, Sequence[str]]):
self._comments = [str(c) for c in comments] if isinstance(comments,list) else [str(comments)]
@property
def cells(self):
def cells(self) -> np.ndarray:
"""Number of cells in x,y,z direction."""
return np.asarray(self.material.shape)
@property
def N_materials(self):
def N_materials(self) -> int:
"""Number of (unique) material indices within grid."""
return np.unique(self.material).size
@staticmethod
def load(fname):
def load(fname: Union[str, Path]) -> "Grid":
"""
Load from VTK image data file.
Parameters
----------
fname : str or or pathlib.Path
fname : str or pathlib.Path
Grid file to read. Valid extension is .vti, which will be appended
if not given.
@ -178,8 +188,9 @@ class Grid:
comments=comments)
@typing. no_type_check
@staticmethod
def load_ASCII(fname):
def load_ASCII(fname)-> "Grid":
"""
Load from geom file.
@ -197,16 +208,18 @@ class Grid:
Grid-based geometry from file.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
try:
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
if isinstance(fname, (str, Path)):
f = open(fname)
except TypeError:
elif isinstance(fname, TextIO):
f = fname
else:
raise TypeError
f.seek(0)
try:
header_length,keyword = f.readline().split()[:2]
header_length = int(header_length)
header_length_,keyword = f.readline().split()[:2]
header_length = int(header_length_)
except ValueError:
header_length,keyword = (-1, 'invalid')
if not keyword.startswith('head') or header_length < 3:
@ -226,19 +239,19 @@ class Grid:
else:
comments.append(line.strip())
material = np.empty(cells.prod()) # initialize as flat array
material = np.empty(int(cells.prod())) # initialize as flat array
i = 0
for line in content[header_length:]:
items = line.split('#')[0].split()
if len(items) == 3:
if items[1].lower() == 'of':
items = np.ones(int(items[0]))*float(items[2])
if items[1].lower() == 'of':
material_entry = np.ones(int(items[0]))*float(items[2])
elif items[1].lower() == 'to':
items = np.linspace(int(items[0]),int(items[2]),
material_entry = np.linspace(int(items[0]),int(items[2]),
abs(int(items[2])-int(items[0]))+1,dtype=float)
else: items = list(map(float,items))
else: items = list(map(float,items))
material[i:i+len(items)] = items
else: material_entry = list(map(float, items))
else: material_entry = list(map(float, items))
material[i:i+len(material_entry)] = material_entry
i += len(items)
if i != cells.prod():
@ -251,13 +264,13 @@ class Grid:
@staticmethod
def load_Neper(fname):
def load_Neper(fname: Union[str, Path]) -> "Grid":
"""
Load from Neper VTK file.
Parameters
----------
fname : str, pathlib.Path, or file handle
fname : str or pathlib.Path
Geometry file to read.
Returns
@ -276,10 +289,10 @@ class Grid:
@staticmethod
def load_DREAM3D(fname,
feature_IDs=None,cell_data=None,
phases='Phases',Euler_angles='EulerAngles',
base_group=None):
def load_DREAM3D(fname: Union[str, Path],
feature_IDs: str = None, cell_data: str = None,
phases: str = 'Phases', Euler_angles: str = 'EulerAngles',
base_group: str = None) -> "Grid":
"""
Load DREAM.3D (HDF5) file.
@ -290,24 +303,24 @@ class Grid:
Parameters
----------
fname : str
fname : str or or pathlib.Path
Filename of the DREAM.3D (HDF5) file.
feature_IDs : str
feature_IDs : str, optional
Name of the dataset containing the mapping between cells and
grain-wise data. Defaults to 'None', in which case cell-wise
data is used.
cell_data : str
cell_data : str, optional
Name of the group (folder) containing cell-wise data. Defaults to
None in wich case it is automatically detected.
phases : str
phases : str, optional
Name of the dataset containing the phase ID. It is not used for
grain-wise data, i.e. when feature_IDs is not None.
Defaults to 'Phases'.
Euler_angles : str
Euler_angles : str, optional
Name of the dataset containing the crystallographic orientation as
Euler angles in radians It is not used for grain-wise data, i.e.
when feature_IDs is not None. Defaults to 'EulerAngles'.
base_group : str
base_group : str, optional
Path to the group (folder) that contains geometry (_SIMPL_GEOMETRY),
and grain- or cell-wise data. Defaults to None, in which case
it is set as the path that contains _SIMPL_GEOMETRY/SPACING.
@ -339,7 +352,9 @@ class Grid:
@staticmethod
def from_table(table,coordinates,labels):
def from_table(table: Table,
coordinates: str,
labels: Union[str, Sequence[str]]) -> "Grid":
"""
Create grid from ASCII table.
@ -350,7 +365,7 @@ class Grid:
coordinates : str
Label of the vector column containing the spatial coordinates.
Need to be ordered (1./x fast, 3./z slow).
labels : str or list of str
labels : (list of) str
Label(s) of the columns containing the material definition.
Each unique combination of values results in one material ID.
@ -372,28 +387,33 @@ class Grid:
@staticmethod
def _find_closest_seed(seeds, weights, point):
def _find_closest_seed(seeds: np.ndarray, weights: np.ndarray, point: np.ndarray) -> np.integer:
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
@staticmethod
def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
def from_Laguerre_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
weights: FloatSequence,
material: IntSequence = None,
periodic: bool = True):
"""
Create grid from Laguerre tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
weights : numpy.ndarray of shape (seeds.shape[0])
weights : sequence of float, len (seeds.shape[0])
Weights of the seeds. Setting all weights to 1.0 gives a standard Voronoi tessellation.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -421,29 +441,33 @@ class Grid:
if periodic: material_ %= len(weights)
return Grid(material = material_ if material is None else material[material_],
return Grid(material = material_ if material is None else np.array(material)[material_],
size = size,
comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
)
@staticmethod
def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
def from_Voronoi_tessellation(cells: IntSequence,
size: FloatSequence,
seeds: np.ndarray,
material: IntSequence = None,
periodic: bool = True) -> "Grid":
"""
Create grid from Voronoi tessellation.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
seeds : numpy.ndarray of shape (:,3)
seeds : numpy.ndarray, shape (:,3)
Position of the seed points in meter. All points need to lay within the box.
material : numpy.ndarray of shape (seeds.shape[0]), optional
material : sequence of int, len (seeds.shape[0]), optional
Material ID of the seeds.
Defaults to None, in which case materials are consecutively numbered.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -460,7 +484,7 @@ class Grid:
except TypeError:
material_ = tree.query(coords, n_jobs = int(os.environ.get('OMP_NUM_THREADS',4)))[1] # scipy <1.6
return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
return Grid(material = (material_ if material is None else np.array(material)[material_]).reshape(cells),
size = size,
comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
)
@ -509,15 +533,20 @@ class Grid:
@staticmethod
def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
def from_minimal_surface(cells: IntSequence,
size: FloatSequence,
surface: str,
threshold: float = 0.0,
periods: int = 1,
materials: IntSequence = (0,1)) -> "Grid":
"""
Create grid from definition of triply periodic minimal surface.
Parameters
----------
cells : int numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
size : list or numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the grid in meter.
surface : str
Type of the minimal surface. See notes for details.
@ -525,7 +554,7 @@ class Grid:
Threshold of the minimal surface. Defaults to 0.0.
periods : integer, optional.
Number of periods per unit cell. Defaults to 1.
materials : (int, int), optional
materials : sequence of int, len (2)
Material IDs. Defaults to (0,1).
Returns
@ -566,22 +595,21 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([64]*3,int),np.ones(3),
... 'Gyroid')
cells a b c: 64 x 64 x 64
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
>>> damask.Grid.from_minimal_surface([64]*3,np.ones(3)*1.e-4,'Gyroid')
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
Minimal surface of 'Neovius' type. non-default material IDs.
>>> import numpy as np
>>> import damask
>>> damask.Grid.from_minimal_surface(np.array([80]*3,int),np.ones(3),
>>> damask.Grid.from_minimal_surface([80]*3,np.ones(3)*5.e-4,
... 'Neovius',materials=(1,5))
cells a b c: 80 x 80 x 80
size x y z: 1.0 x 1.0 x 1.0
origin x y z: 0.0 0.0 0.0
cells : 80 x 80 x 80
size : 0.0005 x 0.0005 x 0.0005 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2 (min: 1, max: 5)
"""
@ -595,7 +623,7 @@ class Grid:
)
def save(self,fname,compress=True):
def save(self, fname: Union[str, Path], compress: bool = True):
"""
Save as VTK image data file.
@ -611,10 +639,10 @@ class Grid:
v.add(self.material.flatten(order='F'),'material')
v.add_comments(self.comments)
v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
v.save(fname,parallel=False,compress=compress)
def save_ASCII(self,fname):
def save_ASCII(self, fname: Union[str, TextIO]):
"""
Save as geom file.
@ -629,7 +657,7 @@ class Grid:
Compress geometry with 'x of y' and 'a to b'.
"""
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning,2)
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.0.0', DeprecationWarning,2)
header = [f'{len(self.comments)+4} header'] + self.comments \
+ ['grid a {} b {} c {}'.format(*self.cells),
'size x {} y {} z {}'.format(*self.size),
@ -644,26 +672,33 @@ class Grid:
header='\n'.join(header), fmt=format_string, comments='')
def show(self):
def show(self) -> None:
"""Show on screen."""
VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
def add_primitive(self,dimension,center,exponent,
fill=None,R=Rotation(),inverse=False,periodic=True):
def add_primitive(self,
dimension: Union[FloatSequence, IntSequence],
center: Union[FloatSequence, IntSequence],
exponent: Union[FloatSequence, float],
fill: int = None,
R: Rotation = Rotation(),
inverse: bool = False,
periodic: bool = True) -> "Grid":
"""
Insert a primitive geometric object at a given position.
Parameters
----------
dimension : int or float numpy.ndarray of shape (3)
Dimension (diameter/side length) of the primitive. If given as
integers, cell centers are addressed.
If given as floats, coordinates are addressed.
center : int or float numpy.ndarray of shape (3)
Center of the primitive. If given as integers, cell centers are addressed.
If given as floats, coordinates in space are addressed.
exponent : numpy.ndarray of shape (3) or float
dimension : sequence of int or float, len (3)
Dimension (diameter/side length) of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
center : sequence of int or float, len (3)
Center of the primitive.
If given as integers, cell centers are addressed.
If given as floats, physical coordinates are addressed.
exponent : float or sequence of float, len (3)
Exponents for the three axes.
0 gives octahedron (ǀxǀ^(2^0) + ǀyǀ^(2^0) + ǀzǀ^(2^0) < 1)
1 gives sphere (ǀxǀ^(2^1) + ǀyǀ^(2^1) + ǀzǀ^(2^1) < 1)
@ -671,10 +706,10 @@ class Grid:
Fill value for primitive. Defaults to material.max()+1.
R : damask.Rotation, optional
Rotation of primitive. Defaults to no rotation.
inverse : Boolean, optional
inverse : bool, optional
Retain original materials within primitive and fill outside.
Defaults to False.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -690,9 +725,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3)*5e-5,np.ones(3)*5e-5,1)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
Add a cube at the origin.
@ -701,9 +736,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([64]*3,int), np.ones(3)*1e-4)
>>> g.add_primitive(np.ones(3,int)*32,np.zeros(3),np.inf)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 2
"""
@ -734,13 +769,13 @@ class Grid:
)
def mirror(self,directions,reflect=False):
def mirror(self, directions: Sequence[str], reflect: bool = False) -> "Grid":
"""
Mirror grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) str
Direction(s) along which the grid is mirrored.
Valid entries are 'x', 'y', 'z'.
reflect : bool, optional
@ -759,9 +794,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int), np.ones(3)*1e-4)
>>> g.mirror('xy',True)
cells a b c: 64 x 64 x 32
size x y z: 0.0002 x 0.0002 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 32
size : 0.0002 x 0.0002 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
@ -769,7 +804,7 @@ class Grid:
if not set(directions).issubset(valid):
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
limits = [None,None] if reflect else [-2,0]
limits: Sequence[Optional[int]] = [None,None] if reflect else [-2,0]
mat = self.material.copy()
if 'x' in directions:
@ -786,13 +821,13 @@ class Grid:
)
def flip(self,directions):
def flip(self, directions: Sequence[str]) -> "Grid":
"""
Flip grid along given directions.
Parameters
----------
directions : iterable containing str
directions : (sequence of) str
Direction(s) along which the grid is flipped.
Valid entries are 'x', 'y', 'z'.
@ -815,15 +850,15 @@ class Grid:
)
def scale(self,cells,periodic=True):
def scale(self, cells: IntSequence, periodic: bool = True) -> "Grid":
"""
Scale grid to new cells.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells in x,y,z direction.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -839,9 +874,9 @@ class Grid:
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.scale(g.cells*2)
cells a b c: 64 x 64 x 64
size x y z: 0.0001 x 0.0001 x 0.0001
origin x y z: 0.0 0.0 0.0
cells : 64 x 64 x 64
size : 0.0001 x 0.0001 x 0.0001 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
@ -859,7 +894,10 @@ class Grid:
)
def clean(self,stencil=3,selection=None,periodic=True):
def clean(self,
stencil: int = 3,
selection: IntSequence = None,
periodic: bool = True) -> "Grid":
"""
Smooth grid by selecting most frequent material index within given stencil at each location.
@ -867,9 +905,9 @@ class Grid:
----------
stencil : int, optional
Size of smoothing stencil.
selection : list, optional
selection : sequence of int, optional
Field values that can be altered. Defaults to all.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -878,7 +916,7 @@ class Grid:
Updated grid-based geometry.
"""
def mostFrequent(arr,selection=None):
def mostFrequent(arr: np.ndarray, selection = None):
me = arr[arr.size//2]
if selection is None or me in selection:
unique, inverse = np.unique(arr, return_inverse=True)
@ -899,7 +937,7 @@ class Grid:
)
def renumber(self):
def renumber(self) -> "Grid":
"""
Renumber sorted material indices as 0,...,N-1.
@ -918,7 +956,7 @@ class Grid:
)
def rotate(self,R,fill=None):
def rotate(self, R: Rotation, fill: int = None) -> "Grid":
"""
Rotate grid (pad if required).
@ -926,7 +964,7 @@ class Grid:
----------
R : damask.Rotation
Rotation to apply to the grid.
fill : int or float, optional
fill : int, optional
Material index to fill the corners. Defaults to material.max() + 1.
Returns
@ -956,17 +994,20 @@ class Grid:
)
def canvas(self,cells=None,offset=None,fill=None):
def canvas(self,
cells: IntSequence = None,
offset: IntSequence = None,
fill: int = None) -> "Grid":
"""
Crop or enlarge/pad grid.
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3), optional
Number of cells x,y,z direction.
offset : numpy.ndarray of shape (3)
offset : sequence of int, len (3), optional
Offset (measured in cells) from old to new grid [0,0,0].
fill : int or float, optional
fill : int, optional
Material index to fill the background. Defaults to material.max() + 1.
Returns
@ -981,42 +1022,43 @@ class Grid:
>>> import numpy as np
>>> import damask
>>> g = damask.Grid(np.zeros([32]*3,int),np.ones(3)*1e-4)
>>> g.canvas(np.array([32,32,16],int))
cells a b c: 33 x 32 x 16
size x y z: 0.0001 x 0.0001 x 5e-05
origin x y z: 0.0 0.0 0.0
>>> g.canvas([32,32,16])
cells : 33 x 32 x 16
size : 0.0001 x 0.0001 x 5e-05 / m³
origin: 0.0 0.0 0.0 / m
# materials: 1
"""
if offset is None: offset = 0
offset_ = np.array(offset,int) if offset is not None else np.zeros(3,int)
cells_ = np.array(cells,int) if cells is not None else self.cells
if fill is None: fill = np.nanmax(self.material) + 1
dtype = float if int(fill) != fill or self.material.dtype in np.sctypes['float'] else int
canvas = np.full(self.cells if cells is None else cells,fill,dtype)
canvas = np.full(cells_,fill,dtype)
LL = np.clip( offset, 0,np.minimum(self.cells, cells+offset))
UR = np.clip( offset+cells, 0,np.minimum(self.cells, cells+offset))
ll = np.clip(-offset, 0,np.minimum( cells,self.cells-offset))
ur = np.clip(-offset+self.cells,0,np.minimum( cells,self.cells-offset))
LL = np.clip( offset_, 0,np.minimum(self.cells, cells_+offset_))
UR = np.clip( offset_+cells_, 0,np.minimum(self.cells, cells_+offset_))
ll = np.clip(-offset_, 0,np.minimum( cells_,self.cells-offset_))
ur = np.clip(-offset_+self.cells,0,np.minimum( cells_,self.cells-offset_))
canvas[ll[0]:ur[0],ll[1]:ur[1],ll[2]:ur[2]] = self.material[LL[0]:UR[0],LL[1]:UR[1],LL[2]:UR[2]]
return Grid(material = canvas,
size = self.size/self.cells*np.asarray(canvas.shape),
origin = self.origin+offset*self.size/self.cells,
origin = self.origin+offset_*self.size/self.cells,
comments = self.comments+[util.execution_stamp('Grid','canvas')],
)
def substitute(self,from_material,to_material):
def substitute(self, from_material: IntSequence, to_material: IntSequence) -> "Grid":
"""
Substitute material indices.
Parameters
----------
from_material : iterable of ints
from_material : sequence of int
Material indices to be substituted.
to_material : iterable of ints
to_material : sequence of int
New material indices.
Returns
@ -1025,7 +1067,7 @@ class Grid:
Updated grid-based geometry.
"""
def mp(entry,mapper):
def mp(entry, mapper):
return mapper[entry] if entry in mapper else entry
mp = np.vectorize(mp)
@ -1038,7 +1080,7 @@ class Grid:
)
def sort(self):
def sort(self) -> "Grid":
"""
Sort material indices such that min(material) is located at (0,0,0).
@ -1060,7 +1102,11 @@ class Grid:
)
def vicinity_offset(self,vicinity=1,offset=None,trigger=[],periodic=True):
def vicinity_offset(self,
vicinity: int = 1,
offset: int = None,
trigger: IntSequence = [],
periodic: bool = True) -> "Grid":
"""
Offset material index of points in the vicinity of xxx.
@ -1076,10 +1122,10 @@ class Grid:
offset : int, optional
Offset (positive or negative) to tag material indices,
defaults to material.max()+1.
trigger : list of ints, optional
trigger : sequence of int, optional
List of material indices that trigger a change.
Defaults to [], meaning that any different neighbor triggers a change.
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
Returns
@ -1088,8 +1134,7 @@ class Grid:
Updated grid-based geometry.
"""
def tainted_neighborhood(stencil,trigger):
def tainted_neighborhood(stencil: np.ndarray, trigger):
me = stencil[stencil.shape[0]//2]
return np.any(stencil != me if len(trigger) == 0 else
np.in1d(stencil,np.array(list(set(trigger) - {me}))))
@ -1108,15 +1153,15 @@ class Grid:
)
def get_grain_boundaries(self,periodic=True,directions='xyz'):
def get_grain_boundaries(self, periodic: bool = True, directions: Sequence[str] = 'xyz'):
"""
Create VTK unstructured grid containing grain boundaries.
Parameters
----------
periodic : Boolean, optional
periodic : bool, optional
Assume grid to be periodic. Defaults to True.
directions : iterable containing str, optional
directions : (sequence of) string, optional
Direction(s) along which the boundaries are determined.
Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.

