Merge branch 'development' into new-gmsh-version
This commit is contained in:
Sharan Roongta
commit
793e5d0d2b
|
|
@ -60,11 +60,11 @@ variables:
|
|||
MPI_Intel: "$IMPI2020Intel19_1"
|
||||
MPI_GNU: "$OMPI4_0GNU10"
|
||||
# ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
||||
PETSc3_14_0IMPI2020Intel19_1: "Libraries/PETSc/3.14.0/Intel-19.1.2-IntelMPI-2019"
|
||||
PETSc3_14_0OMPI4_0GNU10: "Libraries/PETSc/3.14.0/GNU-10-OpenMPI-4.0.5"
|
||||
PETSc3_14_2IMPI2020Intel19_1: "Libraries/PETSc/3.14.2/Intel-19.1.2-IntelMPI-2019"
|
||||
PETSc3_14_2OMPI4_0GNU10: "Libraries/PETSc/3.14.2/GNU-10-OpenMPI-4.0.5"
|
||||
# ------------ Defaults ----------------------------------------------
|
||||
PETSc_Intel: "$PETSc3_14_0IMPI2020Intel19_1"
|
||||
PETSc_GNU: "$PETSc3_14_0OMPI4_0GNU10"
|
||||
PETSc_Intel: "$PETSc3_14_2IMPI2020Intel19_1"
|
||||
PETSc_GNU: "$PETSc3_14_2OMPI4_0GNU10"
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||||
# ++++++++++++ commercial FEM ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
|
||||
MSC2020: "FEM/MSC/2020"
|
||||
# ------------ Defaults ----------------------------------------------
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||||
|
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@ -262,20 +262,6 @@ Pytest_grid:
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- master
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- release
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||||
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||||
Thermal:
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||||
stage: grid
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||||
script: Thermal/test.py
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||||
except:
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||||
- master
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||||
- release
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||||
|
||||
Nonlocal_Damage_DetectChanges:
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||||
stage: grid
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||||
script: Nonlocal_Damage_DetectChanges/test.py
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||||
except:
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||||
- master
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||||
- release
|
||||
|
||||
Plasticity_DetectChanges:
|
||||
stage: grid
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||||
script: Plasticity_DetectChanges/test.py
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||||
|
|
@ -353,7 +339,6 @@ backupData:
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|||
- mkdir $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}
|
||||
- mv $LOCAL_HOME/performance/time.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
|
||||
- mv $LOCAL_HOME/performance/memory.png $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
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||||
- mv $DAMASKROOT/PRIVATE/documenting/DAMASK_* $BACKUP/${CI_PIPELINE_ID}_${CI_COMMIT_SHA}/
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||||
only:
|
||||
- development
|
||||
|
||||
|
|
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|||
|
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@ -2,3 +2,4 @@
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|||
path = PRIVATE
|
||||
url = ../PRIVATE.git
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||||
branch = master
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||||
shallow = true
|
||||
|
|
|
|||
|
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@ -1,6 +1,18 @@
|
|||
########################################################################################
|
||||
# Compiler options for building DAMASK
|
||||
cmake_minimum_required (VERSION 3.10.0 FATAL_ERROR)
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cmake_minimum_required (VERSION 3.10.0)
|
||||
include (FindPkgConfig REQUIRED)
|
||||
|
||||
# Dummy project to determine compiler names and version
|
||||
project (Prerequisites LANGUAGES)
|
||||
set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig")
|
||||
pkg_check_modules (PETSC REQUIRED PETSc>=3.12.0 PETSc<3.15.0)
|
||||
pkg_get_variable (CMAKE_Fortran_COMPILER PETSc fcompiler)
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||||
pkg_get_variable (CMAKE_C_COMPILER PETSc ccompiler)
|
||||
|
||||
find_program (CAT_EXECUTABLE NAMES cat)
|
||||
execute_process (COMMAND ${CAT_EXECUTABLE} ${PROJECT_SOURCE_DIR}/VERSION
|
||||
RESULT_VARIABLE DAMASK_VERSION_RETURN
|
||||
OUTPUT_VARIABLE DAMASK_VERSION
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
|
||||
#---------------------------------------------------------------------------------------
|
||||
# Find PETSc from system environment
|
||||
|
|
@ -28,19 +40,10 @@ include ${petsc_conf_rules}
|
|||
include ${petsc_conf_variables}
|
||||
INCLUDE_DIRS := \${PETSC_FC_INCLUDES}
|
||||
LIBRARIES := \${PETSC_WITH_EXTERNAL_LIB}
|
||||
COMPILERF := \${FC}
|
||||
COMPILERC := \${CC}
|
||||
LINKERNAME := \${FLINKER}
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||||
includes:
|
||||
\t@echo \${INCLUDE_DIRS}
|
||||
extlibs:
|
||||
\t@echo \${LIBRARIES}
|
||||
compilerf:
|
||||
\t@echo \${COMPILERF}
|
||||
compilerc:
|
||||
\t@echo \${COMPILERC}
|
||||
linker:
|
||||
\t@echo \${LINKERNAME}
|
||||
")
|
||||
|
||||
# CMake will execute each target in the ${petsc_config_makefile}
|
||||
|
|
@ -52,26 +55,10 @@ execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_conf
|
|||
OUTPUT_VARIABLE petsc_includes
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
# Find the PETSc external linking directory settings
|
||||
# required for final linking, must be appended after the executable
|
||||
execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} "extlibs"
|
||||
RESULT_VARIABLE PETSC_EXTERNAL_LIB_RETURN
|
||||
OUTPUT_VARIABLE petsc_external_lib
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
# PETSc specified fortran compiler
|
||||
execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} "compilerf"
|
||||
RESULT_VARIABLE PETSC_MPIFC_RETURN
|
||||
OUTPUT_VARIABLE PETSC_MPIFC
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
# PETSc specified C compiler
|
||||
execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} "compilerc"
|
||||
RESULT_VARIABLE PETSC_MPICC_RETURN
|
||||
OUTPUT_VARIABLE PETSC_MPICC
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
# PETSc specified linker (Fortran compiler + PETSc linking flags)
|
||||
execute_process (COMMAND ${MAKE_EXECUTABLE} --no-print-directory -f ${petsc_config_makefile} "linker"
|
||||
RESULT_VARIABLE PETSC_LINKER_RETURN
|
||||
OUTPUT_VARIABLE PETSC_LINKER
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
# Remove temporary makefile, no need to keep it anymore.
|
||||
file (REMOVE_RECURSE ${TEMPDIR})
|
||||
|
||||
|
|
@ -90,14 +77,6 @@ endforeach (exlib)
|
|||
message ("Found PETSC_DIR:\n${PETSC_DIR}\n" )
|
||||
message ("Found PETSC_INCLUDES:\n${PETSC_INCLUDES}\n" )
|
||||
message ("Found PETSC_EXTERNAL_LIB:\n${PETSC_EXTERNAL_LIB}\n")
|
||||
message ("Found PETSC_LINKER:\n${PETSC_LINKER}\n" )
|
||||
message ("Found MPI Fortran Compiler:\n${PETSC_MPIFC}\n" )
|
||||
message ("Found MPI C Compiler:\n${PETSC_MPICC}\n" )
|
||||
|
||||
# set compiler commands to match PETSc (needs to be done before defining the project)
|
||||
# https://cmake.org/Wiki/CMake_FAQ#How_do_I_use_a_different_compiler.3F
|
||||
set (CMAKE_Fortran_COMPILER "${PETSC_MPIFC}")
|
||||
set (CMAKE_C_COMPILER "${PETSC_MPICC}")
|
||||
|
||||
#---------------------------------------------------------------------------------------
|
||||
# Now start to care about DAMASK
|
||||
|
|
@ -105,17 +84,18 @@ set (CMAKE_C_COMPILER "${PETSC_MPICC}")
|
|||
# DAMASK solver defines project to build
|
||||
string(TOLOWER ${DAMASK_SOLVER} DAMASK_SOLVER)
|
||||
if (DAMASK_SOLVER STREQUAL "grid")
|
||||
project (damask-grid Fortran C)
|
||||
project (damask-grid HOMEPAGE_URL https://damask.mpie.de LANGUAGES Fortran C)
|
||||
add_definitions (-DGrid)
|
||||
message ("Building Grid Solver\n")
|
||||
elseif (DAMASK_SOLVER STREQUAL "mesh")
|
||||
project (damask-mesh Fortran C)
|
||||
project (damask-mesh HOMEPAGE_URL https://damask.mpie.de LANGUAGES Fortran C)
|
||||
add_definitions (-DMesh)
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||||
message ("Building Mesh Solver\n")
|
||||
else ()
|
||||
message (FATAL_ERROR "Build target (DAMASK_SOLVER) is not defined")
|
||||
endif ()
|
||||
list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
|
||||
add_definitions (-DDAMASKVERSION="${DAMASK_VERSION}")
|
||||
add_definitions (-DPETSc)
|
||||
|
||||
message ("\nBuilding ${CMAKE_PROJECT_NAME}\n")
|
||||
|
||||
if (CMAKE_BUILD_TYPE STREQUAL "")
|
||||
set (CMAKE_BUILD_TYPE "RELEASE")
|
||||
|
|
@ -153,17 +133,8 @@ if (CMAKE_BUILD_TYPE STREQUAL "SYNTAXONLY")
|
|||
set (BUILDCMD_POST "${BUILDCMD_POST} -fsyntax-only")
|
||||
endif ()
|
||||
|
||||
# Parse DAMASK version from VERSION file
|
||||
find_program (CAT_EXECUTABLE NAMES cat)
|
||||
execute_process (COMMAND ${CAT_EXECUTABLE} ${PROJECT_SOURCE_DIR}/VERSION
|
||||
RESULT_VARIABLE DAMASK_VERSION_RETURN
|
||||
OUTPUT_VARIABLE DAMASK_V
|
||||
OUTPUT_STRIP_TRAILING_WHITESPACE)
|
||||
add_definitions (-DDAMASKVERSION="${DAMASK_V}")
|
||||
|
||||
# definition of other macros
|
||||
add_definitions (-DPETSc)
|
||||
|
||||
list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
|
||||
if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")
|
||||
include (Compiler-Intel)
|
||||
elseif(CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
|
||||
|
|
@ -174,9 +145,8 @@ else ()
|
|||
message (FATAL_ERROR "Compiler type (CMAKE_Fortran_COMPILER_ID) not recognized")
|
||||
endif ()
|
||||
|
||||
|
