Merge branch 'development' of git.damask.mpie.de:damask/DAMASK into typehints_orientation_rotation
This commit is contained in:
Daniel Otto de Mentock
commit
4ba9935ccc
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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_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_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 ${TESTROOT}/compile_mesh_Intel
|
||||
|
||||
test_Marc:
|
||||
stage: compile
|
||||
script:
|
||||
|
|
|
|||
|
|
@ -82,20 +82,18 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
|
|||
include(Compiler-Intel)
|
||||
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
|
||||
include(Compiler-GNU)
|
||||
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "IntelLLVM")
|
||||
include(Compiler-IntelLLVM)
|
||||
else()
|
||||
message(FATAL_ERROR "Compiler type(CMAKE_Fortran_COMPILER_ID) not recognized")
|
||||
endif()
|
||||
|
||||
file(STRINGS "$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_${CMAKE_BUILD_TYPE}}\n")
|
||||
|
|
|
|||
6
Makefile
6
Makefile
|
|
@ -10,14 +10,12 @@ all: grid mesh
|
|||
.PHONY: grid
|
||||
grid:
|
||||
@cmake -B build/grid -DDAMASK_SOLVER=grid -DCMAKE_INSTALL_PREFIX=${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=${OPENMP}
|
||||
@cmake --build build/mesh --parallel
|
||||
@cmake --install build/mesh
|
||||
@cmake --build build/mesh --parallel --target install
|
||||
|
||||
.PHONY: clean
|
||||
clean:
|
||||
|
|
|
|||
2
PRIVATE
2
PRIVATE
|
|
@ -1 +1 @@
|
|||
Subproject commit e6e1f93a36d63348359a81d7c373083a39977694
|
||||
Subproject commit b898a8b5552bd9d1c555edc3d8134564dd32fe53
|
||||
|
|
@ -106,8 +106,9 @@ set (DEBUG_FLAGS "${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
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
@ -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]
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -0,0 +1,4 @@
|
|||
references:
|
||||
- https://en.wikipedia.org/wiki/Silver
|
||||
lattice: cF
|
||||
rho: 10490.0
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -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]
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -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*')) +
|
||||
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]')))
|
||||
|
||||
for file in files:
|
||||
glob.glob(str(marc_root/f'mentat{marc_version}/bin/submit[4-6]'))):
|
||||
os.chmod(file , 0o755)
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
|
|
@ -1 +1 @@
|
|||
v3.0.0-alpha5-272-g3192a31e1
|
||||
v3.0.0-alpha5-379-g731222d09
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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([
|
||||
|
|
|
|||
|
|
@ -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],
|
||||
|
|
@ -543,6 +544,73 @@ class Crystal():
|
|||
[ 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':
|
||||
|
|
|
|||
|
|
@ -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])
|
||||
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'.
|
||||
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
|
|
|||
|
|
@ -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]
|
||||
|
|
@ -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.
|
||||
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -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.
|
||||
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -22,7 +22,7 @@ __all__=[
|
|||
'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,
|
||||
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])]),
|
||||
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]
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -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)))
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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)))])
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
|
|
@ -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')
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
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,
|
||||
|
|
|
|||
|
|
@ -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()
|
||||
|
|
|
|||
|
|
@ -59,8 +59,21 @@ 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,
|
||||
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',
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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)
|
||||
|
|
|
|||
79
src/math.f90
79
src/math.f90
|
|
@ -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
|
||||
|
|
@ -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
|
||||
|
||||
if (present(sigma)) then
|
||||
sigma_ = sigma
|
||||
else
|
||||
sigma_ = 1.0_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
|
||||
x = mu_ + sigma_ * sqrt(-2.0_pReal*log(1.0_pReal-rnd(1)))*cos(2.0_pReal*PI*(1.0_pReal - rnd(2)))
|
||||
|
||||
math_sampleGaussVar = scatter * sigma
|
||||
endif
|
||||
|
||||
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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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, &
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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 &
|
||||
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,&
|
||||
f_matrix,StressRatio_p,&
|
||||
E_kB_T, &
|
||||
ddot_gamma_dtau, &
|
||||
tau
|
||||
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) :: &
|
||||
|
|
@ -556,15 +556,17 @@ 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
|
||||
|
||||
associate(prm => param(ph), stt => state(ph))
|
||||
|
||||
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,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)
|
||||
|
|
@ -589,8 +591,8 @@ module subroutine dislotwin_LpAndItsTangent(Lp,dLp_dMp,Mp,T,ph,en)
|
|||
+ ddot_gamma_dtau_tr(i)* prm%P_tr(k,l,i)*prm%P_tr(m,n,i)
|
||||
end do transContibution
|
||||
|
||||
Lp = Lp * f_unrotated
|
||||
dLp_dMp = dLp_dMp * f_unrotated
|
||||
Lp = Lp * f_matrix
|
||||
dLp_dMp = dLp_dMp * f_matrix
|
||||
|
||||
shearBandingContribution: if (dNeq0(prm%v_sb)) then
|
||||
|
||||
|
|
@ -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, &
|
||||
|
|
@ -661,7 +663,7 @@ module subroutine dislotwin_dotState(Mp,T,ph,en)
|
|||
mu = elastic_mu(ph,en)
|
||||
nu = elastic_nu(ph,en)
|
||||
|
||||
f_unrotated = 1.0_pReal &
|
||||
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))
|
||||
|
||||
|
|
@ -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
|
||||
|
||||
|
|
|
|||
|
|
@ -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))
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
@ -771,6 +768,13 @@ 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))
|
||||
|
||||
|
|
@ -820,8 +824,6 @@ module subroutine nonlocal_LpAndItsTangent(Lp,dLp_dMp, &
|
|||
|
||||
dot_gamma = sum(rhoSgl(:,1:4) * v, 2) * prm%b_sl
|
||||
|
||||
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) &
|
||||
|
|
@ -871,6 +873,7 @@ module subroutine plastic_nonlocal_deltaState(Mp,ph,en)
|
|||
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)
|
||||
|
|
@ -1394,6 +1397,7 @@ module subroutine plastic_nonlocal_updateCompatibility(orientation,ph,i,e)
|
|||
belowThreshold
|
||||
type(rotation) :: mis
|
||||
|
||||
|
||||
associate(prm => param(ph))
|
||||
ns = prm%sum_N_sl
|
||||
|
||||
|
|
@ -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
|
||||
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
|
||||
|
||||
|
|
@ -1652,11 +1650,13 @@ 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
|
||||
|
||||
associate(prm => param(ph))
|
||||
|
||||
do s = 1,prm%sum_N_sl
|
||||
if (abs(tau(s)) > tauThreshold(s)) then
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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), &
|
||||
|
|
|
|||
Loading…
Reference in New Issue