23
python/damask/_orientation.py
View File

@ -412,8 +412,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into fundamental zone.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into fundamental zone.
Notes
-----
@ -456,8 +456,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of quaternion.shape
Boolean array indicating whether Rodrigues-Frank vector falls into disorientation FZ.
in : numpy.ndarray of bool, quaternion.shape
Whether Rodrigues-Frank vector falls into disorientation FZ.
References
----------
@ -532,6 +532,17 @@ class Orientation(Rotation,Crystal):
[ 0.07359167 -0.36505797 0.92807163]]
Bunge Eulers / deg: (11.40, 21.86, 0.60)
Plot a sample from the Mackenzie distribution.
>>> import matplotlib.pyplot as plt
>>> import damask
>>> N = 10000
>>> a = damask.Orientation.from_random(shape=N,family='cubic')
>>> b = damask.Orientation.from_random(shape=N,family='cubic')
>>> d = a.disorientation(b).as_axis_angle(degrees=True,pair=True)[1]
>>> plt.hist(d,25)
>>> plt.show()
"""
if self.family != other.family:
raise NotImplementedError('disorientation between different crystal families')
@ -660,8 +671,8 @@ class Orientation(Rotation,Crystal):
Returns
-------
in : numpy.ndarray of shape (...)
Boolean array indicating whether vector falls into SST.
in : numpy.ndarray, shape (...)
Whether vector falls into SST.
"""
if not isinstance(vector,np.ndarray) or vector.shape[-1] != 3:

175
python/damask/_result.py
View File

@ -4,6 +4,7 @@ import fnmatch
import os
import copy
import datetime
import warnings
import xml.etree.ElementTree as ET
import xml.dom.minidom
from pathlib import Path
@ -27,6 +28,20 @@ h5py3 = h5py.__version__[0] == '3'
chunk_size = 1024**2//8 # for compression in HDF5
def _view_transition(what,datasets,increments,times,phases,homogenizations,fields):
if (datasets is not None and what is None) or (what is not None and datasets is None):
raise ValueError('"what" and "datasets" need to be used as a pair')
if datasets is not None or what is not None:
warnings.warn('Arguments "what" and "datasets" will be removed in DAMASK v3.0.0-alpha7', DeprecationWarning,2)
return what,datasets
if sum(1 for _ in filter(None.__ne__, [increments,times,phases,homogenizations,fields])) > 1:
raise ValueError('Only one out of "increments", "times", "phases", "homogenizations", and "fields" can be used')
else:
if increments is not None: return "increments", increments
if times is not None: return "times", times
if phases is not None: return "phases", phases
if homogenizations is not None: return "homogenizations", homogenizations
if fields is not None: return "fields", fields
def _read(dataset):
"""Read a dataset and its metadata into a numpy.ndarray."""
@ -79,7 +94,7 @@ class Result:
>>> r.add_Cauchy()
>>> r.add_equivalent_Mises('sigma')
>>> r.export_VTK()
>>> r_last = r.view('increments',-1)
>>> r_last = r.view(increments=-1)
>>> sigma_vM_last = r_last.get('sigma_vM')
"""
@ -141,7 +156,7 @@ class Result:
self.fname = Path(fname).absolute()
self._allow_modification = False
self._protected = True
def __copy__(self):
@ -155,10 +170,10 @@ class Result:
"""Show summary of file content."""
visible_increments = self.visible['increments']
first = self.view('increments',visible_increments[0:1]).list_data()
first = self.view(increments=visible_increments[0:1]).list_data()
last = '' if len(visible_increments) < 2 else \
self.view('increments',visible_increments[-1:]).list_data()
self.view(increments=visible_increments[-1:]).list_data()
in_between = '' if len(visible_increments) < 3 else \
''.join([f'\n{inc}\n ...\n' for inc in visible_increments[1:-1]])
@ -231,36 +246,6 @@ class Result:
return dup
def modification_enable(self):
"""
Allow modification of existing data.
Returns
-------
modified_view : damask.Result
View without write-protection of existing data.
"""
print(util.warn('Warning: Modification of existing datasets allowed!'))
dup = self.copy()
dup._allow_modification = True
return dup
def modification_disable(self):
"""
Prevent modification of existing data (default case).
Returns
-------
modified_view : damask.Result
View with write-protection of existing data.
"""
dup = self.copy()
dup._allow_modification = False
return dup
def increments_in_range(self,start,end):
"""
Get all increments within a given range.
@ -285,7 +270,6 @@ class Result:
selected.append(self.increments[i])
return selected
def times_in_range(self,start,end):
"""
Get all increments within a given time range.
@ -310,17 +294,38 @@ class Result:
return selected
def view(self,what,datasets):
def view(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None,
protected=None):
"""
Set view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
protected: bool, optional.
Protection status of existing data.
Returns
-------
@ -333,29 +338,61 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_first = r.view('increment',0)
>>> r_first = r.view(increment=0)
Get a view that shows all results between simulation times of 10 to 40:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_t10to40 = r.view('times',r.times_in_range(10.0,40.0))
>>> r_t10to40 = r.view(times=r.times_in_range(10.0,40.0))
"""
return self._manage_view('set',what,datasets)
v = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
if protected is not None:
if v is None:
dup = self.copy()
else:
what_,datasets_ = v
dup = self._manage_view('set',what_,datasets_)
if not protected:
print(util.warn('Warning: Modification of existing datasets allowed!'))
dup._protected = protected
else:
what_,datasets_ = v
dup = self._manage_view('set',what_,datasets_)
return dup
def view_more(self,what,datasets):
def view_more(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None):
"""
Add to view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
Returns
-------
@ -367,25 +404,44 @@ class Result:
Get a view that shows only results from first and last increment:
>>> import damask
>>> r_empty = damask.Result('my_file.hdf5').view('increments',False)
>>> r_first = r_empty.view_more('increments',0)
>>> r_first_and_last = r.first.view_more('increments',-1)
>>> r_empty = damask.Result('my_file.hdf5').view(increments=False)
>>> r_first = r_empty.view_more(increments=0)
>>> r_first_and_last = r.first.view_more(increments=-1)
"""
return self._manage_view('add',what,datasets)
what_, datasets_ = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
return self._manage_view('add',what_,datasets_)
def view_less(self,what,datasets):
def view_less(self,what=None,datasets=None,*,
increments=None,
times=None,
phases=None,
homogenizations=None,
fields=None):
"""
Remove from view.
Wildcard matching with '?' and '*' is supported.
True is equivalent to '*', False is equivalent to [].
Parameters
----------
what : {'increments', 'times', 'phases', 'homogenizations', 'fields'}
Attribute to change.
Attribute to change. DEPRECATED.
datasets : (list of) int (for increments), (list of) float (for times), (list of) str, or bool
Name of datasets; supports '?' and '*' wildcards.
Name of datasets; supports '?' and '*' wildcards. DEPRECATED.
True is equivalent to '*', False is equivalent to [].
increments: (list of) int, (list of) str, or bool, optional.
Number(s) of increments to select.
times: (list of) float, (list of) str, or bool, optional.
Simulation time(s) of increments to select.
phases: (list of) str, or bool, optional.
Name(s) of phases to select.
homogenizations: (list of) str, or bool, optional.
Name(s) of homogenizations to select.
fields: (list of) str, or bool, optional.
Name(s) of fields to select.
Returns
-------
@ -398,10 +454,11 @@ class Result:
>>> import damask
>>> r_all = damask.Result('my_file.hdf5')
>>> r_deformed = r_all.view_less('increments',0)
>>> r_deformed = r_all.view_less(increments=0)
"""
return self._manage_view('del',what,datasets)
what_, datasets_ = _view_transition(what,datasets,increments,times,phases,homogenizations,fields)
return self._manage_view('del',what_,datasets_)
def rename(self,name_src,name_dst):
@ -424,11 +481,11 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable()
>>> r_unprotected = r.view(protected=False)
>>> r_unprotected.rename('F','def_grad')
"""
if not self._allow_modification:
if self._protected:
raise PermissionError('Renaming datasets not permitted')
with h5py.File(self.fname,'a') as f:
@ -463,11 +520,11 @@ class Result:
>>> import damask
>>> r = damask.Result('my_file.hdf5')
>>> r_unprotected = r.modification_enable()
>>> r_unprotected = r.view(protected=False)
>>> r_unprotected.remove('F')
"""
if not self._allow_modification:
if self._protected:
raise PermissionError('Removing datasets not permitted')
with h5py.File(self.fname,'a') as f:
@ -1358,7 +1415,7 @@ class Result:
lock.acquire()
with h5py.File(self.fname, 'a') as f:
try:
if self._allow_modification and '/'.join([group,result['label']]) in f:
if not self._protected and '/'.join([group,result['label']]) in f:
dataset = f['/'.join([group,result['label']])]
dataset[...] = result['data']
dataset.attrs['overwritten'] = True
@ -1760,7 +1817,7 @@ class Result:
output : (list of) str, optional
Names of the datasets to export to the file.
Defaults to '*', in which case all datasets are exported.
overwrite : boolean, optional
overwrite : bool, optional
Overwrite existing configuration files.
Defaults to False.