||||
set (CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${BUILDCMD_PRE} ${OPENMP_FLAGS} ${STANDARD_CHECK} ${OPTIMIZATION_FLAGS} ${COMPILE_FLAGS} ${PRECISION_FLAGS}")
|
||||
set (CMAKE_Fortran_LINK_EXECUTABLE "${BUILDCMD_PRE} ${PETSC_LINKER} ${OPENMP_FLAGS} ${OPTIMIZATION_FLAGS} ${LINKER_FLAGS}")
|
||||
set (CMAKE_Fortran_LINK_EXECUTABLE "${BUILDCMD_PRE} ${CMAKE_Fortran_COMPILER} ${OPENMP_FLAGS} ${OPTIMIZATION_FLAGS} ${LINKER_FLAGS}")
|
||||
|
||||
if (CMAKE_BUILD_TYPE STREQUAL "DEBUG")
|
||||
set (CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${DEBUG_FLAGS}")
|
||||
|
|
|
|||
23
Makefile
23
Makefile
|
|
@ -2,27 +2,20 @@ SHELL = /bin/sh
|
|||
########################################################################################
|
||||
# Makefile for the installation of DAMASK
|
||||
########################################################################################
|
||||
DAMASK_ROOT = $(shell python3 -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))")
|
||||
.PHONY: all
|
||||
all: grid mesh processing
|
||||
|
||||
.PHONY: grid
|
||||
grid: build/grid
|
||||
@(cd build/grid;make -j${DAMASK_NUM_THREADS} all install;)
|
||||
grid:
|
||||
@cmake -B build/grid -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
|
||||
@cmake --build build/grid --parallel ${DAMASK_NUM_THRADS}
|
||||
@cmake --install build/grid
|
||||
|
||||
.PHONY: mesh
|
||||
mesh: build/mesh
|
||||
@(cd build/mesh; make -j${DAMASK_NUM_THREADS} all install;)
|
||||
|
||||
.PHONY: build/grid
|
||||
build/grid:
|
||||
@mkdir -p build/grid
|
||||
@(cd build/grid; cmake -Wno-dev -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
|
||||
|
||||
.PHONY: build/mesh
|
||||
build/mesh:
|
||||
@mkdir -p build/mesh
|
||||
@(cd build/mesh; cmake -Wno-dev -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
|
||||
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 ${DAMASK_NUM_THRADS}
|
||||
@cmake --install build/mesh
|
||||
|
||||
.PHONY: clean
|
||||
clean:
|
||||
|
|
|
|||
|
|
@ -20,7 +20,7 @@ endif ()
|
|||
|
||||
# -assume std_mod_proc_name (included in -standard-semantics) causes problems if other modules
|
||||
# (PETSc, HDF5) are not compiled with this option (https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/62172)
|
||||
set (STANDARD_CHECK "-stand f15 -standard-semantics -assume nostd_mod_proc_name")
|
||||
set (STANDARD_CHECK "-stand f18 -standard-semantics -assume nostd_mod_proc_name")
|
||||
set (LINKER_FLAGS "${LINKER_FLAGS} -shared-intel")
|
||||
# Link against shared Intel libraries instead of static ones
|
||||
|
||||
|
|
|
|||
|
|
@ -5,8 +5,8 @@ homogenization:
|
|||
|
||||
phase:
|
||||
Aluminum:
|
||||
lattice: cF
|
||||
mechanics:
|
||||
lattice: cF
|
||||
output: [F, P, F_e, F_p, L_p]
|
||||
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
|
||||
plasticity:
|
||||
|
|
|
|||
|
|
@ -33,12 +33,12 @@ for filename in options.filenames:
|
|||
results = damask.Result(filename)
|
||||
|
||||
if not results.structured: continue
|
||||
coords = damask.grid_filters.cell_coord0(results.grid,results.size,results.origin).reshape(-1,3,order='F')
|
||||
coords = damask.grid_filters.coordinates0_point(results.cells,results.size,results.origin).reshape(-1,3,order='F')
|
||||
|
||||
N_digits = int(np.floor(np.log10(int(results.increments[-1][3:]))))+1
|
||||
N_digits = 5 # hack to keep test intact
|
||||
for inc in damask.util.show_progress(results.iterate('increments'),len(results.increments)):
|
||||
table = damask.Table(np.ones(np.product(results.grid),dtype=int)*int(inc[3:]),{'inc':(1,)})\
|
||||
table = damask.Table(np.ones(np.product(results.cells),dtype=int)*int(inc[3:]),{'inc':(1,)})\
|
||||
.add('pos',coords.reshape(-1,3))
|
||||
|
||||
results.pick('homogenizations',False)
|
||||
|
|
@ -46,14 +46,14 @@ for filename in options.filenames:
|
|||
for label in options.con:
|
||||
x = results.get_dataset_location(label)
|
||||
if len(x) != 0:
|
||||
table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1))
|
||||
table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.cells.prod(),-1))
|
||||
|
||||
results.pick('phases',False)
|
||||
results.pick('homogenizations',True)
|
||||
for label in options.mat:
|
||||
x = results.get_dataset_location(label)
|
||||
if len(x) != 0:
|
||||
table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.grid.prod(),-1))
|
||||
table = table.add(label,results.read_dataset(x,0,plain=True).reshape(results.cells.prod(),-1))
|
||||
|
||||
dirname = os.path.abspath(os.path.join(os.path.dirname(filename),options.dir))
|
||||
if not os.path.isdir(dirname):
|
||||
|
|
|
|||
|
|
@ -71,13 +71,13 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
|
||||
|
||||
F = table.get(options.defgrad).reshape(tuple(grid)+(-1,),order='F').reshape(tuple(grid)+(3,3))
|
||||
nodes = damask.grid_filters.node_coord(size,F)
|
||||
nodes = damask.grid_filters.coordinates_node(size,F)
|
||||
|
||||
if options.shape:
|
||||
centers = damask.grid_filters.cell_coord(size,F)
|
||||
centers = damask.grid_filters.coordinates_point(size,F)
|
||||
shapeMismatch = shapeMismatch(size,F,nodes,centers)
|
||||
table = table.add('shapeMismatch(({}))'.format(options.defgrad),
|
||||
shapeMismatch.reshape(-1,1,order='F'),
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
|
||||
|
||||
for label in options.labels:
|
||||
field = table.get(label)
|
||||
|
|
|
|||
|
|
@ -48,24 +48,24 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
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.node_coord0(grid,size).reshape(-1,3,order='F'),
|
||||
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.node_displacement_avg(size,F).reshape(-1,3,order='F'),
|
||||
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.node_displacement_fluct(size,F).reshape(-1,3,order='F'),
|
||||
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.cell_displacement_avg(size,F).reshape(-1,3,order='F'),
|
||||
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.cell_displacement_fluct(size,F).reshape(-1,3,order='F'),
|
||||
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))
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
|
||||
|
||||
for label in options.labels:
|
||||
field = table.get(label)
|
||||
|
|
|
|||
|
|
@ -143,7 +143,7 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
|
||||
|
||||
neighborhood = neighborhoods[options.neighborhood]
|
||||
diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@ 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.cell_coord0_gridSizeOrigin(table.get(options.pos))
|
||||
grid,size,origin = damask.grid_filters.cellsSizeOrigin_coordinates0_point(table.get(options.pos))
|
||||
|
||||
for label in options.labels:
|
||||
field = table.get(label)
|
||||
|
|
|
|||
|
|
@ -65,7 +65,7 @@ if filenames == []: parser.error('no input file specified.')
|
|||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.load_DREAM3D(name,options.basegroup,options.pointwise)
|
||||
geom = damask.Grid.load_DREAM3D(name,options.basegroup,options.pointwise)
|
||||
damask.util.croak(geom)
|
||||
|
||||
geom.save_ASCII(os.path.splitext(name)[0]+'.geom')
|
||||
|
|
|
|||
|
|
@ -133,7 +133,7 @@ for i in range(3,np.max(microstructure)):
|
|||
|
||||
header = [scriptID + ' ' + ' '.join(sys.argv[1:])]\
|
||||
+ config_header
|
||||
geom = damask.Geom(microstructure.reshape(grid),
|
||||
geom = damask.Grid(microstructure.reshape(grid),
|
||||
size,-size/2,
|
||||
comments=header)
|
||||
damask.util.croak(geom)
|
||||
|
|
|
|||
|
|
@ -62,9 +62,9 @@ if filenames == []: filenames = [None]
|
|||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
|
||||
grid_original = geom.grid
|
||||
grid_original = geom.cells
|
||||
damask.util.croak(geom)
|
||||
material = np.tile(geom.material,np.where(grid_original == 1, 2,1)) # make one copy along dimensions with grid == 1
|
||||
grid = np.array(material.shape)
|
||||
|
|
@ -169,7 +169,7 @@ for name in filenames:
|
|||
# undo any changes involving immutable materials
|
||||
material = np.where(immutable, material_original,material)
|
||||
|
||||
damask.Geom(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
|
||||
damask.Grid(material = material[0:grid_original[0],0:grid_original[1],0:grid_original[2]],
|
||||
size = geom.size,
|
||||
origin = geom.origin,
|
||||
comments = geom.comments + [scriptID + ' ' + ' '.join(sys.argv[1:])],
|
||||
|
|
|
|||
|
|
@ -196,12 +196,12 @@ if filenames == []: filenames = [None]
|
|||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
geom = damask.Geom.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
geom = damask.Grid.load(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
material = geom.material.flatten(order='F')
|
||||
|
||||
cmds = [\
|
||||
init(),
|
||||
mesh(geom.grid,geom.size),
|
||||
mesh(geom.cells,geom.size),
|
||||
materials(),
|
||||
geometry(),
|
||||
initial_conditions(material),
|
||||
|
|
|
|||
|
|
@ -91,7 +91,7 @@ class myThread (threading.Thread):
|
|||
perturbedSeedsTable.set('pos',coords).save(perturbedSeedsVFile,legacy=True)
|
||||
|
||||
#--- do tesselation with perturbed seed file ------------------------------------------------------
|
||||
perturbedGeom = damask.Geom.from_Voronoi_tessellation(options.grid,np.ones(3),coords)
|
||||
perturbedGeom = damask.Grid.from_Voronoi_tessellation(options.grid,np.ones(3),coords)
|
||||
|
||||
|
||||
#--- evaluate current seeds file ------------------------------------------------------------------
|
||||
|
|
@ -210,9 +210,9 @@ baseFile = os.path.splitext(os.path.basename(options.seedFile))[0]
|
|||
points = np.array(options.grid).prod().astype('float')
|
||||
|
||||
# ----------- calculate target distribution and bin edges
|
||||
targetGeom = damask.Geom.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
|
||||
targetGeom = damask.Grid.load_ASCII(os.path.splitext(os.path.basename(options.target))[0]+'.geom')
|
||||
nMaterials = len(np.unique(targetGeom.material))
|
||||
targetVolFrac = np.bincount(targetGeom.material.flatten())/targetGeom.grid.prod().astype(np.float)
|
||||
targetVolFrac = np.bincount(targetGeom.material.flatten())/targetGeom.cells.prod().astype(np.float)
|
||||
target = []
|
||||
for i in range(1,nMaterials+1):
|
||||
targetHist,targetBins = np.histogram(targetVolFrac,bins=i) #bin boundaries
|
||||
|
|
@ -229,7 +229,7 @@ bestSeedsUpdate = time.time()
|
|||
|
||||
# ----------- tessellate initial seed file to get and evaluate geom file
|
||||
bestSeedsVFile.seek(0)
|
||||
initialGeom = damask.Geom.from_Voronoi_tessellation(options.grid,np.ones(3),initial_seeds)
|
||||
initialGeom = damask.Grid.from_Voronoi_tessellation(options.grid,np.ones(3),initial_seeds)
|
||||
|
||||
if len(np.unique(targetGeom.material)) != nMaterials:
|
||||
damask.util.croak('error. Material count mismatch')
|
||||
|
|
|
|||
|
|
@ -52,15 +52,15 @@ options.box = np.array(options.box).reshape(3,2)
|
|||
|
||||
for name in filenames:
|
||||
damask.util.report(scriptName,name)
|
||||
geom = damask.Geom.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
geom = damask.Grid.load_ASCII(StringIO(''.join(sys.stdin.read())) if name is None else name)
|
||||
|
||||
offset =(np.amin(options.box, axis=1)*geom.grid/geom.size).astype(int)
|
||||
offset =(np.amin(options.box, axis=1)*geom.cells/geom.size).astype(int)
|
||||
box = np.amax(options.box, axis=1) \
|
||||
- np.amin(options.box, axis=1)
|
||||
|
||||
Nx = int(options.N/np.sqrt(options.N*geom.size[1]*box[1]/geom.size[0]/box[0]))
|
||||
Ny = int(options.N/np.sqrt(options.N*geom.size[0]*box[0]/geom.size[1]/box[1]))
|
||||
Nz = int(box[2]*geom.grid[2])
|
||||
Nz = int(box[2]*geom.cells[2])
|
||||
|
||||
damask.util.croak('poking {} x {} x {} in box {} {} {}...'.format(Nx,Ny,Nz,*box))
|
||||
|
||||
|
|
@ -70,12 +70,12 @@ for name in filenames:
|
|||
n = 0
|
||||
for i in range(Nx):
|
||||
for j in range(Ny):
|
||||
g[0] = round((i+0.5)*box[0]*geom.grid[0]/Nx-0.5)+offset[0]
|
||||
g[1] = round((j+0.5)*box[1]*geom.grid[1]/Ny-0.5)+offset[1]
|
||||
g[0] = round((i+0.5)*box[0]*geom.cells[0]/Nx-0.5)+offset[0]
|
||||
g[1] = round((j+0.5)*box[1]*geom.cells[1]/Ny-0.5)+offset[1]
|
||||
for k in range(Nz):
|
||||
g[2] = k + offset[2]
|
||||
g %= geom.grid
|
||||
seeds[n,0:3] = (g+0.5)/geom.grid # normalize coordinates to box
|
||||
g %= geom.cells
|
||||
seeds[n,0:3] = (g+0.5)/geom.cells # normalize coordinates to box
|
||||
seeds[n, 3] = geom.material[g[0],g[1],g[2]]
|
||||
if options.x: g[0] += 1
|
||||
if options.y: g[1] += 1
|
||||
|
|
@ -85,7 +85,7 @@ for name in filenames:
|
|||
comments = geom.comments \
|
||||
+ [scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
'poking\ta {}\tb {}\tc {}'.format(Nx,Ny,Nz),
|
||||
'grid\ta {}\tb {}\tc {}'.format(*geom.grid),
|
||||
'grid\ta {}\tb {}\tc {}'.format(*geom.cells),
|
||||
'size\tx {}\ty {}\tz {}'.format(*geom.size),
|
||||
'origin\tx {}\ty {}\tz {}'.format(*geom.origin),
|
||||
]
|
||||
|
|
|
|||
|
|
@ -32,7 +32,7 @@ from ._vtk import VTK # noqa
|
|||
from ._colormap import Colormap # noqa
|
||||
from ._config import Config # noqa
|
||||
from ._configmaterial import ConfigMaterial # noqa
|
||||
from ._geom import Geom # noqa
|
||||
from ._grid import Grid # noqa
|
||||
from ._result import Result # noqa
|
||||
|
||||
|
||||
|
|
|
|||
|
|
@ -57,7 +57,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
ax1.imshow(np.linspace(0,1,self.N).reshape(1,-1),
|
||||
aspect='auto', cmap=self, interpolation='nearest')
|
||||
plt.show(block = False)
|
||||
return self.name
|
||||
return 'Colormap: '+self.name
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -225,7 +225,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
def save_paraview(self,fname=None):
|
||||
"""
|
||||
Write colormap to JSON file for Paraview.
|
||||
Save as JSON file for use in Paraview.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -260,7 +260,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
def save_ASCII(self,fname=None):
|
||||
"""
|
||||
Write colormap to ASCII table.
|
||||
Save as ASCII file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -286,7 +286,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
def save_GOM(self,fname=None):
|
||||
"""
|
||||
Write colormap to GOM Aramis compatible format.
|
||||
Save as ASCII file for use in GOM Aramis.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -314,7 +314,7 @@ class Colormap(mpl.colors.ListedColormap):
|
|||
|
||||
def save_gmsh(self,fname=None):
|
||||
"""
|
||||
Write colormap to Gmsh compatible format.
|
||||
Save as ASCII file for use in gmsh.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -21,6 +21,9 @@ class NiceDumper(yaml.SafeDumper):
|
|||
return self.represent_data(dict(data)) if isinstance(data, dict) and type(data) != dict else \
|
||||
super().represent_data(data)
|
||||
|
||||
def ignore_aliases(self, data):
|
||||
"""No references."""
|
||||
return True
|
||||
|
||||
class Config(dict):
|
||||
"""YAML-based configuration."""
|
||||
|
|
|
|||
|
|
@ -9,6 +9,16 @@ from . import Orientation
|
|||
class ConfigMaterial(Config):
|
||||
"""Material configuration."""
|
||||
|
||||
_defaults = {'material': [],
|
||||
'homogenization': {},
|
||||
'phase': {}}
|
||||
|
||||
def __init__(self,d={}):
|
||||
"""Initialize object with default dictionary keys."""
|
||||
super().__init__(d)
|
||||
for k,v in self._defaults.items():
|
||||
if k not in self: self[k] = v
|
||||
|
||||
def save(self,fname='material.yaml',**kwargs):
|
||||
"""
|
||||
Save to yaml file.
|
||||
|
|
@ -75,6 +85,8 @@ class ConfigMaterial(Config):
|
|||
fraction: 1.0
|
||||
phase: Steel
|
||||
homogenization: SX
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
"""
|
||||
constituents_ = {k:table.get(v) for k,v in constituents.items()}
|
||||
|
|
@ -261,6 +273,8 @@ class ConfigMaterial(Config):
|
|||
fraction: 1.0
|
||||
phase: Aluminum
|
||||
homogenization: SX
|
||||
homogenization: {}
|
||||
phase: {}
|
||||
|
||||
"""
|
||||
length = -1
|
||||
|
|
@ -274,6 +288,7 @@ class ConfigMaterial(Config):
|
|||
|
||||
c = [{} for _ in range(length)] if constituents is None else \
|
||||
[{'constituents':u} for u in ConfigMaterial._constituents(**constituents)]
|
||||
|
||||
if len(c) == 1: c = [copy.deepcopy(c[0]) for _ in range(length)]
|
||||
|
||||
if length != 1 and length != len(c):
|
||||
|
|
|
|||
|
|
@ -7,7 +7,8 @@ import warnings
|
|||
import numpy as np
|
||||
import pandas as pd
|
||||
import h5py
|
||||
from scipy import ndimage,spatial
|
||||
from scipy import ndimage, spatial
|
||||
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
|
||||
|
||||
from . import environment
|
||||
from . import VTK
|
||||
|
|
@ -16,21 +17,21 @@ from . import grid_filters
|
|||
from . import Rotation
|
||||
|
||||
|
||||
class Geom:
|
||||
class Grid:
|
||||
"""Geometry definition for grid solvers."""
|
||||
|
||||
def __init__(self,material,size,origin=[0.0,0.0,0.0],comments=[]):
|
||||
"""
|
||||
New geometry definition from array of materials, size, and origin.
|
||||
New grid definition from array of materials, size, and origin.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
material : numpy.ndarray
|
||||
Material index array (3D).
|
||||
size : list or numpy.ndarray
|
||||
Physical size of the geometry in meter.
|
||||
Physical size of the grid in meter.
|
||||
origin : list or numpy.ndarray, optional
|
||||
Physical origin of the geometry in meter.
|
||||
Physical origin of the grid in meter.
|
||||
comments : list of str, optional
|
||||
Comment lines.
|
||||
|
||||
|
|
@ -42,23 +43,26 @@ class Geom:
|
|||
|
||||
|
||||
def __repr__(self):
|
||||
"""Basic information on geometry definition."""
|
||||
"""Basic information on grid definition."""
|
||||
mat_min = np.nanmin(self.material)
|
||||
mat_max = np.nanmax(self.material)
|
||||
mat_N = self.N_materials
|
||||
return util.srepr([
|
||||
f'grid a b c: {util.srepr(self.grid, " x ")}',
|
||||
f'size x y z: {util.srepr(self.size, " x ")}',
|
||||
f'origin x y z: {util.srepr(self.origin," ")}',
|
||||
f'# materials: {self.N_materials}',
|
||||
f'max material: {np.nanmax(self.material)}',
|
||||
f'cells a b c: {util.srepr(self.cells, " x ")}',
|
||||
f'size x y z: {util.srepr(self.size, " x ")}',
|
||||
f'origin x y z: {util.srepr(self.origin," ")}',
|
||||
f'# materials: {mat_N}' + ('' if mat_min == 0 and mat_max+1 == mat_N else
|
||||
f' (min: {mat_min}, max: {mat_max})')
|
||||
])
|
||||
|
||||
|
||||
def __copy__(self):
|
||||
"""Copy geometry."""
|
||||
"""Copy grid."""
|
||||
return copy.deepcopy(self)
|
||||
|
||||
|
||||
def copy(self):
|
||||
"""Copy geometry."""
|
||||
"""Copy grid."""
|
||||
return self.__copy__()
|
||||
|
||||
|
||||
|
|
@ -68,14 +72,14 @@ class Geom:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
other : Geom
|
||||
Geometry to compare self against.
|
||||
other : damask.Grid
|
||||
Grid to compare self against.
|
||||
|
||||
"""
|
||||
message = []
|
||||
if np.any(other.grid != self.grid):
|
||||
message.append(util.deemph(f'grid a b c: {util.srepr(other.grid," x ")}'))
|
||||
message.append(util.emph( f'grid a b c: {util.srepr( self.grid," x ")}'))
|
||||
if np.any(other.cells != self.cells):
|
||||
message.append(util.deemph(f'cells a b c: {util.srepr(other.cells," x ")}'))
|
||||
message.append(util.emph( f'cells a b c: {util.srepr( self.cells," x ")}'))
|
||||
|
||||
if not np.allclose(other.size,self.size):
|
||||
message.append(util.deemph(f'size x y z: {util.srepr(other.size," x ")}'))
|
||||
|
|
@ -104,9 +108,9 @@ class Geom:
|
|||
@material.setter
|
||||
def material(self,material):
|
||||
if len(material.shape) != 3:
|
||||
raise ValueError(f'Invalid material shape {material.shape}.')