22
python/damask/_rotation.py
View File

@ -678,7 +678,7 @@ class Rotation:
----------
q : numpy.ndarray of shape (...,4)
Unit quaternion (q_0, q_1, q_2, q_3) in positive real hemisphere, i.e. ǀqǀ = 1, q_0 ≥ 0.
accept_homomorph : boolean, optional
accept_homomorph : bool, optional
Allow homomorphic variants, i.e. q_0 < 0 (negative real hemisphere).
Defaults to False.
P : int ∈ {-1,1}, optional
@ -713,7 +713,7 @@ class Rotation:
phi : numpy.ndarray of shape (...,3)
Euler angles (φ_1 ∈ [0,2π], ϕ ∈ [0,π], φ_2 ∈ [0,2π])
or (φ_1 ∈ [0,360], ϕ ∈ [0,180], φ_2 ∈ [0,360]) if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Euler angles are given in degrees. Defaults to False.
Notes
@ -744,9 +744,9 @@ class Rotation:
axis_angle : numpy.ndarray of shape (...,4)
Axis and angle (n_1, n_2, n_3, ω) with ǀnǀ = 1 and ω ∈ [0,π]
or ω ∈ [0,180] if degrees == True.
degrees : boolean, optional
degrees : bool, optional
Angle ω is given in degrees. Defaults to False.
normalize: boolean, optional
normalize: bool, optional
Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1.
@ -780,9 +780,9 @@ class Rotation:
----------
basis : numpy.ndarray of shape (...,3,3)
Three three-dimensional lattice basis vectors.
orthonormal : boolean, optional
orthonormal : bool, optional
Basis is strictly orthonormal, i.e. is free of stretch components. Defaults to True.
reciprocal : boolean, optional
reciprocal : bool, optional
Basis vectors are given in reciprocal (instead of real) space. Defaults to False.
"""
@ -858,7 +858,7 @@ class Rotation:
----------
rho : numpy.ndarray of shape (...,4)
Rodrigues–Frank vector (n_1, n_2, n_3, tan(ω/2)) with ǀnǀ = 1 and ω ∈ [0,π].
normalize : boolean, optional
normalize : bool, optional
Allow ǀnǀ ≠ 1. Defaults to False.
P : int ∈ {-1,1}, optional
Sign convention. Defaults to -1.
@ -983,9 +983,9 @@ class Rotation:
N : integer, optional
Number of discrete orientations to be sampled from the given ODF.
Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
Euler space grid coordinates are in degrees. Defaults to True.
fractions : boolean, optional
fractions : bool, optional
ODF values correspond to volume fractions, not probability densities.
Defaults to True.
rng_seed: {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -1039,7 +1039,7 @@ class Rotation:
Standard deviation of (Gaussian) misorientation distribution.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma is given in degrees. Defaults to True.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.
@ -1078,7 +1078,7 @@ class Rotation:
Defaults to 0.
N : int, optional
Number of samples. Defaults to 500.
degrees : boolean, optional
degrees : bool, optional
sigma, alpha, and beta are given in degrees.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator.

11
python/damask/_typehints.py Normal file
View File

@ -0,0 +1,11 @@
"""Functionality for typehints."""
from typing import Sequence, Union, TextIO
from pathlib import Path
import numpy as np
FloatSequence = Union[np.ndarray,Sequence[float]]
IntSequence = Union[np.ndarray,Sequence[int]]
FileHandle = Union[TextIO, str, Path]

8
python/damask/_vtk.py
View File

@ -28,8 +28,8 @@ class VTK:
----------
vtk_data : subclass of vtk.vtkDataSet
Description of geometry and topology, optionally with attached data.
Valid types are vtk.vtkRectilinearGrid, vtk.vtkUnstructuredGrid,
or vtk.vtkPolyData.
Valid types are vtk.vtkImageData, vtk.vtkUnstructuredGrid,
vtk.vtkPolyData, and vtk.vtkRectilinearGrid.
"""
self.vtk_data = vtk_data
@ -242,7 +242,7 @@ class VTK:
----------
fname : str or pathlib.Path
Filename for writing.
parallel : boolean, optional
parallel : bool, optional
Write data in parallel background process. Defaults to True.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.
@ -419,7 +419,7 @@ class VTK:
return writer.GetOutputString()
def show(self):
def show(self) -> None:
"""
Render.

171
python/damask/grid_filters.py
View File

@ -12,21 +12,23 @@ the following operations are required for tensorial data:
"""
from typing import Sequence, Tuple, Union
from typing import Tuple as _Tuple
from scipy import spatial as _spatial
import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order: bool = False) -> _np.ndarray:
def _ks(size: _FloatSequence, cells: _IntSequence, first_order: bool = False) -> _np.ndarray:
"""
Get wave numbers operator.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
first_order : bool, optional
Correction for first order derivatives, defaults to False.
@ -45,20 +47,20 @@ def _ks(size: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]], first_order:
return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def curl(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
u"""
Calculate curl of a vector or tensor field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Periodic field of which the curl is calculated.
Returns
-------
∇ × f : numpy.ndarray
∇ × f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Curl of f.
"""
@ -76,20 +78,20 @@ def curl(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(curl_,axes=(0,1,2),s=f.shape[:3])
def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def divergence(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
u"""
Calculate divergence of a vector or tensor field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Periodic field of which the divergence is calculated.
Returns
-------
∇ · f : numpy.ndarray
∇ · f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
Divergence of f.
"""
@ -103,20 +105,20 @@ def divergence(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(div_,axes=(0,1,2),s=f.shape[:3])
def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
def gradient(size: _FloatSequence, f: _np.ndarray) -> _np.ndarray:
u"""
Calculate gradient of a scalar or vector fieldin Fourier space.
Calculate gradient of a scalar or vector field in Fourier space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
f : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
f : numpy.ndarray, shape (:,:,:,1) or (:,:,:,3)
Periodic field of which the gradient is calculated.
Returns
-------
∇ f : numpy.ndarray
∇ f : numpy.ndarray, shape (:,:,:,3) or (:,:,:,3,3)
Divergence of f.
"""
@ -130,29 +132,30 @@ def gradient(size: _np.ndarray, f: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(grad_,axes=(0,1,2),s=f.shape[:3])
def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
size: _np.ndarray,
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates0_point(cells: _IntSequence,
size: _FloatSequence,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Cell center positions (undeformed).
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
origin : numpy.ndarray, optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_p_0 : numpy.ndarray
x_p_0 : numpy.ndarray, shape (:,:,:,3)
Undeformed cell center coordinates.
"""
start = origin + size/_np.array(cells)*.5
end = origin + size - size/_np.array(cells)*.5
size_ = _np.array(size,float)
start = origin + size_/_np.array(cells,int)*.5
end = origin + size_ - size_/_np.array(cells,int)*.5
return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
_np.linspace(start[1],end[1],cells[1]),
@ -160,24 +163,24 @@ def coordinates0_point(cells: Union[ _np.ndarray,Sequence[int]],
axis = -1)
def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_fluct_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from fluctuation part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p_fluct : numpy.ndarray
u_p_fluct : numpy.ndarray, shape (:,:,:,3)
Fluctuating part of the cell center displacements.
"""
integrator = 0.5j*size/_np.pi
integrator = 0.5j*_np.array(size,float)/_np.pi
k_s = _ks(size,F.shape[:3],False)
k_s_squared = _np.einsum('...l,...l',k_s,k_s)
@ -192,20 +195,20 @@ def displacement_fluct_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_avg_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from average part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p_avg : numpy.ndarray
u_p_avg : numpy.ndarray, shape (:,:,:,3)
Average part of the cell center displacements.
"""
@ -213,42 +216,42 @@ def displacement_avg_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
def displacement_point(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_point(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Cell center displacement field from deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p : numpy.ndarray
u_p : numpy.ndarray, shape (:,:,:,3)
Cell center displacements.
"""
return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates_point(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Cell center positions.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_p : numpy.ndarray
x_p : numpy.ndarray, shape (:,:,:,3)
Cell center coordinates.
"""
@ -256,14 +259,14 @@ def coordinates_point(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _
def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
"""
Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
Parameters
----------
coordinates0 : numpy.ndarray of shape (:,3)
Undeformed cell coordinates.
coordinates0 : numpy.ndarray, shape (:,3)
Undeformed cell center coordinates.
ordered : bool, optional
Expect coordinates0 data to be ordered (x fast, z slow).
Defaults to True.
@ -277,7 +280,7 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
mincorner = _np.array(list(map(min,coords)))
maxcorner = _np.array(list(map(max,coords)))
cells = _np.array(list(map(len,coords)),'i')
cells = _np.array(list(map(len,coords)),int)
size = cells/_np.maximum(cells-1,1) * (maxcorner-mincorner)
delta = size/cells
origin = mincorner - delta*.5
@ -305,24 +308,24 @@ def cellsSizeOrigin_coordinates0_point(coordinates0: _np.ndarray,
return (cells,size,origin)
def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
size: _np.ndarray,
origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates0_node(cells: _IntSequence,
size: _FloatSequence,
origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Nodal positions (undeformed).
Parameters
----------
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Number of cells.
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_n_0 : numpy.ndarray
x_n_0 : numpy.ndarray, shape (:,:,:,3)
Undeformed nodal coordinates.
"""
@ -332,40 +335,40 @@ def coordinates0_node(cells: Union[_np.ndarray,Sequence[int]],
axis = -1)
def displacement_fluct_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_fluct_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from fluctuation part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_n_fluct : numpy.ndarray
u_n_fluct : numpy.ndarray, shape (:,:,:,3)
Fluctuating part of the nodal displacements.
"""
return point_to_node(displacement_fluct_point(size,F))
def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_avg_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from average part of the deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_n_avg : numpy.ndarray
u_n_avg : numpy.ndarray, shape (:,:,:,3)
Average part of the nodal displacements.
"""
@ -373,42 +376,42 @@ def displacement_avg_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
def displacement_node(size: _np.ndarray, F: _np.ndarray) -> _np.ndarray:
def displacement_node(size: _FloatSequence, F: _np.ndarray) -> _np.ndarray:
"""
Nodal displacement field from deformation gradient field.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
Returns
-------
u_p : numpy.ndarray
u_p : numpy.ndarray, shape (:,:,:,3)
Nodal displacements.
"""
return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _np.zeros(3)) -> _np.ndarray:
def coordinates_node(size: _FloatSequence, F: _np.ndarray, origin: _FloatSequence = _np.zeros(3)) -> _np.ndarray:
"""
Nodal positions.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the periodic field.
F : numpy.ndarray
F : numpy.ndarray, shape (:,:,:,3,3)
Deformation gradient field.
origin : numpy.ndarray of shape (3), optional
origin : sequence of float, len(3), optional
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
Returns
-------
x_n : numpy.ndarray
x_n : numpy.ndarray, shape (:,:,:,3)
Nodal coordinates.
"""
@ -416,13 +419,13 @@ def coordinates_node(size: _np.ndarray, F: _np.ndarray, origin: _np.ndarray = _n
def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
ordered: bool = True) -> Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
ordered: bool = True) -> _Tuple[_np.ndarray,_np.ndarray,_np.ndarray]:
"""
Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
Parameters
----------
coordinates0 : numpy.ndarray of shape (:,3)
coordinates0 : numpy.ndarray, shape (:,3)
Undeformed nodal coordinates.
ordered : bool, optional
Expect coordinates0 data to be ordered (x fast, z slow).
@ -437,7 +440,7 @@ def cellsSizeOrigin_coordinates0_node(coordinates0: _np.ndarray,
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
mincorner = _np.array(list(map(min,coords)))
maxcorner = _np.array(list(map(max,coords)))
cells = _np.array(list(map(len,coords)),'i') - 1
cells = _np.array(list(map(len,coords)),int) - 1
size = maxcorner-mincorner
origin = mincorner
@ -463,12 +466,12 @@ def point_to_node(cell_data: _np.ndarray) -> _np.ndarray:
Parameters
----------
cell_data : numpy.ndarray of shape (:,:,:,...)
cell_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the cell centers of a periodic grid.
Returns
-------
node_data : numpy.ndarray of shape (:,:,:,...)
node_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the nodes of a periodic grid.
"""
@ -485,12 +488,12 @@ def node_to_point(node_data: _np.ndarray) -> _np.ndarray:
Parameters
----------
node_data : numpy.ndarray of shape (:,:,:,...)
node_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the nodes of a periodic grid.
Returns
-------
cell_data : numpy.ndarray of shape (:,:,:,...)
cell_data : numpy.ndarray, shape (:,:,:,...)
Data defined on the cell centers of a periodic grid.
"""
@ -507,7 +510,7 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
Parameters
----------
coordinates0 : numpy.ndarray
coordinates0 : numpy.ndarray, shape (:,3)
Array of undeformed cell coordinates.
Returns
@ -523,17 +526,17 @@ def coordinates0_valid(coordinates0: _np.ndarray) -> bool:
return False
def regrid(size: _np.ndarray, F: _np.ndarray, cells: Union[_np.ndarray,Sequence[int]]) -> _np.ndarray:
def regrid(size: _FloatSequence, F: _np.ndarray, cells: _IntSequence) -> _np.ndarray:
"""
Return mapping from coordinates in deformed configuration to a regular grid.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size.
F : numpy.ndarray of shape (:,:,:,3,3)
F : numpy.ndarray, shape (:,:,:,3,3), shape (:,:,:,3,3)
Deformation gradient field.
cells : numpy.ndarray of shape (3)
cells : sequence of int, len (3)
Cell count along x,y,z of remapping grid.
"""

4
python/damask/mechanics.py
View File

@ -5,7 +5,7 @@ All routines operate on numpy.ndarrays of shape (...,3,3).
"""
from typing import Sequence
from typing import Sequence as _Sequence
import numpy as _np
@ -243,7 +243,7 @@ def stretch_right(T: _np.ndarray) -> _np.ndarray:
return _polar_decomposition(T,'U')[0]
def _polar_decomposition(T: _np.ndarray, requested: Sequence[str]) -> tuple:
def _polar_decomposition(T: _np.ndarray, requested: _Sequence[str]) -> tuple:
"""
Perform singular value decomposition.

43
python/damask/seeds.py
View File

@ -1,25 +1,27 @@
"""Functionality for generation of seed points for Voronoi or Laguerre tessellation."""
from typing import Sequence,Tuple
from typing import Tuple as _Tuple
from scipy import spatial as _spatial
import numpy as _np
from ._typehints import FloatSequence as _FloatSequence, IntSequence as _IntSequence
from . import util as _util
from . import grid_filters as _grid_filters
def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_seed=None) -> _np.ndarray:
def from_random(size: _FloatSequence, N_seeds: int, cells: _IntSequence = None,
rng_seed=None) -> _np.ndarray:
"""
Place seeds randomly in space.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the seeding domain.
N_seeds : int
Number of seeds.
cells : numpy.ndarray of shape (3), optional.
cells : sequence of int, len (3), optional.
If given, ensures that each seed results in a grain when a standard Voronoi
tessellation is performed using the given grid resolution (i.e. size/cells).
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
@ -28,29 +30,30 @@ def from_random(size: _np.ndarray, N_seeds: int, cells: _np.ndarray = None, rng_
Returns
-------
coords : numpy.ndarray of shape (N_seeds,3)
coords : numpy.ndarray, shape (N_seeds,3)
Seed coordinates in 3D space.
"""
size_ = _np.array(size,float)
rng = _np.random.default_rng(rng_seed)
if cells is None:
coords = rng.random((N_seeds,3)) * size
coords = rng.random((N_seeds,3)) * size_
else:
grid_coords = _grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
coords = grid_coords[rng.choice(_np.prod(cells),N_seeds, replace=False)] \
+ _np.broadcast_to(size/cells,(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble without leaving cells
+ _np.broadcast_to(size_/_np.array(cells,int),(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble w/o leaving grid
return coords
def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distance: float,
def from_Poisson_disc(size: _FloatSequence, N_seeds: int, N_candidates: int, distance: float,
periodic: bool = True, rng_seed=None) -> _np.ndarray:
"""
Place seeds according to a Poisson disc distribution.
Parameters
----------
size : numpy.ndarray of shape (3)
size : sequence of float, len (3)
Physical size of the seeding domain.
N_seeds : int
Number of seeds.
@ -58,7 +61,7 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
Number of candidates to consider for finding best candidate.
distance : float
Minimum acceptable distance to other seeds.
periodic : boolean, optional
periodic : bool, optional
Calculate minimum distance for periodically repeated grid.
rng_seed : {None, int, array_like[ints], SeedSequence, BitGenerator, Generator}, optional
A seed to initialize the BitGenerator. Defaults to None.
@ -66,13 +69,13 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
Returns
-------
coords : numpy.ndarray of shape (N_seeds,3)
coords : numpy.ndarray, shape (N_seeds,3)
Seed coordinates in 3D space.
"""
rng = _np.random.default_rng(rng_seed)
coords = _np.empty((N_seeds,3))
coords[0] = rng.random(3) * size
coords[0] = rng.random(3) * _np.array(size,float)
s = 1
i = 0
@ -96,8 +99,8 @@ def from_Poisson_disc(size: _np.ndarray, N_seeds: int, N_candidates: int, distan
return coords
def from_grid(grid, selection: Sequence[int] = None,
invert: bool = False, average: bool = False, periodic: bool = True) -> Tuple[_np.ndarray, _np.ndarray]:
def from_grid(grid, selection: _IntSequence = None, invert_selection: bool = False,
average: bool = False, periodic: bool = True) -> _Tuple[_np.ndarray, _np.ndarray]:
"""
Create seeds from grid description.
@ -105,24 +108,24 @@ def from_grid(grid, selection: Sequence[int] = None,
----------
grid : damask.Grid
Grid from which the material IDs are used as seeds.
selection : iterable of integers, optional
selection : sequence of int, optional
Material IDs to consider.
invert : boolean, false
invert_selection : bool, optional
Consider all material IDs except those in selection. Defaults to False.
average : boolean, optional
average : bool, optional
Seed corresponds to center of gravity of material ID cloud.
periodic : boolean, optional
periodic : bool, optional
Center of gravity accounts for periodic boundaries.
Returns
-------
coords, materials : numpy.ndarray of shape (:,3), numpy.ndarray of shape (:)
coords, materials : numpy.ndarray, shape (:,3); numpy.ndarray, shape (:)
Seed coordinates in 3D space, material IDs.
"""
material = grid.material.reshape((-1,1),order='F')
mask = _np.full(grid.cells.prod(),True,dtype=bool) if selection is None else \
_np.isin(material,selection,invert=invert).flatten()
_np.isin(material,selection,invert=invert_selection).flatten()
coords = _grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
if not average:

70
python/damask/util.py
View File

@ -18,11 +18,11 @@ from . import version
__all__=[
'srepr',
'emph', 'deemph', 'warn', 'strikeout',
'run',
'run',
'natural_sort',
'show_progress',
'scale_to_coprime',
'project_stereographic',
'project_equal_angle', 'project_equal_area',
'hybrid_IA',
'execution_stamp',
'shapeshifter', 'shapeblender',
@ -267,13 +267,13 @@ def scale_to_coprime(v):
return m
def project_stereographic(vector,direction='z',normalize=True,keepdims=False):
def project_equal_angle(vector,direction='z',normalize=True,keepdims=False):
"""
Apply stereographic projection to vector.
Apply equal-angle projection to vector.
Parameters
----------
vector : numpy.ndarray of shape (...,3)
vector : numpy.ndarray, shape (...,3)
Vector coordinates to be projected.
direction : str
Projection direction 'x', 'y', or 'z'.
@ -281,32 +281,74 @@ def project_stereographic(vector,direction='z',normalize=True,keepdims=False):
normalize : bool
Ensure unit length of input vector. Defaults to True.
keepdims : bool
Maintain three-dimensional output coordinates.
Default two-dimensional output uses right-handed frame spanned by
Maintain three-dimensional output coordinates. Defaults to False.
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Returns
-------
coordinates : numpy.ndarray of shape (...,2 | 3)
coordinates : numpy.ndarray, shape (...,2 | 3)
Projected coordinates.
Examples
--------
>>> import damask
>>> import numpy as np
>>> project_stereographic(np.ones(3))
>>> project_equal_angle(np.ones(3))
[0.3660254, 0.3660254]
>>> project_stereographic(np.ones(3),direction='x',normalize=False,keepdims=True)
>>> project_equal_angle(np.ones(3),direction='x',normalize=False,keepdims=True)
[0, 0.5, 0.5]
>>> project_stereographic([0,1,1],direction='y',normalize=True,keepdims=False)
>>> project_equal_angle([0,1,1],direction='y',normalize=True,keepdims=False)
[0.41421356, 0]
"""
shift = 'zyx'.index(direction)
v_ = np.roll(vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector,
shift,axis=-1)
return np.roll(np.block([v_[...,:2]/(1+np.abs(v_[...,2:3])),np.zeros_like(v_[...,2:3])]),
v = np.roll(vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector,
shift,axis=-1)
return np.roll(np.block([v[...,:2]/(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]
def project_equal_area(vector,direction='z',normalize=True,keepdims=False):
"""
Apply equal-area projection to vector.
Parameters
----------
vector : numpy.ndarray, shape (...,3)
Vector coordinates to be projected.
direction : str
Projection direction 'x', 'y', or 'z'.
Defaults to 'z'.
normalize : bool
Ensure unit length of input vector. Defaults to True.
keepdims : bool
Maintain three-dimensional output coordinates. Defaults to False.
Two-dimensional output uses right-handed frame spanned by
the next and next-next axis relative to the projection direction,
e.g. x-y when projecting along z and z-x when projecting along y.
Returns
-------
coordinates : numpy.ndarray, shape (...,2 | 3)
Projected coordinates.
Examples
--------
>>> import damask
>>> import numpy as np
>>> project_equal_area(np.ones(3))
[0.45970084, 0.45970084]
>>> project_equal_area(np.ones(3),direction='x',normalize=False,keepdims=True)
[0.0, 0.70710678, 0.70710678]
>>> project_equal_area([0,1,1],direction='y',normalize=True,keepdims=False)
[0.5411961, 0.0]
"""
shift = 'zyx'.index(direction)
v = np.roll(vector/np.linalg.norm(vector,axis=-1,keepdims=True) if normalize else vector,
shift,axis=-1)
return np.roll(np.block([v[...,:2]/np.sqrt(1.0+np.abs(v[...,2:3])),np.zeros_like(v[...,2:3])]),
-shift if keepdims else 0,axis=-1)[...,:3 if keepdims else 2]

10
python/tests/test_Colormap.py
View File

@ -139,6 +139,16 @@ class TestColormap:
c += c
assert (np.allclose(c.colors[:len(c.colors)//2],c.colors[len(c.colors)//2:]))
@pytest.mark.parametrize('N,cmap,at,result',[
(8,'gray',0.5,[0.5,0.5,0.5]),
(17,'gray',0.5,[0.5,0.5,0.5]),
(17,'gray',[0.5,0.75],[[0.5,0.5,0.5],[0.75,0.75,0.75]]),
])
def test_at_value(self, N, cmap, at, result):
assert np.allclose(Colormap.from_predefined(cmap,N=N).at(at)[...,:3],
result,
rtol=0.005)
@pytest.mark.parametrize('bounds',[None,[2,10]])
def test_shade(self,ref_path,update,bounds):
data = np.add(*np.indices((10, 11)))

20
python/tests/test_Crystal.py
View File

@ -79,3 +79,23 @@ class TestCrystal:
a=a,b=b,c=c,
alpha=alpha,beta=beta,gamma=gamma)
assert np.allclose(points,c.lattice_points)
@pytest.mark.parametrize('crystal,length',
[(Crystal(lattice='cF'),[12,6]),
(Crystal(lattice='cI'),[12,12,24]),
(Crystal(lattice='hP'),[3,3,6,12,6]),
(Crystal(lattice='tI',c=1.2),[2,2,2,4,2,4,2,2,4,8,4,8,8])
])
def test_N_slip(self,crystal,length):
assert [len(s) for s in crystal.kinematics('slip')['direction']] == length
assert [len(s) for s in crystal.kinematics('slip')['plane']] == length
@pytest.mark.parametrize('crystal,length',
[(Crystal(lattice='cF'),[12]),
(Crystal(lattice='cI'),[12]),
(Crystal(lattice='hP'),[6,6,6,6]),
])
def test_N_twin(self,crystal,length):
assert [len(s) for s in crystal.kinematics('twin')['direction']] == length
assert [len(s) for s in crystal.kinematics('twin')['plane']] == length

21
python/tests/test_Grid.py
View File

@ -237,12 +237,27 @@ class TestGrid:
modified)
def test_canvas(self,default):
def test_canvas_extend(self,default):
cells = default.cells
grid_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + grid_add)
cells_add = np.random.randint(0,30,(3))
modified = default.canvas(cells + cells_add)
assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)
@pytest.mark.parametrize('sign',[+1,-1])
@pytest.mark.parametrize('extra_offset',[0,-1])
def test_canvas_move_out(self,sign,extra_offset):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
o = sign*np.ones(3)*g.cells.min() +extra_offset*sign
if extra_offset == 0:
assert np.all(g.canvas(offset=o).material == 1)
else:
assert np.all(np.unique(g.canvas(offset=o).material) == (0,1))
def test_canvas_cells(self,default):
g = Grid(np.zeros(np.random.randint(3,30,(3)),int),np.ones(3))
cells = np.random.randint(1,30,(3))
offset = np.random.randint(-30,30,(3))
assert np.all(g.canvas(cells,offset).cells == cells)
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
(np.random.randint(4,8,(3)),np.random.randint(9,12,(3)))])

32
python/tests/test_Result.py
View File

@ -25,7 +25,7 @@ def default(tmp_path,ref_path):
fname = '12grains6x7x8_tensionY.hdf5'
shutil.copy(ref_path/fname,tmp_path)
f = Result(tmp_path/fname)
return f.view('times',20.0)
return f.view(times=20.0)
@pytest.fixture
def single_phase(tmp_path,ref_path):
@ -58,14 +58,14 @@ class TestResult:
def test_view_all(self,default):
a = default.view('increments',True).get('F')
a = default.view(increments=True).get('F')
assert dict_equal(a,default.view('increments','*').get('F'))
assert dict_equal(a,default.view('increments',default.increments_in_range(0,np.iinfo(int).max)).get('F'))
assert dict_equal(a,default.view(increments='*').get('F'))
assert dict_equal(a,default.view(increments=default.increments_in_range(0,np.iinfo(int).max)).get('F'))
assert dict_equal(a,default.view('times',True).get('F'))
assert dict_equal(a,default.view('times','*').get('F'))
assert dict_equal(a,default.view('times',default.times_in_range(0.0,np.inf)).get('F'))
assert dict_equal(a,default.view(times=True).get('F'))
assert dict_equal(a,default.view(times='*').get('F'))
assert dict_equal(a,default.view(times=default.times_in_range(0.0,np.inf)).get('F'))
@pytest.mark.parametrize('what',['increments','times','phases','fields']) # ToDo: discuss homogenizations
def test_view_none(self,default,what):
@ -314,7 +314,7 @@ class TestResult:
@pytest.mark.parametrize('overwrite',['off','on'])
def test_add_overwrite(self,default,overwrite):
last = default.view('increments',-1)
last = default.view(increments=-1)
last.add_stress_Cauchy()
@ -322,9 +322,9 @@ class TestResult:
created_first = datetime.strptime(created_first,'%Y-%m-%d %H:%M:%S%z')
if overwrite == 'on':
last = last.modification_enable()
last = last.view(protected=False)
else:
last = last.modification_disable()
last = last.view(protected=True)
time.sleep(2.)
try:
@ -344,10 +344,10 @@ class TestResult:
def test_rename(self,default,allowed):
if allowed == 'on':
F = default.place('F')
default = default.modification_enable()
default = default.view(protected=False)
default.rename('F','new_name')
assert np.all(F == default.place('new_name'))
default = default.modification_disable()
default = default.view(protected=True)
with pytest.raises(PermissionError):
default.rename('P','another_new_name')
@ -355,7 +355,7 @@ class TestResult:
@pytest.mark.parametrize('allowed',['off','on'])
def test_remove(self,default,allowed):
if allowed == 'on':
unsafe = default.modification_enable()
unsafe = default.view(protected=False)
unsafe.remove('F')
assert unsafe.get('F') is None
else:
@ -377,7 +377,7 @@ class TestResult:
@pytest.mark.parametrize('inc',[4,0],ids=range(2))
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<9, reason='missing "Direction" attribute')
def test_vtk(self,request,tmp_path,ref_path,update,patch_execution_stamp,patch_datetime_now,output,fname,inc):
result = Result(ref_path/fname).view('increments',inc)
result = Result(ref_path/fname).view(increments=inc)
os.chdir(tmp_path)
result.export_VTK(output,parallel=False)
fname = fname.split('.')[0]+f'_inc{(inc if type(inc) == int else inc[0]):0>2}.vti'
@ -400,7 +400,7 @@ class TestResult:
result.export_VTK(output,mode)
def test_marc_coordinates(self,ref_path):
result = Result(ref_path/'check_compile_job1.hdf5').view('increments',-1)
result = Result(ref_path/'check_compile_job1.hdf5').view(increments=-1)
c_n = result.coordinates0_node + result.get('u_n')
c_p = result.coordinates0_point + result.get('u_p')
assert len(c_n) > len(c_p)
@ -440,7 +440,7 @@ class TestResult:
dim_xdmf = reader_xdmf.GetOutput().GetDimensions()
bounds_xdmf = reader_xdmf.GetOutput().GetBounds()
single_phase.view('increments',0).export_VTK(parallel=False)
single_phase.view(increments=0).export_VTK(parallel=False)
fname = os.path.splitext(os.path.basename(single_phase.fname))[0]+'_inc00.vti'
reader_vti = vtk.vtkXMLImageDataReader()
reader_vti.SetFileName(fname)