|
||||
raise ValueError(f'invalid material shape {material.shape}')
|
||||
elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
|
||||
raise TypeError(f'Invalid material data type {material.dtype}.')
|
||||
raise TypeError(f'invalid material data type {material.dtype}')
|
||||
else:
|
||||
self._material = np.copy(material)
|
||||
|
||||
|
|
@ -117,31 +121,31 @@ class Geom:
|
|||
|
||||
@property
|
||||
def size(self):
|
||||
"""Physical size of geometry in meter."""
|
||||
"""Physical size of grid in meter."""
|
||||
return self._size
|
||||
|
||||
@size.setter
|
||||
def size(self,size):
|
||||
if len(size) != 3 or any(np.array(size) <= 0):
|
||||
raise ValueError(f'Invalid size {size}.')
|
||||
raise ValueError(f'invalid size {size}')
|
||||
else:
|
||||
self._size = np.array(size)
|
||||
|
||||
@property
|
||||
def origin(self):
|
||||
"""Coordinates of geometry origin in meter."""
|
||||
"""Coordinates of grid origin in meter."""
|
||||
return self._origin
|
||||
|
||||
@origin.setter
|
||||
def origin(self,origin):
|
||||
if len(origin) != 3:
|
||||
raise ValueError(f'Invalid origin {origin}.')
|
||||
raise ValueError(f'invalid origin {origin}')
|
||||
else:
|
||||
self._origin = np.array(origin)
|
||||
|
||||
@property
|
||||
def comments(self):
|
||||
"""Comments/history of geometry."""
|
||||
"""Comments, e.g. history of operations."""
|
||||
return self._comments
|
||||
|
||||
@comments.setter
|
||||
|
|
@ -150,35 +154,39 @@ class Geom:
|
|||
|
||||
|
||||
@property
|
||||
def grid(self):
|
||||
"""Grid dimension of geometry."""
|
||||
def cells(self):
|
||||
"""Number of cells in x,y,z direction."""
|
||||
return np.asarray(self.material.shape)
|
||||
|
||||
|
||||
@property
|
||||
def N_materials(self):
|
||||
"""Number of (unique) material indices within geometry."""
|
||||
"""Number of (unique) material indices within grid."""
|
||||
return np.unique(self.material).size
|
||||
|
||||
|
||||
@staticmethod
|
||||
def load(fname):
|
||||
"""
|
||||
Read a VTK rectilinear grid.
|
||||
Load from VTK rectilinear grid file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
fname : str or or pathlib.Path
|
||||
Geometry file to read.
|
||||
Valid extension is .vtr, which will be appended if not given.
|
||||
Grid file to read. Valid extension is .vtr, which will be appended
|
||||
if not given.
|
||||
|
||||
"""
|
||||
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
|
||||
comments = v.get_comments()
|
||||
grid = np.array(v.vtk_data.GetDimensions())-1
|
||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
||||
cells = np.array(v.vtk_data.GetDimensions())-1
|
||||
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
|
||||
|
||||
return Geom(material = v.get('material').reshape(grid,order='F'),
|
||||
for i,c in enumerate([v.vtk_data.GetXCoordinates(),v.vtk_data.GetYCoordinates(),v.vtk_data.GetZCoordinates()]):
|
||||
if not np.allclose(vtk_to_np(c),np.linspace(bbox[0][i],bbox[1][i],cells[i]+1)):
|
||||
raise ValueError('regular grid spacing violated')
|
||||
|
||||
return Grid(material = v.get('material').reshape(cells,order='F'),
|
||||
size = bbox[1] - bbox[0],
|
||||
origin = bbox[0],
|
||||
comments=comments)
|
||||
|
|
@ -187,7 +195,7 @@ class Geom:
|
|||
@staticmethod
|
||||
def load_ASCII(fname):
|
||||
"""
|
||||
Read a geom file.
|
||||
Load from geom file.
|
||||
|
||||
Storing geometry files in ASCII format is deprecated.
|
||||
This function will be removed in a future version of DAMASK.
|
||||
|
|
@ -211,7 +219,7 @@ class Geom:
|
|||
except ValueError:
|
||||
header_length,keyword = (-1, 'invalid')
|
||||
if not keyword.startswith('head') or header_length < 3:
|
||||
raise TypeError('Header length information missing or invalid')
|
||||
raise TypeError('header length information missing or invalid')
|
||||
|
||||
comments = []
|
||||
content = f.readlines()
|
||||
|
|
@ -219,7 +227,7 @@ class Geom:
|
|||
items = line.split('#')[0].lower().strip().split()
|
||||
key = items[0] if items else ''
|
||||
if key == 'grid':
|
||||
grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||
cells = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
|
||||
elif key == 'size':
|
||||
size = np.array([float(dict(zip(items[1::2],items[2::2]))[i]) for i in ['x','y','z']])
|
||||
elif key == 'origin':
|
||||
|
|
@ -227,7 +235,7 @@ class Geom:
|
|||
else:
|
||||
comments.append(line.strip())
|
||||
|
||||
material = np.empty(grid.prod()) # initialize as flat array
|
||||
material = np.empty(cells.prod()) # initialize as flat array
|
||||
i = 0
|
||||
for line in content[header_length:]:
|
||||
items = line.split('#')[0].split()
|
||||
|
|
@ -242,19 +250,19 @@ class Geom:
|
|||
material[i:i+len(items)] = items
|
||||
i += len(items)
|
||||
|
||||
if i != grid.prod():
|
||||
raise TypeError(f'Invalid file: expected {grid.prod()} entries, found {i}')
|
||||
if i != cells.prod():
|
||||
raise TypeError(f'invalid file: expected {cells.prod()} entries, found {i}')
|
||||
|
||||
if not np.any(np.mod(material,1) != 0.0): # no float present
|
||||
material = material.astype('int') - (1 if material.min() > 0 else 0)
|
||||
|
||||
return Geom(material.reshape(grid,order='F'),size,origin,comments)
|
||||
return Grid(material.reshape(cells,order='F'),size,origin,comments)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def load_DREAM3D(fname,base_group,point_data=None,material='FeatureIds'):
|
||||
"""
|
||||
Load a DREAM.3D file.
|
||||
Load from DREAM.3D file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -274,21 +282,21 @@ class Geom:
|
|||
root_dir ='DataContainers'
|
||||
f = h5py.File(fname, 'r')
|
||||
g = path.join(root_dir,base_group,'_SIMPL_GEOMETRY')
|
||||
grid = f[path.join(g,'DIMENSIONS')][()]
|
||||
size = f[path.join(g,'SPACING')][()] * grid
|
||||
cells = f[path.join(g,'DIMENSIONS')][()]
|
||||
size = f[path.join(g,'SPACING')][()] * cells
|
||||
origin = f[path.join(g,'ORIGIN')][()]
|
||||
|
||||
ma = np.arange(grid.prod(),dtype=int) \
|
||||
ma = np.arange(cells.prod(),dtype=int) \
|
||||
if point_data is None else \
|
||||
np.reshape(f[path.join(root_dir,base_group,point_data,material)],grid.prod())
|
||||
np.reshape(f[path.join(root_dir,base_group,point_data,material)],cells.prod())
|
||||
|
||||
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','load_DREAM3D'))
|
||||
return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','load_DREAM3D'))
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_table(table,coordinates,labels):
|
||||
"""
|
||||
Derive geometry from an ASCII table.
|
||||
Generate grid from ASCII table.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -302,15 +310,15 @@ class Geom:
|
|||
Each unique combintation of values results in one material ID.
|
||||
|
||||
"""
|
||||
grid,size,origin = grid_filters.cell_coord0_gridSizeOrigin(table.get(coordinates))
|
||||
cells,size,origin = grid_filters.cellsSizeOrigin_coordinates0_point(table.get(coordinates))
|
||||
|
||||
labels_ = [labels] if isinstance(labels,str) else labels
|
||||
unique,unique_inverse = np.unique(np.hstack([table.get(l) for l in labels_]),return_inverse=True,axis=0)
|
||||
|
||||
ma = np.arange(grid.prod()) if len(unique) == grid.prod() else \
|
||||
ma = np.arange(cells.prod()) if len(unique) == cells.prod() else \
|
||||
np.arange(unique.size)[np.argsort(pd.unique(unique_inverse))][unique_inverse]
|
||||
|
||||
return Geom(ma.reshape(grid,order='F'),size,origin,util.execution_stamp('Geom','from_table'))
|
||||
return Grid(ma.reshape(cells,order='F'),size,origin,util.execution_stamp('Grid','from_table'))
|
||||
|
||||
|
||||
@staticmethod
|
||||
|
|
@ -318,16 +326,16 @@ class Geom:
|
|||
return np.argmin(np.sum((np.broadcast_to(point,(len(seeds),3))-seeds)**2,axis=1) - weights)
|
||||
|
||||
@staticmethod
|
||||
def from_Laguerre_tessellation(grid,size,seeds,weights,material=None,periodic=True):
|
||||
def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
|
||||
"""
|
||||
Generate geometry from Laguerre tessellation.
|
||||
Generate grid from Laguerre tessellation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : int numpy.ndarray of shape (3)
|
||||
Number of grid points in x,y,z direction.
|
||||
cells : int numpy.ndarray of shape (3)
|
||||
Number of cells in x,y,z direction.
|
||||
size : list or numpy.ndarray of shape (3)
|
||||
Physical size of the geometry in meter.
|
||||
Physical size of the grid in meter.
|
||||
seeds : numpy.ndarray of 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])
|
||||
|
|
@ -336,7 +344,7 @@ class Geom:
|
|||
Material ID of the seeds.
|
||||
Defaults to None, in which case materials are consecutively numbered.
|
||||
periodic : Boolean, optional
|
||||
Perform a periodic tessellation. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
if periodic:
|
||||
|
|
@ -344,57 +352,57 @@ class Geom:
|
|||
seeds_p = np.vstack((seeds -np.array([size[0],0.,0.]),seeds, seeds +np.array([size[0],0.,0.])))
|
||||
seeds_p = np.vstack((seeds_p-np.array([0.,size[1],0.]),seeds_p,seeds_p+np.array([0.,size[1],0.])))