6
python/tests/test_VTK.py
View File

@ -20,7 +20,7 @@ def default():
"""Simple VTK."""
cells = np.array([5,6,7],int)
size = np.array([.6,1.,.5])
return VTK.from_rectilinear_grid(cells,size)
return VTK.from_image_data(cells,size)
class TestVTK:
@ -116,7 +116,7 @@ class TestVTK:
def test_add_extension(self,tmp_path,default):
default.save(tmp_path/'default.txt',parallel=False)
assert os.path.isfile(tmp_path/'default.txt.vtr')
assert os.path.isfile(tmp_path/'default.txt.vti')
def test_invalid_get(self,default):
@ -160,7 +160,7 @@ class TestVTK:
def test_comments(self,tmp_path,default):
default.add_comments(['this is a comment'])
default.save(tmp_path/'with_comments',parallel=False)
new = VTK.load(tmp_path/'with_comments.vtr')
new = VTK.load(tmp_path/'with_comments.vti')
assert new.get_comments() == ['this is a comment']
@pytest.mark.xfail(int(vtk.vtkVersion.GetVTKVersion().split('.')[0])<8, reason='missing METADATA')

13
python/tests/test_grid_filters.py
View File

@ -2,6 +2,8 @@ import pytest
import numpy as np
from damask import grid_filters
from damask import Grid
from damask import seeds
class TestGridFilters:
@ -139,12 +141,19 @@ class TestGridFilters:
else:
function(unordered,mode)
def test_regrid(self):
def test_regrid_identity(self):
size = np.random.random(3)
cells = np.random.randint(8,32,(3))
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
assert all(grid_filters.regrid(size,F,cells) == np.arange(cells.prod()))
def test_regrid_double_cells(self):
size = np.random.random(3)
cells = np.random.randint(8,32,(3))
g = Grid.from_Voronoi_tessellation(cells,size,seeds.from_random(size,10))
F = np.broadcast_to(np.eye(3), tuple(cells)+(3,3))
assert all(g.scale(cells*2).material.flatten() ==
g.material.flatten()[grid_filters.regrid(size,F,cells*2)])
@pytest.mark.parametrize('differential_operator',[grid_filters.curl,
grid_filters.divergence,

2
python/tests/test_seeds.py
View File

@ -67,5 +67,5 @@ class TestSeeds:
coords = seeds.from_random(size,N_seeds,cells)
grid = Grid.from_Voronoi_tessellation(cells,size,coords)
selection=np.random.randint(N_seeds)+1
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert=invert,selection=[selection])
coords,material = seeds.from_grid(grid,average=average,periodic=periodic,invert_selection=invert,selection=[selection])
assert selection not in material if invert else (selection==material).all()

19
python/tests/test_util.py
View File

@ -59,9 +59,22 @@ class TestUtil:
([1,1,0],'x',False,False,[0.5,0]),
([1,1,1],'y',True, True, [0.3660254, 0,0.3660254]),
])
def test_project_stereographic(self,point,direction,normalize,keepdims,answer):
assert np.allclose(util.project_stereographic(np.array(point),direction=direction,
normalize=normalize,keepdims=keepdims),answer)
def test_project_equal_angle(self,point,direction,normalize,keepdims,answer):
assert np.allclose(util.project_equal_angle(np.array(point),direction=direction,
normalize=normalize,keepdims=keepdims),answer)
@pytest.mark.parametrize('point,direction,normalize,keepdims,answer',
[
([1,0,0],'z',False,True, [1,0,0]),
([1,0,0],'z',True, False,[1,0]),
([0,1,1],'z',False,True, [0,0.70710678,0]),
([0,1,1],'y',True, False,[0.5411961,0]),
([1,1,0],'x',False,False,[0.70710678,0]),
([1,1,1],'y',True, True, [0.45970084,0,0.45970084]),
])
def test_project_equal_area(self,point,direction,normalize,keepdims,answer):
assert np.allclose(util.project_equal_area(np.array(point),direction=direction,
normalize=normalize,keepdims=keepdims),answer)
@pytest.mark.parametrize('fro,to,mode,answer',
[

14
src/LAPACK_interface.f90
View File

@ -6,7 +6,7 @@
module LAPACK_interface
interface
subroutine dgeev(jobvl,jobvr,n,a,lda,wr,wi,vl,ldvl,vr,ldvr,work,lwork,info)
pure subroutine dgeev(jobvl,jobvr,n,a,lda,wr,wi,vl,ldvl,vr,ldvr,work,lwork,info)
use prec
character, intent(in) :: jobvl,jobvr
integer, intent(in) :: n,lda,ldvl,ldvr,lwork
@ -18,16 +18,16 @@ module LAPACK_interface
integer, intent(out) :: info
end subroutine dgeev
subroutine dgesv(n,nrhs,a,lda,ipiv,b,ldb,info)
pure subroutine dgesv(n,nrhs,a,lda,ipiv,b,ldb,info)
use prec
integer, intent(in) :: n,nrhs,lda,ldb
real(pReal), intent(inout), dimension(lda,n) :: a
integer, intent(out), dimension(n) :: ipiv
real(pReal), intent(out), dimension(ldb,nrhs) :: b
real(pReal), intent(inout), dimension(ldb,nrhs) :: b
integer, intent(out) :: info
end subroutine dgesv
subroutine dgetrf(m,n,a,lda,ipiv,info)
pure subroutine dgetrf(m,n,a,lda,ipiv,info)
use prec
integer, intent(in) :: m,n,lda
real(pReal), intent(inout), dimension(lda,n) :: a
@ -35,16 +35,16 @@ module LAPACK_interface
integer, intent(out) :: info
end subroutine dgetrf
subroutine dgetri(n,a,lda,ipiv,work,lwork,info)
pure subroutine dgetri(n,a,lda,ipiv,work,lwork,info)
use prec
integer, intent(in) :: n,lda,lwork
real(pReal), intent(inout), dimension(lda,n) :: a
integer, intent(out), dimension(n) :: ipiv
integer, intent(in), dimension(n) :: ipiv
real(pReal), intent(out), dimension(max(1,lwork)) :: work
integer, intent(out) :: info
end subroutine dgetri
subroutine dsyev(jobz,uplo,n,a,lda,w,work,lwork,info)
pure subroutine dsyev(jobz,uplo,n,a,lda,w,work,lwork,info)
use prec
character, intent(in) :: jobz,uplo
integer, intent(in) :: n,lda,lwork

5
src/constants.f90
View File

@ -9,7 +9,8 @@ module constants
public
real(pReal), parameter :: &
T_ROOM = 300.0_pReal, & !< Room temperature in K
K_B = 1.38e-23_pReal !< Boltzmann constant in J/Kelvin
T_ROOM = 300.0_pReal, & !< Room temperature in K. ToDo: IUPAC: 298.15
K_B = 1.38e-23_pReal, & !< Boltzmann constant in J/Kelvin
N_A = 6.02214076e23_pReal !< Avogadro constant in 1/mol
end module constants

4
src/lattice.f90
View File

@ -2070,7 +2070,7 @@ end function getlabels
!> @brief Equivalent Poisson's ratio (ν)
!> @details https://doi.org/10.1143/JPSJ.20.635
!--------------------------------------------------------------------------------------------------
function lattice_equivalent_nu(C,assumption) result(nu)
pure function lattice_equivalent_nu(C,assumption) result(nu)
real(pReal), dimension(6,6), intent(in) :: C !< Stiffness tensor (Voigt notation)
character(len=5), intent(in) :: assumption !< Assumption ('Voigt' = isostrain, 'Reuss' = isostress)
@ -2103,7 +2103,7 @@ end function lattice_equivalent_nu
!> @brief Equivalent shear modulus (μ)
!> @details https://doi.org/10.1143/JPSJ.20.635
!--------------------------------------------------------------------------------------------------
function lattice_equivalent_mu(C,assumption) result(mu)
pure function lattice_equivalent_mu(C,assumption) result(mu)
real(pReal), dimension(6,6), intent(in) :: C !< Stiffness tensor (Voigt notation)
character(len=5), intent(in) :: assumption !< Assumption ('Voigt' = isostrain, 'Reuss' = isostress)

83
src/math.f90
View File

@ -512,7 +512,7 @@ end subroutine math_invert33
!--------------------------------------------------------------------------------------------------
!> @brief Inversion of symmetriced 3x3x3x3 matrix
!--------------------------------------------------------------------------------------------------
function math_invSym3333(A)
pure function math_invSym3333(A)
real(pReal),dimension(3,3,3,3) :: math_invSym3333
@ -538,7 +538,7 @@ end function math_invSym3333
!--------------------------------------------------------------------------------------------------
!> @brief invert quadratic matrix of arbitrary dimension
!--------------------------------------------------------------------------------------------------
subroutine math_invert(InvA, error, A)
pure subroutine math_invert(InvA, error, A)
real(pReal), dimension(:,:), intent(in) :: A
real(pReal), dimension(size(A,1),size(A,1)), intent(out) :: invA
@ -895,7 +895,7 @@ pure function math_33toVoigt6_stress(sigma) result(sigma_tilde)
sigma_tilde = [sigma(1,1), sigma(2,2), sigma(3,3), &
sigma(3,2), sigma(3,1), sigma(1,2)]
sigma(3,2), sigma(3,1), sigma(1,2)]
end function math_33toVoigt6_stress
@ -910,7 +910,7 @@ pure function math_33toVoigt6_strain(epsilon) result(epsilon_tilde)
epsilon_tilde = [ epsilon(1,1), epsilon(2,2), epsilon(3,3), &
2.0_pReal*epsilon(3,2), 2.0_pReal*epsilon(3,1), 2.0_pReal*epsilon(1,2)]
2.0_pReal*epsilon(3,2), 2.0_pReal*epsilon(3,1), 2.0_pReal*epsilon(1,2)]
end function math_33toVoigt6_strain
@ -961,45 +961,42 @@ pure function math_3333toVoigt66(m3333)
end function math_3333toVoigt66
!--------------------------------------------------------------------------------------------------
!> @brief draw a random sample from Gauss variable
!> @brief Draw a sample from a normal distribution.
!> @details https://en.wikipedia.org/wiki/Box%E2%80%93Muller_transform
!> https://masuday.github.io/fortran_tutorial/random.html
!--------------------------------------------------------------------------------------------------
real(pReal) function math_sampleGaussVar(mu, sigma, width)
impure elemental subroutine math_normal(x,mu,sigma)
real(pReal), intent(in) :: mu, & !< mean
sigma !< standard deviation
real(pReal), intent(in), optional :: width !< cut off as multiples of standard deviation
real(pReal), intent(out) :: x
real(pReal), intent(in), optional :: mu, sigma
real(pReal), dimension(2) :: rnd ! random numbers
real(pReal) :: scatter, & ! normalized scatter around mean
width_
real(pReal) :: sigma_, mu_
real(pReal), dimension(2) :: rnd
if (abs(sigma) < tol_math_check) then
math_sampleGaussVar = mu
if (present(mu)) then
mu_ = mu
else
if (present(width)) then
width_ = width
else
width_ = 3.0_pReal ! use +-3*sigma as default scatter
endif
mu_ = 0.0_pReal
end if
do
call random_number(rnd)
scatter = width_ * (2.0_pReal * rnd(1) - 1.0_pReal)
if (rnd(2) <= exp(-0.5_pReal * scatter**2)) exit ! test if scattered value is drawn
enddo
if (present(sigma)) then
sigma_ = sigma
else
sigma_ = 1.0_pReal
end if
math_sampleGaussVar = scatter * sigma
endif
call random_number(rnd)
x = mu_ + sigma_ * sqrt(-2.0_pReal*log(1.0_pReal-rnd(1)))*cos(2.0_pReal*PI*(1.0_pReal - rnd(2)))
end function math_sampleGaussVar
end subroutine math_normal
!--------------------------------------------------------------------------------------------------
!> @brief eigenvalues and eigenvectors of symmetric matrix
!--------------------------------------------------------------------------------------------------
subroutine math_eigh(w,v,error,m)
pure subroutine math_eigh(w,v,error,m)
real(pReal), dimension(:,:), intent(in) :: m !< quadratic matrix to compute eigenvectors and values of
real(pReal), dimension(size(m,1)), intent(out) :: w !< eigenvalues
@ -1024,7 +1021,7 @@ end subroutine math_eigh
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
!> @details See http://arxiv.org/abs/physics/0610206 (DSYEVH3)
!--------------------------------------------------------------------------------------------------
subroutine math_eigh33(w,v,m)
pure subroutine math_eigh33(w,v,m)
real(pReal), dimension(3,3),intent(in) :: m !< 3x3 matrix to compute eigenvectors and values of
real(pReal), dimension(3), intent(out) :: w !< eigenvalues
@ -1117,7 +1114,7 @@ end function math_rotationalPart
!> @brief Eigenvalues of symmetric matrix
! will return NaN on error
!--------------------------------------------------------------------------------------------------
function math_eigvalsh(m)
pure function math_eigvalsh(m)
real(pReal), dimension(:,:), intent(in) :: m !< symmetric matrix to compute eigenvalues of
real(pReal), dimension(size(m,1)) :: math_eigvalsh
@ -1140,7 +1137,7 @@ end function math_eigvalsh
!> but apparently more stable solution and has general LAPACK powered version for arbritrary sized
!> matrices as fallback
!--------------------------------------------------------------------------------------------------
function math_eigvalsh33(m)
pure function math_eigvalsh33(m)
real(pReal), intent(in), dimension(3,3) :: m !< 3x3 symmetric matrix to compute eigenvalues of
real(pReal), dimension(3) :: math_eigvalsh33,I
@ -1434,6 +1431,28 @@ subroutine selfTest
if (dNeq0(math_LeviCivita(ijk(1),ijk(2),ijk(3)))) &
error stop 'math_LeviCivita'
normal_distribution: block
integer, parameter :: N = 1000000
real(pReal), dimension(:), allocatable :: r
real(pReal) :: mu, sigma
allocate(r(N))
call random_number(mu)
call random_number(sigma)
sigma = 1.0_pReal + sigma*5.0_pReal
mu = (mu-0.5_pReal)*10_pReal
call math_normal(r,mu,sigma)
if (abs(mu -sum(r)/real(N,pReal))>5.0e-2_pReal) &
error stop 'math_normal(mu)'
mu = sum(r)/real(N,pReal)
if (abs(sigma**2 -1.0_pReal/real(N-1,pReal) * sum((r-mu)**2))/sigma > 5.0e-2_pReal) &
error stop 'math_normal(sigma)'
end block normal_distribution
end subroutine selfTest
end module math

2
src/phase.f90
View File

@ -155,7 +155,7 @@ module phase
real(pReal), dimension(3,3) :: P
end function phase_P
module function thermal_T(ph,en) result(T)
pure module function thermal_T(ph,en) result(T)
integer, intent(in) :: ph,en
real(pReal) :: T
end function thermal_T

6
src/phase_mechanical.f90
View File

@ -168,17 +168,17 @@ submodule(phase) mechanical
integer, intent(in) :: ph,en
end function plastic_dislotwin_homogenizedC
module function elastic_C66(ph,en) result(C66)
pure module function elastic_C66(ph,en) result(C66)
real(pReal), dimension(6,6) :: C66
integer, intent(in) :: ph, en
end function elastic_C66
module function elastic_mu(ph,en) result(mu)
pure module function elastic_mu(ph,en) result(mu)
real(pReal) :: mu
integer, intent(in) :: ph, en
end function elastic_mu
module function elastic_nu(ph,en) result(nu)
pure module function elastic_nu(ph,en) result(nu)
real(pReal) :: nu
integer, intent(in) :: ph, en
end function elastic_nu

8
src/phase_mechanical_elastic.f90
View File

@ -30,7 +30,7 @@ module subroutine elastic_init(phases)
phase, &
mech, &
elastic
logical :: thermal_active
print'(/,1x,a)', '<<<+- phase:mechanical:elastic init -+>>>'
print'(/,1x,a)', '<<<+- phase:mechanical:elastic:Hooke init -+>>>'
@ -86,7 +86,7 @@ end subroutine elastic_init
!--------------------------------------------------------------------------------------------------
!> @brief return 6x6 elasticity tensor
!--------------------------------------------------------------------------------------------------
module function elastic_C66(ph,en) result(C66)
pure module function elastic_C66(ph,en) result(C66)
integer, intent(in) :: &
ph, &
@ -140,7 +140,7 @@ end function elastic_C66
!--------------------------------------------------------------------------------------------------
!> @brief return shear modulus
!--------------------------------------------------------------------------------------------------
module function elastic_mu(ph,en) result(mu)
pure module function elastic_mu(ph,en) result(mu)
integer, intent(in) :: &
ph, &
@ -157,7 +157,7 @@ end function elastic_mu
!--------------------------------------------------------------------------------------------------
!> @brief return Poisson ratio
!--------------------------------------------------------------------------------------------------
module function elastic_nu(ph,en) result(nu)
pure module function elastic_nu(ph,en) result(nu)
integer, intent(in) :: &
ph, &

22
src/phase_mechanical_plastic.f90
View File

@ -73,47 +73,37 @@ submodule(phase:mechanical) plastic
en
end subroutine kinehardening_LpAndItsTangent
module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,T,ph,en)
module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: &
Lp
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLp_dMp
real(pReal), dimension(3,3), intent(in) :: &
Mp
real(pReal), intent(in) :: &
T
integer, intent(in) :: &
ph, &
en
end subroutine dislotwin_LpAndItsTangent
pure module subroutine dislotungsten_LpAndItsTangent(Lp,dLp_dMp,Mp,T,ph,en)
pure module subroutine dislotungsten_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: &
Lp
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLp_dMp
real(pReal), dimension(3,3), intent(in) :: &
Mp
real(pReal), intent(in) :: &
T
integer, intent(in) :: &
ph, &
en
end subroutine dislotungsten_LpAndItsTangent
module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp, &
Mp,Temperature,ph,en)
module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: &
Lp
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLp_dMp
real(pReal), dimension(3,3), intent(in) :: &
Mp !< Mandel stress
real(pReal), intent(in) :: &
Temperature
integer, intent(in) :: &
ph, &
en
@ -282,13 +272,13 @@ module subroutine plastic_LpAndItsTangents(Lp, dLp_dS, dLp_dFi, &
call kinehardening_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
case (PLASTIC_NONLOCAL_ID) plasticType
call nonlocal_LpAndItsTangent(Lp,dLp_dMp,Mp, thermal_T(ph,en),ph,en)
call nonlocal_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
case (PLASTIC_DISLOTWIN_ID) plasticType
call dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp, thermal_T(ph,en),ph,en)
call dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
case (PLASTIC_DISLOTUNGSTEN_ID) plasticType
call dislotungsten_LpAndItsTangent(Lp,dLp_dMp,Mp, thermal_T(ph,en),ph,en)
call dislotungsten_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
end select plasticType

8
src/phase_mechanical_plastic_dislotungsten.f90
View File

@ -257,27 +257,27 @@ end function plastic_dislotungsten_init
!> @brief Calculate plastic velocity gradient and its tangent.
!--------------------------------------------------------------------------------------------------
pure module subroutine dislotungsten_LpAndItsTangent(Lp,dLp_dMp, &
Mp,T,ph,en)
Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: &
Lp !< plastic velocity gradient
real(pReal), dimension(3,3,3,3), intent(out) :: &
dLp_dMp !< derivative of Lp with respect to the Mandel stress
real(pReal), dimension(3,3), intent(in) :: &
Mp !< Mandel stress
real(pReal), intent(in) :: &
T !< temperature
integer, intent(in) :: &
ph, &
en
integer :: &
i,k,l,m,n
real(pReal) :: &
T !< temperature
real(pReal), dimension(param(ph)%sum_N_sl) :: &
dot_gamma_pos,dot_gamma_neg, &
ddot_gamma_dtau_pos,ddot_gamma_dtau_neg
T = thermal_T(ph,en)
Lp = 0.0_pReal
dLp_dMp = 0.0_pReal

134
src/phase_mechanical_plastic_dislotwin.f90
View File

@ -476,18 +476,18 @@ module function plastic_dislotwin_homogenizedC(ph,en) result(homogenizedC)
C66_tw, &
C66_tr
integer :: i
real(pReal) :: f_unrotated
real(pReal) :: f_matrix
C = elastic_C66(ph,en)
associate(prm => param(ph), stt => state(ph))
f_unrotated = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
f_matrix = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
homogenizedC = f_unrotated * C
homogenizedC = f_matrix * C
twinActive: if (prm%sum_N_tw > 0) then
C66_tw = lattice_C66_twin(prm%N_tw,C,phase_lattice(ph),phase_cOverA(ph))
@ -513,20 +513,20 @@ end function plastic_dislotwin_homogenizedC
!--------------------------------------------------------------------------------------------------
!> @brief Calculate plastic velocity gradient and its tangent.
!--------------------------------------------------------------------------------------------------
module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,T,ph,en)
module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: Lp
real(pReal), dimension(3,3,3,3), intent(out) :: dLp_dMp
real(pReal), dimension(3,3), intent(in) :: Mp
integer, intent(in) :: ph,en
real(pReal), intent(in) :: T
integer :: i,k,l,m,n
real(pReal) :: &
f_unrotated,StressRatio_p,&
E_kB_T, &
ddot_gamma_dtau, &
tau
f_matrix,StressRatio_p,&
E_kB_T, &
ddot_gamma_dtau, &
tau, &
T
real(pReal), dimension(param(ph)%sum_N_sl) :: &
dot_gamma_sl,ddot_gamma_dtau_sl
real(pReal), dimension(param(ph)%sum_N_tw) :: &
@ -556,69 +556,71 @@ module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,T,ph,en)
0, 1, 1 &
],pReal),[ 3,6])
associate(prm => param(ph), stt => state(ph))
f_unrotated = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
T = thermal_T(ph,en)
Lp = 0.0_pReal
dLp_dMp = 0.0_pReal
call kinetics_sl(Mp,T,ph,en,dot_gamma_sl,ddot_gamma_dtau_sl)
slipContribution: do i = 1, prm%sum_N_sl
Lp = Lp + dot_gamma_sl(i)*prm%P_sl(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_sl(i) * prm%P_sl(k,l,i) * prm%P_sl(m,n,i)
end do slipContribution
associate(prm => param(ph), stt => state(ph))
call kinetics_tw(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tw,ddot_gamma_dtau_tw)
twinContibution: do i = 1, prm%sum_N_tw
Lp = Lp + dot_gamma_tw(i)*prm%P_tw(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_tw(i)* prm%P_tw(k,l,i)*prm%P_tw(m,n,i)
end do twinContibution
f_matrix = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
call kinetics_tr(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tr,ddot_gamma_dtau_tr)
transContibution: do i = 1, prm%sum_N_tr
Lp = Lp + dot_gamma_tr(i)*prm%P_tr(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_tr(i)* prm%P_tr(k,l,i)*prm%P_tr(m,n,i)
end do transContibution
call kinetics_sl(Mp,T,ph,en,dot_gamma_sl,ddot_gamma_dtau_sl)
slipContribution: do i = 1, prm%sum_N_sl
Lp = Lp + dot_gamma_sl(i)*prm%P_sl(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_sl(i) * prm%P_sl(k,l,i) * prm%P_sl(m,n,i)
end do slipContribution
Lp = Lp * f_unrotated
dLp_dMp = dLp_dMp * f_unrotated
call kinetics_tw(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tw,ddot_gamma_dtau_tw)
twinContibution: do i = 1, prm%sum_N_tw
Lp = Lp + dot_gamma_tw(i)*prm%P_tw(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_tw(i)* prm%P_tw(k,l,i)*prm%P_tw(m,n,i)
end do twinContibution
shearBandingContribution: if (dNeq0(prm%v_sb)) then
call kinetics_tr(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tr,ddot_gamma_dtau_tr)
transContibution: do i = 1, prm%sum_N_tr
Lp = Lp + dot_gamma_tr(i)*prm%P_tr(1:3,1:3,i)
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau_tr(i)* prm%P_tr(k,l,i)*prm%P_tr(m,n,i)
end do transContibution
E_kB_T = prm%E_sb/(K_B*T)
call math_eigh33(eigValues,eigVectors,Mp) ! is Mp symmetric by design?
Lp = Lp * f_matrix
dLp_dMp = dLp_dMp * f_matrix
do i = 1,6
P_sb = 0.5_pReal * math_outer(matmul(eigVectors,sb_sComposition(1:3,i)),&
matmul(eigVectors,sb_mComposition(1:3,i)))
tau = math_tensordot(Mp,P_sb)
shearBandingContribution: if (dNeq0(prm%v_sb)) then
significantShearBandStress: if (abs(tau) > tol_math_check) then
StressRatio_p = (abs(tau)/prm%xi_sb)**prm%p_sb
dot_gamma_sb = sign(prm%v_sb*exp(-E_kB_T*(1-StressRatio_p)**prm%q_sb), tau)
ddot_gamma_dtau = abs(dot_gamma_sb)*E_kB_T*prm%p_sb*prm%q_sb/prm%xi_sb &
* (abs(tau)/prm%xi_sb)**(prm%p_sb-1.0_pReal) &
* (1.0_pReal-StressRatio_p)**(prm%q_sb-1.0_pReal)
E_kB_T = prm%E_sb/(K_B*T)
call math_eigh33(eigValues,eigVectors,Mp) ! is Mp symmetric by design?
Lp = Lp + dot_gamma_sb * P_sb
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau * P_sb(k,l) * P_sb(m,n)
end if significantShearBandStress
end do
do i = 1,6
P_sb = 0.5_pReal * math_outer(matmul(eigVectors,sb_sComposition(1:3,i)),&
matmul(eigVectors,sb_mComposition(1:3,i)))
tau = math_tensordot(Mp,P_sb)
end if shearBandingContribution
significantShearBandStress: if (abs(tau) > tol_math_check) then
StressRatio_p = (abs(tau)/prm%xi_sb)**prm%p_sb
dot_gamma_sb = sign(prm%v_sb*exp(-E_kB_T*(1-StressRatio_p)**prm%q_sb), tau)
ddot_gamma_dtau = abs(dot_gamma_sb)*E_kB_T*prm%p_sb*prm%q_sb/prm%xi_sb &
* (abs(tau)/prm%xi_sb)**(prm%p_sb-1.0_pReal) &
* (1.0_pReal-StressRatio_p)**(prm%q_sb-1.0_pReal)
end associate
Lp = Lp + dot_gamma_sb * P_sb
forall (k=1:3,l=1:3,m=1:3,n=1:3) &
dLp_dMp(k,l,m,n) = dLp_dMp(k,l,m,n) &
+ ddot_gamma_dtau * P_sb(k,l) * P_sb(m,n)
end if significantShearBandStress
end do
end if shearBandingContribution
end associate
end subroutine dislotwin_LpAndItsTangent
@ -638,7 +640,7 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
integer :: i
real(pReal) :: &
f_unrotated, &
f_matrix, &
d_hat, &
v_cl, & !< climb velocity
tau, &
@ -661,9 +663,9 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
mu = elastic_mu(ph,en)
nu = elastic_nu(ph,en)
f_unrotated = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
f_matrix = 1.0_pReal &
- sum(stt%f_tw(1:prm%sum_N_tw,en)) &
- sum(stt%f_tr(1:prm%sum_N_tr,en))
call kinetics_sl(Mp,T,ph,en,dot_gamma_sl)
dot%gamma_sl(:,en) = abs(dot_gamma_sl)
@ -709,10 +711,10 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
- dot_rho_dip_climb
call kinetics_tw(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tw)
dot%f_tw(:,en) = f_unrotated*dot_gamma_tw/prm%gamma_char
dot%f_tw(:,en) = f_matrix*dot_gamma_tw/prm%gamma_char
call kinetics_tr(Mp,T,dot_gamma_sl,ph,en,dot_gamma_tr)
dot%f_tr(:,en) = f_unrotated*dot_gamma_tr
dot%f_tr(:,en) = f_matrix*dot_gamma_tr
end associate