|
||||
seeds_p = np.vstack((seeds_p-np.array([0.,0.,size[2]]),seeds_p,seeds_p+np.array([0.,0.,size[2]])))
|
||||
coords = grid_filters.cell_coord0(grid*3,size*3,-size).reshape(-1,3)
|
||||
coords = grid_filters.coordinates0_point(cells*3,size*3,-size).reshape(-1,3)
|
||||
else:
|
||||
weights_p = weights
|
||||
seeds_p = seeds
|
||||
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
|
||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||
|
||||
pool = mp.Pool(processes = int(environment.options['DAMASK_NUM_THREADS']))
|
||||
result = pool.map_async(partial(Geom._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
|
||||
result = pool.map_async(partial(Grid._find_closest_seed,seeds_p,weights_p), [coord for coord in coords])
|
||||
pool.close()
|
||||
pool.join()
|
||||
material_ = np.array(result.get())
|
||||
|
||||
if periodic:
|
||||
material_ = material_.reshape(grid*3)
|
||||
material_ = material_[grid[0]:grid[0]*2,grid[1]:grid[1]*2,grid[2]:grid[2]*2]%seeds.shape[0]
|
||||
material_ = material_.reshape(cells*3)
|
||||
material_ = material_[cells[0]:cells[0]*2,cells[1]:cells[1]*2,cells[2]:cells[2]*2]%seeds.shape[0]
|
||||
else:
|
||||
material_ = material_.reshape(grid)
|
||||
material_ = material_.reshape(cells)
|
||||
|
||||
return Geom(material = material_ if material is None else material[material_],
|
||||
return Grid(material = material_ if material is None else material[material_],
|
||||
size = size,
|
||||
comments = util.execution_stamp('Geom','from_Laguerre_tessellation'),
|
||||
comments = util.execution_stamp('Grid','from_Laguerre_tessellation'),
|
||||
)
|
||||
|
||||
|
||||
@staticmethod
|
||||
def from_Voronoi_tessellation(grid,size,seeds,material=None,periodic=True):
|
||||
def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
|
||||
"""
|
||||
Generate geometry from Voronoi tessellation.
|
||||
Generate grid from Voronoi tessellation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : int numpy.ndarray of shape (3)
|
||||
Number of grid points in x,y,z direction.
|
||||
cells : int numpy.ndarray of shape (3)
|
||||
Number of cells in x,y,z direction.
|
||||
size : list or numpy.ndarray of shape (3)
|
||||
Physical size of the geometry in meter.
|
||||
Physical size of the grid in meter.
|
||||
seeds : numpy.ndarray of 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 ID of the seeds.
|
||||
Defaults to None, in which case materials are consecutively numbered.
|
||||
periodic : Boolean, optional
|
||||
Perform a periodic tessellation. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3)
|
||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3)
|
||||
KDTree = spatial.cKDTree(seeds,boxsize=size) if periodic else spatial.cKDTree(seeds)
|
||||
devNull,material_ = KDTree.query(coords)
|
||||
|
||||
return Geom(material = (material_ if material is None else material[material_]).reshape(grid),
|
||||
return Grid(material = (material_ if material is None else material[material_]).reshape(cells),
|
||||
size = size,
|
||||
comments = util.execution_stamp('Geom','from_Voronoi_tessellation'),
|
||||
comments = util.execution_stamp('Grid','from_Voronoi_tessellation'),
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -441,16 +449,16 @@ class Geom:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def from_minimal_surface(grid,size,surface,threshold=0.0,periods=1,materials=(0,1)):
|
||||
def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
|
||||
"""
|
||||
Generate geometry from definition of triply periodic minimal surface.
|
||||
Generate grid from definition of triply periodic minimal surface.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : int numpy.ndarray of shape (3)
|
||||
Number of grid points in x,y,z direction.
|
||||
cells : int numpy.ndarray of shape (3)
|
||||
Number of cells in x,y,z direction.
|
||||
size : list or numpy.ndarray of shape (3)
|
||||
Physical size of the geometry in meter.
|
||||
Physical size of the grid in meter.
|
||||
surface : str
|
||||
Type of the minimal surface. See notes for details.
|
||||
threshold : float, optional.
|
||||
|
|
@ -493,19 +501,19 @@ class Geom:
|
|||
https://doi.org/10.1016/j.simpa.2020.100026
|
||||
|
||||
"""
|
||||
x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(grid[0])+0.5)/grid[0],
|
||||
periods*2.0*np.pi*(np.arange(grid[1])+0.5)/grid[1],
|
||||
periods*2.0*np.pi*(np.arange(grid[2])+0.5)/grid[2],
|
||||
x,y,z = np.meshgrid(periods*2.0*np.pi*(np.arange(cells[0])+0.5)/cells[0],
|
||||
periods*2.0*np.pi*(np.arange(cells[1])+0.5)/cells[1],
|
||||
periods*2.0*np.pi*(np.arange(cells[2])+0.5)/cells[2],
|
||||
indexing='ij',sparse=True)
|
||||
return Geom(material = np.where(threshold < Geom._minimal_surface[surface](x,y,z),materials[1],materials[0]),
|
||||
return Grid(material = np.where(threshold < Grid._minimal_surface[surface](x,y,z),materials[1],materials[0]),
|
||||
size = size,
|
||||
comments = util.execution_stamp('Geom','from_minimal_surface'),
|
||||
comments = util.execution_stamp('Grid','from_minimal_surface'),
|
||||
)
|
||||
|
||||
|
||||
def save(self,fname,compress=True):
|
||||
"""
|
||||
Store as VTK rectilinear grid.
|
||||
Save as VTK rectilinear grid file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -515,7 +523,7 @@ class Geom:
|
|||
Compress with zlib algorithm. Defaults to True.
|
||||
|
||||
"""
|
||||
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
|
||||
v = VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
|
||||
v.add(self.material.flatten(order='F'),'material')
|
||||
v.add_comments(self.comments)
|
||||
|
||||
|
|
@ -524,7 +532,7 @@ class Geom:
|
|||
|
||||
def save_ASCII(self,fname):
|
||||
"""
|
||||
Write a geom file.
|
||||
Save as geom file.
|
||||
|
||||
Storing geometry files in ASCII format is deprecated.
|
||||
This function will be removed in a future version of DAMASK.
|
||||
|
|
@ -539,7 +547,7 @@ class Geom:
|
|||
"""
|
||||
warnings.warn('Support for ASCII-based geom format will be removed in DAMASK 3.1.0', DeprecationWarning)
|
||||
header = [f'{len(self.comments)+4} header'] + self.comments \
|
||||
+ ['grid a {} b {} c {}'.format(*self.grid),
|
||||
+ ['grid a {} b {} c {}'.format(*self.cells),
|
||||
'size x {} y {} z {}'.format(*self.size),
|
||||
'origin x {} y {} z {}'.format(*self.origin),
|
||||
'homogenization 1',
|
||||
|
|
@ -548,13 +556,13 @@ class Geom:
|
|||
format_string = '%g' if self.material.dtype in np.sctypes['float'] else \
|
||||
'%{}i'.format(1+int(np.floor(np.log10(np.nanmax(self.material)))))
|
||||
np.savetxt(fname,
|
||||
self.material.reshape([self.grid[0],np.prod(self.grid[1:])],order='F').T,
|
||||
self.material.reshape([self.cells[0],np.prod(self.cells[1:])],order='F').T,
|
||||
header='\n'.join(header), fmt=format_string, comments='')
|
||||
|
||||
|
||||
def show(self):
|
||||
"""Show on screen."""
|
||||
VTK.from_rectilinear_grid(self.grid,self.size,self.origin).show()
|
||||
VTK.from_rectilinear_grid(self.cells,self.size,self.origin).show()
|
||||
|
||||
|
||||
def add_primitive(self,dimension,center,exponent,
|
||||
|
|
@ -566,11 +574,10 @@ class Geom:
|
|||
----------
|
||||
dimension : int or float numpy.ndarray of shape (3)
|
||||
Dimension (diameter/side length) of the primitive. If given as
|
||||
integers, grid point locations (cell centers) are addressed.
|
||||
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, grid point
|
||||
coordinates (cell centers) are addressed.
|
||||
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
|
||||
Exponents for the three axes.
|
||||
|
|
@ -584,44 +591,44 @@ class Geom:
|
|||
Retain original materials within primitive and fill outside.
|
||||
Defaults to False.
|
||||
periodic : Boolean, optional
|
||||
Repeat primitive over boundaries. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
# radius and center
|
||||
r = np.array(dimension)/2.0*self.size/self.grid if np.array(dimension).dtype in np.sctypes['int'] else \
|
||||
r = np.array(dimension)/2.0*self.size/self.cells if np.array(dimension).dtype in np.sctypes['int'] else \
|
||||
np.array(dimension)/2.0
|
||||
c = (np.array(center) + .5)*self.size/self.grid if np.array(center).dtype in np.sctypes['int'] else \
|
||||
c = (np.array(center) + .5)*self.size/self.cells if np.array(center).dtype in np.sctypes['int'] else \
|
||||
(np.array(center) - self.origin)
|
||||
|
||||
coords = grid_filters.cell_coord0(self.grid,self.size,
|
||||
-(0.5*(self.size + (self.size/self.grid
|
||||
coords = grid_filters.coordinates0_point(self.cells,self.size,
|
||||
-(0.5*(self.size + (self.size/self.cells
|
||||
if np.array(center).dtype in np.sctypes['int'] else
|
||||
0)) if periodic else c))
|
||||
coords_rot = R.broadcast_to(tuple(self.grid))@coords
|
||||
coords_rot = R.broadcast_to(tuple(self.cells))@coords
|
||||
|
||||
with np.errstate(all='ignore'):
|
||||
mask = np.sum(np.power(coords_rot/r,2.0**np.array(exponent)),axis=-1) > 1.0
|
||||
|
||||
if periodic: # translate back to center
|
||||
mask = np.roll(mask,((c/self.size-0.5)*self.grid).round().astype(int),(0,1,2))
|
||||
mask = np.roll(mask,((c/self.size-0.5)*self.cells).round().astype(int),(0,1,2))
|
||||
|
||||
return Geom(material = np.where(np.logical_not(mask) if inverse else mask,
|
||||
return Grid(material = np.where(np.logical_not(mask) if inverse else mask,
|
||||
self.material,
|
||||
np.nanmax(self.material)+1 if fill is None else fill),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','add_primitive')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','add_primitive')],
|
||||
)
|
||||
|
||||
|
||||
def mirror(self,directions,reflect=False):
|
||||
"""
|
||||
Mirror geometry along given directions.
|
||||
Mirror grid along given directions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
directions : iterable containing str
|
||||
Direction(s) along which the geometry is mirrored.
|
||||
Direction(s) along which the grid is mirrored.
|
||||
Valid entries are 'x', 'y', 'z'.
|
||||
reflect : bool, optional
|
||||
Reflect (include) outermost layers. Defaults to False.
|
||||
|
|
@ -629,7 +636,7 @@ class Geom:
|
|||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
|
||||
|
||||
limits = [None,None] if reflect else [-2,0]
|
||||
mat = self.material.copy()
|
||||
|
|
@ -641,52 +648,52 @@ class Geom:
|
|||
if 'z' in directions:
|
||||
mat = np.concatenate([mat,mat[:,:,limits[0]:limits[1]:-1]],2)
|
||||
|
||||
return Geom(material = mat,
|
||||
size = self.size/self.grid*np.asarray(mat.shape),
|
||||
return Grid(material = mat,
|
||||
size = self.size/self.cells*np.asarray(mat.shape),
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','mirror')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','mirror')],
|
||||
)
|
||||
|
||||
|
||||
def flip(self,directions):
|
||||
"""
|
||||
Flip geometry along given directions.