2
src/phase_mechanical_plastic_kinehardening.f90
View File

@ -86,6 +86,8 @@ module function plastic_kinehardening_init() result(myPlasticity)
print'(/,1x,a)', '<<<+- phase:mechanical:plastic:kinehardening init -+>>>'
print'(/,a,i0)', ' # phases: ',count(myPlasticity); flush(IO_STDOUT)
print'(/,1x,a)', 'J.A. Wollmershauser et al., International Journal of Fatigue 36:181–193, 2012'
print'( 1x,a)', 'https://doi.org/10.1016/j.ijfatigue.2011.07.008'
phases => config_material%get('phase')
allocate(param(phases%length))

344
src/phase_mechanical_plastic_nonlocal.f90
View File

@ -741,7 +741,7 @@ end subroutine nonlocal_dependentState
!> @brief calculates plastic velocity gradient and its tangent
!--------------------------------------------------------------------------------------------------
module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp, &
Mp,Temperature,ph,en)
Mp,ph,en)
real(pReal), dimension(3,3), intent(out) :: &
Lp !< plastic velocity gradient
real(pReal), dimension(3,3,3,3), intent(out) :: &
@ -749,9 +749,6 @@ module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp, &
integer, intent(in) :: &
ph, &
en
real(pReal), intent(in) :: &
Temperature !< temperature
real(pReal), dimension(3,3), intent(in) :: &
Mp
!< derivative of Lp with respect to Mp
@ -771,67 +768,72 @@ module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp, &
real(pReal), dimension(param(ph)%sum_N_sl) :: &
tau, & !< resolved shear stress including backstress terms
dot_gamma !< shear rate
real(pReal) :: &
Temperature !< temperature
Temperature = thermal_T(ph,en)
Lp = 0.0_pReal
dLp_dMp = 0.0_pReal
associate(prm => param(ph),dst=>dependentState(ph),stt=>state(ph))
!*** shortcut to state variables
rho = getRho(ph,en)
rhoSgl = rho(:,sgl)
!*** shortcut to state variables
rho = getRho(ph,en)
rhoSgl = rho(:,sgl)
do s = 1,prm%sum_N_sl
tau(s) = math_tensordot(Mp, prm%P_sl(1:3,1:3,s))
tauNS(s,1) = tau(s)
tauNS(s,2) = tau(s)
if (tau(s) > 0.0_pReal) then
tauNS(s,3) = math_tensordot(Mp, +prm%P_nS_pos(1:3,1:3,s))
tauNS(s,4) = math_tensordot(Mp, -prm%P_nS_neg(1:3,1:3,s))
else
tauNS(s,3) = math_tensordot(Mp, +prm%P_nS_neg(1:3,1:3,s))
tauNS(s,4) = math_tensordot(Mp, -prm%P_nS_pos(1:3,1:3,s))
end if
end do
tauNS = tauNS + spread(dst%tau_back(:,en),2,4)
tau = tau + dst%tau_back(:,en)
! edges
call kinetics(v(:,1), dv_dtau(:,1), dv_dtauNS(:,1), &
tau, tauNS(:,1), dst%tau_pass(:,en),1,Temperature, ph)
v(:,2) = v(:,1)
dv_dtau(:,2) = dv_dtau(:,1)
dv_dtauNS(:,2) = dv_dtauNS(:,1)
!screws
if (prm%nonSchmidActive) then
do t = 3,4
call kinetics(v(:,t), dv_dtau(:,t), dv_dtauNS(:,t), &
tau, tauNS(:,t), dst%tau_pass(:,en),2,Temperature, ph)
do s = 1,prm%sum_N_sl
tau(s) = math_tensordot(Mp, prm%P_sl(1:3,1:3,s))
tauNS(s,1) = tau(s)
tauNS(s,2) = tau(s)
if (tau(s) > 0.0_pReal) then
tauNS(s,3) = math_tensordot(Mp, +prm%P_nS_pos(1:3,1:3,s))
tauNS(s,4) = math_tensordot(Mp, -prm%P_nS_neg(1:3,1:3,s))
else
tauNS(s,3) = math_tensordot(Mp, +prm%P_nS_neg(1:3,1:3,s))
tauNS(s,4) = math_tensordot(Mp, -prm%P_nS_pos(1:3,1:3,s))
end if
end do
else
v(:,3:4) = spread(v(:,1),2,2)
dv_dtau(:,3:4) = spread(dv_dtau(:,1),2,2)
dv_dtauNS(:,3:4) = spread(dv_dtauNS(:,1),2,2)
end if
tauNS = tauNS + spread(dst%tau_back(:,en),2,4)
tau = tau + dst%tau_back(:,en)
stt%v(:,en) = pack(v,.true.)
! edges
call kinetics(v(:,1), dv_dtau(:,1), dv_dtauNS(:,1), &
tau, tauNS(:,1), dst%tau_pass(:,en),1,Temperature, ph)
v(:,2) = v(:,1)
dv_dtau(:,2) = dv_dtau(:,1)
dv_dtauNS(:,2) = dv_dtauNS(:,1)
!*** Bauschinger effect
forall (s = 1:prm%sum_N_sl, t = 5:8, rhoSgl(s,t) * v(s,t-4) < 0.0_pReal) &
rhoSgl(s,t-4) = rhoSgl(s,t-4) + abs(rhoSgl(s,t))
!screws
if (prm%nonSchmidActive) then
do t = 3,4
call kinetics(v(:,t), dv_dtau(:,t), dv_dtauNS(:,t), &
tau, tauNS(:,t), dst%tau_pass(:,en),2,Temperature, ph)
end do
else
v(:,3:4) = spread(v(:,1),2,2)
dv_dtau(:,3:4) = spread(dv_dtau(:,1),2,2)
dv_dtauNS(:,3:4) = spread(dv_dtauNS(:,1),2,2)
end if
dot_gamma = sum(rhoSgl(:,1:4) * v, 2) * prm%b_sl
stt%v(:,en) = pack(v,.true.)
Lp = 0.0_pReal
dLp_dMp = 0.0_pReal
do s = 1,prm%sum_N_sl
Lp = Lp + dot_gamma(s) * prm%P_sl(1:3,1:3,s)
forall (i=1:3,j=1:3,k=1:3,l=1:3) &
dLp_dMp(i,j,k,l) = dLp_dMp(i,j,k,l) &
+ prm%P_sl(i,j,s) * prm%P_sl(k,l,s) &
* sum(rhoSgl(s,1:4) * dv_dtau(s,1:4)) * prm%b_sl(s) &
+ prm%P_sl(i,j,s) &
* (+ prm%P_nS_pos(k,l,s) * rhoSgl(s,3) * dv_dtauNS(s,3) &
- prm%P_nS_neg(k,l,s) * rhoSgl(s,4) * dv_dtauNS(s,4)) * prm%b_sl(s)
end do
!*** Bauschinger effect
forall (s = 1:prm%sum_N_sl, t = 5:8, rhoSgl(s,t) * v(s,t-4) < 0.0_pReal) &
rhoSgl(s,t-4) = rhoSgl(s,t-4) + abs(rhoSgl(s,t))
dot_gamma = sum(rhoSgl(:,1:4) * v, 2) * prm%b_sl
do s = 1,prm%sum_N_sl
Lp = Lp + dot_gamma(s) * prm%P_sl(1:3,1:3,s)
forall (i=1:3,j=1:3,k=1:3,l=1:3) &
dLp_dMp(i,j,k,l) = dLp_dMp(i,j,k,l) &
+ prm%P_sl(i,j,s) * prm%P_sl(k,l,s) &
* sum(rhoSgl(s,1:4) * dv_dtau(s,1:4)) * prm%b_sl(s) &
+ prm%P_sl(i,j,s) &
* (+ prm%P_nS_pos(k,l,s) * rhoSgl(s,3) * dv_dtauNS(s,3) &
- prm%P_nS_neg(k,l,s) * rhoSgl(s,4) * dv_dtauNS(s,4)) * prm%b_sl(s)
end do
end associate
@ -870,7 +872,8 @@ module subroutine plastic_nonlocal_deltaState(Mp,ph,en)
dUpper, & ! current maximum stable dipole distance for edges and screws
dUpperOld, & ! old maximum stable dipole distance for edges and screws
deltaDUpper ! change in maximum stable dipole distance for edges and screws
associate(prm => param(ph),dst => dependentState(ph),del => deltaState(ph))
mu = elastic_mu(ph,en)
@ -1394,78 +1397,79 @@ module subroutine plastic_nonlocal_updateCompatibility(orientation,ph,i,e)
belowThreshold
type(rotation) :: mis
associate(prm => param(ph))
ns = prm%sum_N_sl
ns = prm%sum_N_sl
en = material_phaseMemberAt(1,i,e)
!*** start out fully compatible
my_compatibility = 0.0_pReal
forall(s1 = 1:ns) my_compatibility(:,s1,s1,:) = 1.0_pReal
en = material_phaseMemberAt(1,i,e)
!*** start out fully compatible
my_compatibility = 0.0_pReal
forall(s1 = 1:ns) my_compatibility(:,s1,s1,:) = 1.0_pReal
neighbors: do n = 1,nIPneighbors
neighbor_e = IPneighborhood(1,n,i,e)
neighbor_i = IPneighborhood(2,n,i,e)
neighbor_me = material_phaseMemberAt(1,neighbor_i,neighbor_e)
neighbor_phase = material_phaseAt(1,neighbor_e)
neighbors: do n = 1,nIPneighbors
neighbor_e = IPneighborhood(1,n,i,e)
neighbor_i = IPneighborhood(2,n,i,e)
neighbor_me = material_phaseMemberAt(1,neighbor_i,neighbor_e)
neighbor_phase = material_phaseAt(1,neighbor_e)
if (neighbor_e <= 0 .or. neighbor_i <= 0) then
!* FREE SURFACE
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = sqrt(prm%chi_surface)
elseif (neighbor_phase /= ph) then
!* PHASE BOUNDARY
if (plasticState(neighbor_phase)%nonlocal .and. plasticState(ph)%nonlocal) &
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = 0.0_pReal
elseif (prm%chi_GB >= 0.0_pReal) then
!* GRAIN BOUNDARY
if (any(dNeq(phase_O_0(ph)%data(en)%asQuaternion(), &
phase_O_0(neighbor_phase)%data(neighbor_me)%asQuaternion())) .and. &
plasticState(neighbor_phase)%nonlocal) &
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = sqrt(prm%chi_GB)
else
!* GRAIN BOUNDARY ?
!* Compatibility defined by relative orientation of slip systems:
!* The my_compatibility value is defined as the product of the slip normal projection and the slip direction projection.
!* Its sign is always positive for screws, for edges it has the same sign as the slip normal projection.
!* Since the sum for each slip system can easily exceed one (which would result in a transmissivity larger than one),
!* only values above or equal to a certain threshold value are considered. This threshold value is chosen, such that
!* the number of compatible slip systems is minimized with the sum of the original compatibility values exceeding one.
!* Finally the smallest compatibility value is decreased until the sum is exactly equal to one.
!* All values below the threshold are set to zero.
mis = orientation(ph)%data(en)%misorientation(orientation(neighbor_phase)%data(neighbor_me))
mySlipSystems: do s1 = 1,ns
neighborSlipSystems: do s2 = 1,ns
my_compatibility(1,s2,s1,n) = math_inner(prm%slip_normal(1:3,s1), &
mis%rotate(prm%slip_normal(1:3,s2))) &
* abs(math_inner(prm%slip_direction(1:3,s1), &
mis%rotate(prm%slip_direction(1:3,s2))))
my_compatibility(2,s2,s1,n) = abs(math_inner(prm%slip_normal(1:3,s1), &
mis%rotate(prm%slip_normal(1:3,s2)))) &
* abs(math_inner(prm%slip_direction(1:3,s1), &
mis%rotate(prm%slip_direction(1:3,s2))))
end do neighborSlipSystems
if (neighbor_e <= 0 .or. neighbor_i <= 0) then
!* FREE SURFACE
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = sqrt(prm%chi_surface)
elseif (neighbor_phase /= ph) then
!* PHASE BOUNDARY
if (plasticState(neighbor_phase)%nonlocal .and. plasticState(ph)%nonlocal) &
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = 0.0_pReal
elseif (prm%chi_GB >= 0.0_pReal) then
!* GRAIN BOUNDARY
if (any(dNeq(phase_O_0(ph)%data(en)%asQuaternion(), &
phase_O_0(neighbor_phase)%data(neighbor_me)%asQuaternion())) .and. &
plasticState(neighbor_phase)%nonlocal) &
forall(s1 = 1:ns) my_compatibility(:,s1,s1,n) = sqrt(prm%chi_GB)
else
!* GRAIN BOUNDARY ?
!* Compatibility defined by relative orientation of slip systems:
!* The my_compatibility value is defined as the product of the slip normal projection and the slip direction projection.
!* Its sign is always positive for screws, for edges it has the same sign as the slip normal projection.
!* Since the sum for each slip system can easily exceed one (which would result in a transmissivity larger than one),
!* only values above or equal to a certain threshold value are considered. This threshold value is chosen, such that
!* the number of compatible slip systems is minimized with the sum of the original compatibility values exceeding one.
!* Finally the smallest compatibility value is decreased until the sum is exactly equal to one.
!* All values below the threshold are set to zero.
mis = orientation(ph)%data(en)%misorientation(orientation(neighbor_phase)%data(neighbor_me))
mySlipSystems: do s1 = 1,ns
neighborSlipSystems: do s2 = 1,ns
my_compatibility(1,s2,s1,n) = math_inner(prm%slip_normal(1:3,s1), &
mis%rotate(prm%slip_normal(1:3,s2))) &
* abs(math_inner(prm%slip_direction(1:3,s1), &
mis%rotate(prm%slip_direction(1:3,s2))))
my_compatibility(2,s2,s1,n) = abs(math_inner(prm%slip_normal(1:3,s1), &
mis%rotate(prm%slip_normal(1:3,s2)))) &
* abs(math_inner(prm%slip_direction(1:3,s1), &
mis%rotate(prm%slip_direction(1:3,s2))))
end do neighborSlipSystems
my_compatibilitySum = 0.0_pReal
belowThreshold = .true.
do while (my_compatibilitySum < 1.0_pReal .and. any(belowThreshold))
thresholdValue = maxval(my_compatibility(2,:,s1,n), belowThreshold) ! screws always positive
nThresholdValues = real(count(my_compatibility(2,:,s1,n) >= thresholdValue),pReal)
where (my_compatibility(2,:,s1,n) >= thresholdValue) belowThreshold = .false.
if (my_compatibilitySum + thresholdValue * nThresholdValues > 1.0_pReal) &
where (abs(my_compatibility(:,:,s1,n)) >= thresholdValue) &
my_compatibility(:,:,s1,n) = sign((1.0_pReal - my_compatibilitySum)/nThresholdValues,&
my_compatibility(:,:,s1,n))
my_compatibilitySum = my_compatibilitySum + nThresholdValues * thresholdValue
end do
my_compatibilitySum = 0.0_pReal
belowThreshold = .true.
do while (my_compatibilitySum < 1.0_pReal .and. any(belowThreshold))
thresholdValue = maxval(my_compatibility(2,:,s1,n), belowThreshold) ! screws always positive
nThresholdValues = real(count(my_compatibility(2,:,s1,n) >= thresholdValue),pReal)
where (my_compatibility(2,:,s1,n) >= thresholdValue) belowThreshold = .false.
if (my_compatibilitySum + thresholdValue * nThresholdValues > 1.0_pReal) &
where (abs(my_compatibility(:,:,s1,n)) >= thresholdValue) &
my_compatibility(:,:,s1,n) = sign((1.0_pReal - my_compatibilitySum)/nThresholdValues,&
my_compatibility(:,:,s1,n))
my_compatibilitySum = my_compatibilitySum + nThresholdValues * thresholdValue
end do
where(belowThreshold) my_compatibility(1,:,s1,n) = 0.0_pReal
where(belowThreshold) my_compatibility(2,:,s1,n) = 0.0_pReal
where(belowThreshold) my_compatibility(1,:,s1,n) = 0.0_pReal
where(belowThreshold) my_compatibility(2,:,s1,n) = 0.0_pReal
end do mySlipSystems
end if
end do mySlipSystems
end if
end do neighbors
end do neighbors
compatibility(:,:,:,:,i,e) = my_compatibility
compatibility(:,:,:,:,i,e) = my_compatibility
end associate
@ -1592,21 +1596,15 @@ subroutine stateInit(ini,phase,Nentries)
stt%rhoSglMobile(s,e) = densityBinning
end do
else ! homogeneous distribution with noise
do e = 1, Nentries
do f = 1,size(ini%N_sl,1)
from = 1 + sum(ini%N_sl(1:f-1))
upto = sum(ini%N_sl(1:f))
do s = from,upto
noise = [math_sampleGaussVar(0.0_pReal, ini%sigma_rho_u), &
math_sampleGaussVar(0.0_pReal, ini%sigma_rho_u)]
stt%rho_sgl_mob_edg_pos(s,e) = ini%rho_u_ed_pos_0(f) + noise(1)
stt%rho_sgl_mob_edg_neg(s,e) = ini%rho_u_ed_neg_0(f) + noise(1)
stt%rho_sgl_mob_scr_pos(s,e) = ini%rho_u_sc_pos_0(f) + noise(2)
stt%rho_sgl_mob_scr_neg(s,e) = ini%rho_u_sc_neg_0(f) + noise(2)
end do
stt%rho_dip_edg(from:upto,e) = ini%rho_d_ed_0(f)
stt%rho_dip_scr(from:upto,e) = ini%rho_d_sc_0(f)
end do
do f = 1,size(ini%N_sl,1)
from = 1 + sum(ini%N_sl(1:f-1))
upto = sum(ini%N_sl(1:f))
call math_normal(stt%rho_sgl_mob_edg_pos(from:upto,:),ini%rho_u_ed_pos_0(f),ini%sigma_rho_u)
call math_normal(stt%rho_sgl_mob_edg_neg(from:upto,:),ini%rho_u_ed_neg_0(f),ini%sigma_rho_u)
call math_normal(stt%rho_sgl_mob_scr_pos(from:upto,:),ini%rho_u_sc_pos_0(f),ini%sigma_rho_u)
call math_normal(stt%rho_sgl_mob_scr_neg(from:upto,:),ini%rho_u_sc_neg_0(f),ini%sigma_rho_u)
stt%rho_dip_edg(from:upto,:) = ini%rho_d_ed_0(f)
stt%rho_dip_scr(from:upto,:) = ini%rho_d_sc_0(f)
end do
end if
@ -1652,53 +1650,55 @@ pure subroutine kinetics(v, dv_dtau, dv_dtauNS, tau, tauNS, tauThreshold, c, T,
criticalStress_P, & !< maximum obstacle strength
criticalStress_S !< maximum obstacle strength
associate(prm => param(ph))
v = 0.0_pReal
dv_dtau = 0.0_pReal
dv_dtauNS = 0.0_pReal
do s = 1,prm%sum_N_sl
if (abs(tau(s)) > tauThreshold(s)) then
associate(prm => param(ph))
!* Peierls contribution
tauEff = max(0.0_pReal, abs(tauNS(s)) - tauThreshold(s))
lambda_P = prm%b_sl(s)
activationVolume_P = prm%w *prm%b_sl(s)**3
criticalStress_P = prm%peierlsStress(s,c)
activationEnergy_P = criticalStress_P * activationVolume_P
tauRel_P = min(1.0_pReal, tauEff / criticalStress_P)
tPeierls = 1.0_pReal / prm%nu_a &
* exp(activationEnergy_P / (K_B * T) &
* (1.0_pReal - tauRel_P**prm%p)**prm%q)
dtPeierls_dtau = merge(tPeierls * prm%p * prm%q * activationVolume_P / (K_B * T) &
* (1.0_pReal - tauRel_P**prm%p)**(prm%q-1.0_pReal) * tauRel_P**(prm%p-1.0_pReal), &
0.0_pReal, &
tauEff < criticalStress_P)
do s = 1,prm%sum_N_sl
if (abs(tau(s)) > tauThreshold(s)) then
! Contribution from solid solution strengthening
tauEff = abs(tau(s)) - tauThreshold(s)
lambda_S = prm%b_sl(s) / sqrt(prm%c_sol)
activationVolume_S = prm%f_sol * prm%b_sl(s)**3 / sqrt(prm%c_sol)
criticalStress_S = prm%Q_sol / activationVolume_S
tauRel_S = min(1.0_pReal, tauEff / criticalStress_S)
tSolidSolution = 1.0_pReal / prm%nu_a &
* exp(prm%Q_sol / (K_B * T)* (1.0_pReal - tauRel_S**prm%p)**prm%q)
dtSolidSolution_dtau = merge(tSolidSolution * prm%p * prm%q * activationVolume_S / (K_B * T) &
* (1.0_pReal - tauRel_S**prm%p)**(prm%q-1.0_pReal)* tauRel_S**(prm%p-1.0_pReal), &
0.0_pReal, &
tauEff < criticalStress_S)
!* Peierls contribution
tauEff = max(0.0_pReal, abs(tauNS(s)) - tauThreshold(s))
lambda_P = prm%b_sl(s)
activationVolume_P = prm%w *prm%b_sl(s)**3
criticalStress_P = prm%peierlsStress(s,c)
activationEnergy_P = criticalStress_P * activationVolume_P
tauRel_P = min(1.0_pReal, tauEff / criticalStress_P)
tPeierls = 1.0_pReal / prm%nu_a &
* exp(activationEnergy_P / (K_B * T) &
* (1.0_pReal - tauRel_P**prm%p)**prm%q)
dtPeierls_dtau = merge(tPeierls * prm%p * prm%q * activationVolume_P / (K_B * T) &
* (1.0_pReal - tauRel_P**prm%p)**(prm%q-1.0_pReal) * tauRel_P**(prm%p-1.0_pReal), &
0.0_pReal, &
tauEff < criticalStress_P)
!* viscous glide velocity
tauEff = abs(tau(s)) - tauThreshold(s)
! Contribution from solid solution strengthening
tauEff = abs(tau(s)) - tauThreshold(s)
lambda_S = prm%b_sl(s) / sqrt(prm%c_sol)
activationVolume_S = prm%f_sol * prm%b_sl(s)**3 / sqrt(prm%c_sol)
criticalStress_S = prm%Q_sol / activationVolume_S
tauRel_S = min(1.0_pReal, tauEff / criticalStress_S)
tSolidSolution = 1.0_pReal / prm%nu_a &
* exp(prm%Q_sol / (K_B * T)* (1.0_pReal - tauRel_S**prm%p)**prm%q)
dtSolidSolution_dtau = merge(tSolidSolution * prm%p * prm%q * activationVolume_S / (K_B * T) &
* (1.0_pReal - tauRel_S**prm%p)**(prm%q-1.0_pReal)* tauRel_S**(prm%p-1.0_pReal), &
0.0_pReal, &
tauEff < criticalStress_S)
!* viscous glide velocity
tauEff = abs(tau(s)) - tauThreshold(s)
v(s) = sign(1.0_pReal,tau(s)) &
/ (tPeierls / lambda_P + tSolidSolution / lambda_S + prm%B /(prm%b_sl(s) * tauEff))
dv_dtau(s) = v(s)**2 * (dtSolidSolution_dtau / lambda_S + prm%B / (prm%b_sl(s) * tauEff**2))
dv_dtauNS(s) = v(s)**2 * dtPeierls_dtau / lambda_P
v(s) = sign(1.0_pReal,tau(s)) &
/ (tPeierls / lambda_P + tSolidSolution / lambda_S + prm%B /(prm%b_sl(s) * tauEff))
dv_dtau(s) = v(s)**2 * (dtSolidSolution_dtau / lambda_S + prm%B / (prm%b_sl(s) * tauEff**2))
dv_dtauNS(s) = v(s)**2 * dtPeierls_dtau / lambda_P
end if
end do
end if
end do
end associate

2
src/phase_thermal.f90
View File

@ -271,7 +271,7 @@ end subroutine thermal_forward
!----------------------------------------------------------------------------------------------
!< @brief Get temperature (for use by non-thermal physics)
!----------------------------------------------------------------------------------------------
module function thermal_T(ph,en) result(T)
pure module function thermal_T(ph,en) result(T)
integer, intent(in) :: ph, en
real(pReal) :: T

8
src/rotations.f90
View File

@ -372,7 +372,7 @@ end function rotTensor4
!---------------------------------------------------------------------------------------------------
!> @brief Rotate a rank-4 tensor in Voigt 6x6 notation passively (default) or actively.
!> @brief Rotate a rank-4 stiffness tensor in Voigt 6x6 notation passively (default) or actively.
!> @details: https://scicomp.stackexchange.com/questions/35600
!! ToDo: Need to check active/passive !!!
!---------------------------------------------------------------------------------------------------
@ -393,11 +393,11 @@ pure function rotStiffness(self,C,active) result(cRot)
R = self%asMatrix()
endif
M = reshape([R(1,1)**2.0_pReal, R(2,1)**2.0_pReal, R(3,1)**2.0_pReal, &
M = reshape([R(1,1)**2, R(2,1)**2, R(3,1)**2, &
R(2,1)*R(3,1), R(1,1)*R(3,1), R(1,1)*R(2,1), &
R(1,2)**2.0_pReal, R(2,2)**2.0_pReal, R(3,2)**2.0_pReal, &
R(1,2)**2, R(2,2)**2, R(3,2)**2, &
R(2,2)*R(3,2), R(1,2)*R(3,2), R(1,2)*R(2,2), &
R(1,3)**2.0_pReal, R(2,3)**2.0_pReal, R(3,3)**2.0_pReal, &
R(1,3)**2, R(2,3)**2, R(3,3)**2, &
R(2,3)*R(3,3), R(1,3)*R(3,3), R(1,3)*R(2,3), &
2.0_pReal*R(1,2)*R(1,3), 2.0_pReal*R(2,2)*R(2,3), 2.0_pReal*R(3,2)*R(3,3), &
R(2,2)*R(3,3)+R(2,3)*R(3,2), R(1,2)*R(3,3)+R(1,3)*R(3,2), R(1,2)*R(2,3)+R(1,3)*R(2,2), &