|
||||
Flip grid along given directions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
directions : iterable containing str
|
||||
Direction(s) along which the geometry is flipped.
|
||||
Direction(s) along which the grid is flipped.
|
||||
Valid entries are 'x', 'y', 'z'.
|
||||
|
||||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
|
||||
|
||||
mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
|
||||
|
||||
return Geom(material = mat,
|
||||
return Grid(material = mat,
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','flip')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','flip')],
|
||||
)
|
||||
|
||||
|
||||
def scale(self,grid,periodic=True):
|
||||
def scale(self,cells,periodic=True):
|
||||
"""
|
||||
Scale geometry to new grid.
|
||||
Scale grid to new cells.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : numpy.ndarray of shape (3)
|
||||
Number of grid points in x,y,z direction.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Number of cells in x,y,z direction.
|
||||
periodic : Boolean, optional
|
||||
Assume geometry to be periodic. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
return Geom(material = ndimage.interpolation.zoom(
|
||||
return Grid(material = ndimage.interpolation.zoom(
|
||||
self.material,
|
||||
grid/self.grid,
|
||||
cells/self.cells,
|
||||
output=self.material.dtype,
|
||||
order=0,
|
||||
mode=('wrap' if periodic else 'nearest'),
|
||||
|
|
@ -694,13 +701,13 @@ class Geom:
|
|||
),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','scale')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','scale')],
|
||||
)
|
||||
|
||||
|
||||
def clean(self,stencil=3,selection=None,periodic=True):
|
||||
"""
|
||||
Smooth geometry by selecting most frequent material index within given stencil at each location.
|
||||
Smooth grid by selecting most frequent material index within given stencil at each location.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -709,7 +716,7 @@ class Geom:
|
|||
selection : list, optional
|
||||
Field values that can be altered. Defaults to all.
|
||||
periodic : Boolean, optional
|
||||
Assume geometry to be periodic. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
def mostFrequent(arr,selection=None):
|
||||
|
|
@ -720,7 +727,7 @@ class Geom:
|
|||
else:
|
||||
return me
|
||||
|
||||
return Geom(material = ndimage.filters.generic_filter(
|
||||
return Grid(material = ndimage.filters.generic_filter(
|
||||
self.material,
|
||||
mostFrequent,
|
||||
size=(stencil if selection is None else stencil//2*2+1,)*3,
|
||||
|
|
@ -729,7 +736,7 @@ class Geom:
|
|||
).astype(self.material.dtype),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','clean')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','clean')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -737,21 +744,21 @@ class Geom:
|
|||
"""Renumber sorted material indices as 0,...,N-1."""
|
||||
_,renumbered = np.unique(self.material,return_inverse=True)
|
||||
|
||||
return Geom(material = renumbered.reshape(self.grid),
|
||||
return Grid(material = renumbered.reshape(self.cells),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','renumber')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','renumber')],
|
||||
)
|
||||
|
||||
|
||||
def rotate(self,R,fill=None):
|
||||
"""
|
||||
Rotate geometry (pad if required).
|
||||
Rotate grid (pad if required).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
R : damask.Rotation
|
||||
Rotation to apply to the geometry.
|
||||
Rotation to apply to the grid.
|
||||
fill : int or float, optional
|
||||
Material index to fill the corners. Defaults to material.max() + 1.
|
||||
|
||||
|
|
@ -773,25 +780,25 @@ class Geom:
|
|||
else:
|
||||
material_in = material_out
|
||||
|
||||
origin = self.origin-(np.asarray(material_in.shape)-self.grid)*.5 * self.size/self.grid
|
||||
origin = self.origin-(np.asarray(material_in.shape)-self.cells)*.5 * self.size/self.cells
|
||||
|
||||
return Geom(material = material_in,
|
||||
size = self.size/self.grid*np.asarray(material_in.shape),
|
||||
return Grid(material = material_in,
|
||||
size = self.size/self.cells*np.asarray(material_in.shape),
|
||||
origin = origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','rotate')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','rotate')],
|
||||
)
|
||||
|
||||
|
||||
def canvas(self,grid=None,offset=None,fill=None):
|
||||
def canvas(self,cells=None,offset=None,fill=None):
|
||||
"""
|
||||
Crop or enlarge/pad geometry.
|
||||
Crop or enlarge/pad grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : numpy.ndarray of shape (3)
|
||||
Number of grid points in x,y,z direction.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Number of cells x,y,z direction.
|
||||
offset : numpy.ndarray of shape (3)
|
||||
Offset (measured in grid points) from old to new geometry [0,0,0].
|
||||
Offset (measured in cells) from old to new grid [0,0,0].
|
||||
fill : int or float, optional
|
||||
Material index to fill the background. Defaults to material.max() + 1.
|
||||
|
||||
|
|
@ -800,19 +807,19 @@ class Geom:
|
|||
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.grid if grid is None else grid,fill,dtype)
|
||||
canvas = np.full(self.cells if cells is None else cells,fill,dtype)
|
||||
|
||||
LL = np.clip( offset, 0,np.minimum(self.grid, grid+offset))
|
||||
UR = np.clip( offset+grid, 0,np.minimum(self.grid, grid+offset))
|
||||
ll = np.clip(-offset, 0,np.minimum( grid,self.grid-offset))
|
||||
ur = np.clip(-offset+self.grid,0,np.minimum( grid,self.grid-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 Geom(material = canvas,
|
||||
size = self.size/self.grid*np.asarray(canvas.shape),
|
||||
origin = self.origin+offset*self.size/self.grid,
|
||||
comments = self.comments+[util.execution_stamp('Geom','canvas')],
|
||||
return Grid(material = canvas,
|
||||
size = self.size/self.cells*np.asarray(canvas.shape),
|
||||
origin = self.origin+offset*self.size/self.cells,
|
||||
comments = self.comments+[util.execution_stamp('Grid','canvas')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -834,10 +841,10 @@ class Geom:
|
|||
mp = np.vectorize(mp)
|
||||
mapper = dict(zip(from_material,to_material))
|
||||
|
||||
return Geom(material = mp(self.material,mapper).reshape(self.grid),
|
||||
return Grid(material = mp(self.material,mapper).reshape(self.cells),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','substitute')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','substitute')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -848,10 +855,10 @@ class Geom:
|
|||
sort_idx = np.argsort(from_ma)
|
||||
ma = np.unique(a)[sort_idx][np.searchsorted(from_ma,a,sorter = sort_idx)]
|
||||
|
||||
return Geom(material = ma.reshape(self.grid,order='F'),
|
||||
return Grid(material = ma.reshape(self.cells,order='F'),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','sort')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','sort')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -861,7 +868,7 @@ class Geom:
|
|||
|
||||
Different from themselves (or listed as triggers) within a given (cubic) vicinity,
|
||||
i.e. within the region close to a grain/phase boundary.
|
||||
ToDo: use include/exclude as in seeds.from_geom
|
||||
ToDo: use include/exclude as in seeds.from_grid
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -875,7 +882,7 @@ class Geom:
|
|||
List of material indices that trigger a change.
|
||||
Defaults to [], meaning that any different neighbor triggers a change.
|
||||
periodic : Boolean, optional
|
||||
Assume geometry to be periodic. Defaults to True.
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
|
||||
"""
|
||||
def tainted_neighborhood(stencil,trigger):
|
||||
|
|
@ -892,10 +899,10 @@ class Geom:
|
|||
mode='wrap' if periodic else 'nearest',
|
||||
extra_keywords={'trigger':trigger})
|
||||
|
||||
return Geom(material = np.where(mask, self.material + offset_,self.material),
|
||||
return Grid(material = np.where(mask, self.material + offset_,self.material),
|
||||
size = self.size,
|
||||
origin = self.origin,
|
||||
comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
|
||||
comments = self.comments+[util.execution_stamp('Grid','vicinity_offset')],
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -905,20 +912,20 @@ class Geom:
|
|||
|
||||
Parameters
|
||||
----------
|
||||
periodic : bool, optional
|
||||
Show boundaries across periodicity. Defaults to True.
|
||||
periodic : Boolean, optional
|
||||
Assume grid to be periodic. Defaults to True.
|
||||
directions : iterable containing str, optional
|
||||
Direction(s) along which the geometry is mirrored.
|
||||
Direction(s) along which the boundaries are determined.
|
||||
Valid entries are 'x', 'y', 'z'. Defaults to 'xyz'.
|
||||
|
||||
"""
|
||||
valid = ['x','y','z']
|
||||
if not set(directions).issubset(valid):
|
||||
raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
|
||||
raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
|
||||
|
||||
o = [[0, self.grid[0]+1, np.prod(self.grid[:2]+1)+self.grid[0]+1, np.prod(self.grid[:2]+1)],
|
||||
[0, np.prod(self.grid[:2]+1), np.prod(self.grid[:2]+1)+1, 1],
|
||||
[0, 1, self.grid[0]+1+1, self.grid[0]+1]] # offset for connectivity
|
||||
o = [[0, self.cells[0]+1, np.prod(self.cells[:2]+1)+self.cells[0]+1, np.prod(self.cells[:2]+1)],
|
||||
[0, np.prod(self.cells[:2]+1), np.prod(self.cells[:2]+1)+1, 1],
|
||||
[0, 1, self.cells[0]+1+1, self.cells[0]+1]] # offset for connectivity
|
||||
|
||||
connectivity = []
|
||||
for i,d in enumerate(['x','y','z']):
|
||||
|
|
@ -933,5 +940,5 @@ class Geom:
|
|||
base_nodes = np.argwhere(mask.flatten(order='F')).reshape(-1,1)
|
||||
connectivity.append(np.block([base_nodes + o[i][k] for k in range(4)]))
|
||||
|
||||
coords = grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
|
||||
coords = grid_filters.coordinates0_node(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
return VTK.from_unstructured_grid(coords,np.vstack(connectivity),'QUAD')
|
||||
|
|
@ -226,9 +226,9 @@ class Orientation(Rotation):
|
|||
|
||||
"""
|
||||
return super().__eq__(other) \
|
||||
and self.family == other.family \
|
||||
and self.lattice == other.lattice \
|
||||
and self.parameters == other.parameters
|
||||
and hasattr(other, 'family') and self.family == other.family \
|
||||
and hasattr(other, 'lattice') and self.lattice == other.lattice \
|
||||
and hasattr(other, 'parameters') and self.parameters == other.parameters
|
||||
|
||||
|
||||
def __matmul__(self,other):
|
||||
|
|
|
|||
|
|
@ -46,13 +46,17 @@ class Result:
|
|||
self.version_major = f.attrs['DADF5_version_major']
|
||||
self.version_minor = f.attrs['DADF5_version_minor']
|
||||
|
||||
if self.version_major != 0 or not 7 <= self.version_minor <= 9:
|
||||
if self.version_major != 0 or not 7 <= self.version_minor <= 11:
|
||||
raise TypeError(f'Unsupported DADF5 version {self.version_major}.{self.version_minor}')
|
||||
|
||||
self.structured = 'grid' in f['geometry'].attrs.keys()
|
||||
self.structured = 'grid' in f['geometry'].attrs.keys() or \
|
||||
'cells' in f['geometry'].attrs.keys()
|
||||
|
||||
if self.structured:
|
||||
self.grid = f['geometry'].attrs['grid']
|
||||
try:
|
||||
self.cells = f['geometry'].attrs['cells']
|
||||
except KeyError:
|
||||
self.cells = f['geometry'].attrs['grid']
|
||||
self.size = f['geometry'].attrs['size']
|
||||
self.origin = f['geometry'].attrs['origin']
|
||||
|
||||
|
|
@ -558,19 +562,19 @@ class Result:
|
|||
return dataset
|
||||
|
||||
@property
|
||||
def cell_coordinates(self):
|
||||
def coordinates0_point(self):
|
||||
"""Return initial coordinates of the cell centers."""
|
||||
if self.structured:
|
||||
return grid_filters.cell_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
|
||||
return grid_filters.coordinates0_point(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
else:
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
return f['geometry/x_c'][()]
|
||||
|
||||
@property
|
||||
def node_coordinates(self):
|
||||
def coordinates0_node(self):
|
||||
"""Return initial coordinates of the cell centers."""
|
||||
if self.structured:
|
||||
return grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F')
|
||||
return grid_filters.coordinates0_node(self.cells,self.size,self.origin).reshape(-1,3,order='F')
|
||||
else:
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
return f['geometry/x_n'][()]
|
||||
|
|
@ -780,13 +784,16 @@ class Result:
|
|||
|
||||
|
||||
@staticmethod
|
||||
def _add_IPF_color(q,l):
|
||||
def _add_IPF_color(l,q):
|
||||
m = util.scale_to_coprime(np.array(l))
|
||||
try:
|
||||
lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['Lattice']]
|
||||
except KeyError:
|
||||
lattice = q['meta']['Lattice']
|
||||
o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),lattice=lattice)
|
||||
try:
|
||||
o = Orientation(rotation = (rfn.structured_to_unstructured(q['data'])),lattice=lattice)
|
||||
except ValueError:
|
||||
o = Orientation(rotation = q['data'],lattice=lattice)
|
||||
|
||||
return {
|
||||
'data': np.uint8(o.IPF_color(l)*255),
|
||||
|
|
@ -798,16 +805,17 @@ class Result:
|
|||
'Creator': 'add_IPF_color'
|
||||
}
|
||||
}
|
||||
def add_IPF_color(self,q,l):
|
||||
def add_IPF_color(self,l,q='O'):
|
||||
"""
|
||||
Add RGB color tuple of inverse pole figure (IPF) color.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
q : str
|
||||
Label of the dataset containing the crystallographic orientation as quaternions.
|
||||
l : numpy.array of shape (3)
|
||||
Lab frame direction for inverse pole figure.
|
||||
q : str
|
||||
Label of the dataset containing the crystallographic orientation as quaternions.
|
||||
Defaults to 'O'.
|
||||
|
||||
"""
|
||||
self._add_generic_pointwise(self._add_IPF_color,{'q':q},{'l':l})
|
||||
|
|
@ -1125,6 +1133,7 @@ class Result:
|
|||
Arguments parsed to func.
|
||||
|
||||
"""
|
||||
chunk_size = 1024**2//8
|
||||
num_threads = damask.environment.options['DAMASK_NUM_THREADS']
|
||||
pool = mp.Pool(int(num_threads) if num_threads is not None else None)
|
||||
lock = mp.Manager().Lock()
|
||||
|
|
@ -1148,7 +1157,15 @@ class Result:
|
|||
dataset.attrs['Overwritten'] = 'Yes' if h5py3 else \
|
||||
'Yes'.encode()
|
||||
else:
|
||||
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
|
||||
if result[1]['data'].size >= chunk_size*2:
|
||||
shape = result[1]['data'].shape
|
||||
chunks = (chunk_size//np.prod(shape[1:]),)+shape[1:]
|
||||
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'],
|
||||
maxshape=shape, chunks=chunks,
|
||||
compression='gzip', compression_opts=6,
|
||||
shuffle=True,fletcher32=True)
|
||||
else:
|
||||
dataset = f[result[0]].create_dataset(result[1]['label'],data=result[1]['data'])
|
||||
|
||||
now = datetime.datetime.now().astimezone()
|
||||
dataset.attrs['Created'] = now.strftime('%Y-%m-%d %H:%M:%S%z') if h5py3 else \
|
||||
|
|
@ -1218,7 +1235,7 @@ class Result:
|
|||
|
||||
topology=ET.SubElement(grid, 'Topology')
|
||||
topology.attrib={'TopologyType': '3DCoRectMesh',
|
||||
'Dimensions': '{} {} {}'.format(*self.grid+1)}
|
||||
'Dimensions': '{} {} {}'.format(*self.cells+1)}
|
||||
|
||||
geometry=ET.SubElement(grid, 'Geometry')
|
||||
geometry.attrib={'GeometryType':'Origin_DxDyDz'}
|
||||
|
|
@ -1233,7 +1250,7 @@ class Result:
|
|||
delta.attrib={'Format': 'XML',
|
||||
'NumberType': 'Float',
|
||||
'Dimensions': '3'}
|
||||
delta.text="{} {} {}".format(*(self.size/self.grid))
|
||||
delta.text="{} {} {}".format(*(self.size/self.cells))
|
||||
|
||||
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
|
|
@ -1244,7 +1261,7 @@ class Result:
|
|||
data_items.append(ET.SubElement(attributes[-1], 'DataItem'))
|
||||
data_items[-1].attrib={'Format': 'HDF',
|
||||
'Precision': '8',
|
||||
'Dimensions': '{} {} {} 3'.format(*(self.grid+1))}
|
||||
'Dimensions': '{} {} {} 3'.format(*(self.cells+1))}
|
||||
data_items[-1].text=f'{os.path.split(self.fname)[1]}:/{inc}/geometry/u_n'
|
||||
|
||||
for o,p in zip(['phases','homogenizations'],['out_type_ph','out_type_ho']):
|
||||
|
|
@ -1267,8 +1284,8 @@ class Result:
|
|||
data_items[-1].attrib={'Format': 'HDF',
|
||||
'NumberType': number_type_map(dtype),
|
||||
'Precision': f'{dtype.itemsize}',
|
||||
'Dimensions': '{} {} {} {}'.format(*self.grid,1 if shape == () else
|
||||
np.prod(shape))}
|
||||
'Dimensions': '{} {} {} {}'.format(*self.cells,1 if shape == () else
|
||||
np.prod(shape))}
|
||||
data_items[-1].text=f'{os.path.split(self.fname)[1]}:{name}'
|
||||
|
||||
with open(self.fname.with_suffix('.xdmf').name,'w') as f:
|
||||
|
|
@ -1291,7 +1308,7 @@ class Result:
|
|||
if mode.lower()=='cell':
|
||||
|
||||
if self.structured:
|
||||
v = VTK.from_rectilinear_grid(self.grid,self.size,self.origin)
|
||||
v = VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
|
||||
else:
|
||||
with h5py.File(self.fname,'r') as f:
|
||||
v = VTK.from_unstructured_grid(f['/geometry/x_n'][()],
|
||||
|
|
@ -1299,7 +1316,7 @@ class Result:
|
|||
f['/geometry/T_c'].attrs['VTK_TYPE'] if h5py3 else \
|
||||
f['/geometry/T_c'].attrs['VTK_TYPE'].decode())
|
||||
elif mode.lower()=='point':
|
||||
v = VTK.from_poly_data(self.cell_coordinates)
|
||||
v = VTK.from_poly_data(self.coordinates0_point)
|
||||
|
||||
N_digits = int(np.floor(np.log10(max(1,int(self.increments[-1][3:])))))+1
|
||||
|
||||
|
|
|
|||
|
|
@ -144,6 +144,11 @@ class Rotation:
|
|||
return self.copy(rotation=Rotation(np.block([np.cos(pwr*phi),np.sin(pwr*phi)*p]))._standardize())
|
||||
|
||||
|
||||
def __mul__(self,other):
|
||||
"""Standard multiplication is not implemented."""
|
||||
raise NotImplementedError('Use "R@b", i.e. matmul, to apply rotation "R" to object "b"')
|
||||
|
||||
|
||||
def __matmul__(self,other):
|
||||
"""
|
||||
Rotation of vector, second or fourth order tensor, or rotation object.
|
||||
|
|
@ -199,8 +204,16 @@ class Rotation:
|
|||
|
||||
|
||||
def append(self,other):
|
||||
"""Extend rotation array along first dimension with other array."""
|
||||
return self.copy(rotation=np.vstack((self.quaternion,other.quaternion)))
|
||||
"""
|
||||
Extend rotation array along first dimension with other array(s).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
other : Rotation or list of Rotations.
|
||||
|
||||
"""
|
||||
return self.copy(rotation=np.vstack(tuple(map(lambda x:x.quaternion,
|
||||
[self]+other if isinstance(other,list) else [self,other]))))
|
||||
|
||||
|
||||
def flatten(self,order = 'C'):
|
||||
|
|
@ -258,7 +271,7 @@ class Rotation:
|
|||
"""Intermediate representation supporting quaternion averaging."""
|
||||
return np.einsum('...i,...j',quat,quat)
|
||||
|
||||
if not weights:
|
||||
if weights is None:
|
||||
weights = np.ones(self.shape,dtype=float)
|
||||
|
||||
eig, vec = np.linalg.eig(np.sum(_M(self.quaternion) * weights[...,np.newaxis,np.newaxis],axis=-3) \
|
||||
|
|
@ -763,7 +776,7 @@ class Rotation:
|
|||
def _dg(eu,deg):
|
||||
"""Return infinitesimal Euler space volume of bin(s)."""
|
||||
phi_sorted = eu[np.lexsort((eu[:,0],eu[:,1],eu[:,2]))]
|
||||
steps,size,_ = grid_filters.cell_coord0_gridSizeOrigin(phi_sorted)
|
||||
steps,size,_ = grid_filters.cellsSizeOrigin_coordinates0_point(phi_sorted)
|
||||
delta = np.radians(size/steps) if deg else size/steps
|
||||
return delta[0]*2.0*np.sin(delta[1]/2.0)*delta[2] / 8.0 / np.pi**2 * np.sin(np.radians(eu[:,1]) if deg else eu[:,1])
|
||||
|
||||
|
|
|
|||
|
|
@ -33,6 +33,10 @@ class Table:
|
|||
"""Brief overview."""
|
||||
return '\n'.join(['# '+c for c in self.comments])+'\n'+self.data.__repr__()
|
||||
|
||||
def __getitem__(self,item):
|
||||
"""Return slice according to item."""
|
||||
return self.__class__(data=self.data[item],shapes=self.shapes,comments=self.comments)
|
||||
|
||||
def __len__(self):
|
||||
"""Number of rows."""
|
||||
return len(self.data)
|
||||
|
|
@ -73,7 +77,7 @@ class Table:
|
|||
@staticmethod
|
||||
def load(fname):
|
||||
"""
|
||||
Load ASCII table file.
|
||||
Load from ASCII table file.
|
||||
|
||||
In legacy style, the first line indicates the number of
|
||||
subsequent header lines as "N header", with the last header line being
|
||||
|
|
@ -131,7 +135,7 @@ class Table:
|
|||
@staticmethod
|
||||
def load_ang(fname):
|
||||
"""
|
||||
Load ang file.
|
||||
Load from ang file.
|
||||
|
||||
A valid TSL ang file needs to contains the following columns:
|
||||
* Euler angles (Bunge notation) in radians, 3 floats, label 'eu'.
|
||||
|
|
|
|||
|
|
@ -76,7 +76,8 @@ class VTK:
|
|||
nodes : numpy.ndarray of shape (:,3)
|
||||
Spatial position of the nodes.
|
||||
connectivity : numpy.ndarray of np.dtype = int
|
||||
Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.
|
||||
Cell connectivity (0-based), first dimension determines #Cells,
|
||||
second dimension determines #Nodes/Cell.
|
||||
cell_type : str
|
||||
Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
|
||||
|
||||
|
|
@ -91,7 +92,9 @@ class VTK:
|
|||
|
||||
vtk_data = vtk.vtkUnstructuredGrid()
|
||||
vtk_data.SetPoints(vtk_nodes)
|
||||
vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
|
||||
cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD,
|
||||
'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON}
|
||||
vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
|
||||
|
||||
return VTK(vtk_data)
|
||||
|
||||
|
|
@ -128,7 +131,7 @@ class VTK:
|
|||
@staticmethod
|
||||
def load(fname,dataset_type=None):
|
||||
"""
|
||||
Create VTK from file.
|
||||
Load from VTK file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
@ -181,7 +184,7 @@ class VTK:
|
|||
writer.Write()
|
||||
def save(self,fname,parallel=True,compress=True):
|
||||
"""
|
||||
Write to file.
|
||||
Save as VTK file.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
|
|
|
|||
|
|
@ -4,38 +4,38 @@ Filters for operations on regular grids.
|
|||
Notes
|
||||
-----
|
||||
The grids are defined as (x,y,z,...) where x is fastest and z is slowest.
|
||||
This convention is consistent with the geom file format.
|
||||
This convention is consistent with the layout in grid vtr files.
|
||||
When converting to/from a plain list (e.g. storage in ASCII table),
|
||||
the following operations are required for tensorial data:
|
||||
|
||||
D3 = D1.reshape(grid+(-1,),order='F').reshape(grid+(3,3))
|
||||
D1 = D3.reshape(grid+(-1,)).reshape(-1,9,order='F')
|
||||
D3 = D1.reshape(cells+(-1,),order='F').reshape(cells+(3,3))
|
||||
D1 = D3.reshape(cells+(-1,)).reshape(-1,9,order='F')
|
||||
|
||||
"""
|
||||
from scipy import spatial as _spatial
|
||||
import numpy as _np
|
||||
|
||||
def _ks(size,grid,first_order=False):
|
||||
def _ks(size,cells,first_order=False):
|
||||
"""
|
||||
Get wave numbers operator.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
grid : numpy.ndarray of shape (3)
|
||||
number of grid points.
|
||||
Physical size of the periodic field.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Number of cells.
|
||||
first_order : bool, optional
|
||||
correction for first order derivatives, defaults to False.
|
||||
Correction for first order derivatives, defaults to False.
|
||||
|
||||
"""
|
||||
k_sk = _np.where(_np.arange(grid[0])>grid[0]//2,_np.arange(grid[0])-grid[0],_np.arange(grid[0]))/size[0]
|
||||
if grid[0]%2 == 0 and first_order: k_sk[grid[0]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
|
||||
k_sk = _np.where(_np.arange(cells[0])>cells[0]//2,_np.arange(cells[0])-cells[0],_np.arange(cells[0]))/size[0]
|
||||
if cells[0]%2 == 0 and first_order: k_sk[cells[0]//2] = 0 # Nyquist freq=0 for even cells (Johnson, MIT, 2011)
|
||||
|
||||
k_sj = _np.where(_np.arange(grid[1])>grid[1]//2,_np.arange(grid[1])-grid[1],_np.arange(grid[1]))/size[1]
|
||||
if grid[1]%2 == 0 and first_order: k_sj[grid[1]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
|
||||
k_sj = _np.where(_np.arange(cells[1])>cells[1]//2,_np.arange(cells[1])-cells[1],_np.arange(cells[1]))/size[1]
|
||||
if cells[1]%2 == 0 and first_order: k_sj[cells[1]//2] = 0 # Nyquist freq=0 for even cells (Johnson, MIT, 2011)
|
||||
|
||||
k_si = _np.arange(grid[2]//2+1)/size[2]
|
||||
k_si = _np.arange(cells[2]//2+1)/size[2]
|
||||
|
||||
return _np.stack(_np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij'), axis=-1)
|
||||
|
||||
|
|
@ -47,9 +47,9 @@ def curl(size,field):
|
|||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
periodic field of which the curl is calculated.
|
||||
Periodic field of which the curl is calculated.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
|
|
@ -73,9 +73,9 @@ def divergence(size,field):
|
|||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,3) or (:,:,:,3,3)
|
||||
periodic field of which the divergence is calculated.
|
||||
Periodic field of which the divergence is calculated.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
|
|
@ -95,9 +95,9 @@ def gradient(size,field):
|
|||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
field : numpy.ndarray of shape (:,:,:,1) or (:,:,:,3)
|
||||
periodic field of which the gradient is calculated.
|
||||
Periodic field of which the gradient is calculated.
|
||||
|
||||
"""
|
||||
n = _np.prod(field.shape[3:])
|
||||
|
|
@ -110,39 +110,39 @@ def gradient(size,field):
|
|||
return _np.fft.irfftn(grad_,axes=(0,1,2),s=field.shape[:3])
|
||||
|
||||
|
||||
def cell_coord0(grid,size,origin=_np.zeros(3)):
|
||||
def coordinates0_point(cells,size,origin=_np.zeros(3)):
|
||||
"""
|
||||
Cell center positions (undeformed).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : numpy.ndarray of shape (3)
|
||||
number of grid points.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Number of cells.
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
origin : numpy.ndarray, optional
|
||||
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
"""
|
||||
start = origin + size/grid*.5
|
||||
end = origin + size - size/grid*.5
|
||||
start = origin + size/cells*.5
|
||||
end = origin + size - size/cells*.5
|
||||
|
||||
return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],grid[0]),
|
||||
_np.linspace(start[1],end[1],grid[1]),
|
||||
_np.linspace(start[2],end[2],grid[2]),indexing = 'ij'),
|
||||
return _np.stack(_np.meshgrid(_np.linspace(start[0],end[0],cells[0]),
|
||||
_np.linspace(start[1],end[1],cells[1]),
|
||||
_np.linspace(start[2],end[2],cells[2]),indexing = 'ij'),
|
||||
axis = -1)
|
||||
|
||||
|
||||
def cell_displacement_fluct(size,F):
|
||||
def displacement_fluct_point(size,F):
|
||||
"""
|
||||
Cell center displacement field from fluctuation part of the deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
integrator = 0.5j*size/_np.pi
|
||||
|
|
@ -160,194 +160,196 @@ def cell_displacement_fluct(size,F):
|
|||
return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
|
||||
|
||||
|
||||
def cell_displacement_avg(size,F):
|
||||
def displacement_avg_point(size,F):
|
||||
"""
|
||||
Cell center displacement field from average part of the deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
F_avg = _np.average(F,axis=(0,1,2))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),cell_coord0(F.shape[:3],size))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_point(F.shape[:3],size))
|
||||
|
||||
|
||||
def cell_displacement(size,F):
|
||||
def displacement_point(size,F):
|
||||
"""
|
||||
Cell center displacement field from deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
|
||||
return displacement_avg_point(size,F) + displacement_fluct_point(size,F)
|
||||
|
||||
|
||||
def cell_coord(size,F,origin=_np.zeros(3)):
|
||||
def coordinates_point(size,F,origin=_np.zeros(3)):
|
||||
"""
|
||||
Cell center positions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
origin : numpy.ndarray of shape (3), optional
|
||||
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
"""
|
||||
return cell_coord0(F.shape[:3],size,origin) + cell_displacement(size,F)
|
||||
return coordinates0_point(F.shape[:3],size,origin) + displacement_point(size,F)
|
||||
|
||||
|
||||
def cell_coord0_gridSizeOrigin(coord0,ordered=True):
|
||||
def cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True):
|
||||
"""
|
||||
Return grid 'DNA', i.e. grid, size, and origin from 1D array of cell positions.
|
||||
Return grid 'DNA', i.e. cells, size, and origin from 1D array of point positions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
coord0 : numpy.ndarray of shape (:,3)
|
||||
undeformed cell coordinates.
|
||||
coordinates0 : numpy.ndarray of shape (:,3)
|
||||
Undeformed cell coordinates.
|
||||
ordered : bool, optional
|
||||
expect coord0 data to be ordered (x fast, z slow).
|
||||
Expect coordinates0 data to be ordered (x fast, z slow).
|
||||
Defaults to True.
|
||||
|
||||
"""
|
||||
coords = [_np.unique(coord0[:,i]) for i in range(3)]
|
||||
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
|
||||
mincorner = _np.array(list(map(min,coords)))
|
||||
maxcorner = _np.array(list(map(max,coords)))
|
||||
grid = _np.array(list(map(len,coords)),'i')
|
||||
size = grid/_np.maximum(grid-1,1) * (maxcorner-mincorner)
|
||||
delta = size/grid
|
||||
cells = _np.array(list(map(len,coords)),'i')
|
||||
size = cells/_np.maximum(cells-1,1) * (maxcorner-mincorner)
|
||||
delta = size/cells
|
||||
origin = mincorner - delta*.5
|
||||
|
||||
# 1D/2D: size/origin combination undefined, set origin to 0.0
|
||||
size [_np.where(grid==1)] = origin[_np.where(grid==1)]*2.
|
||||
origin[_np.where(grid==1)] = 0.0
|
||||
size [_np.where(cells==1)] = origin[_np.where(cells==1)]*2.
|
||||
origin[_np.where(cells==1)] = 0.0
|
||||
|
||||
if grid.prod() != len(coord0):
|
||||
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
|
||||
if cells.prod() != len(coordinates0):
|
||||
raise ValueError(f'Data count {len(coordinates0)} does not match cells {cells}.')
|
||||
|
||||
start = origin + delta*.5
|
||||
end = origin - delta*.5 + size
|
||||
|
||||
atol = _np.max(size)*5e-2
|
||||
if not (_np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0]),atol=atol) and \
|
||||
_np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1]),atol=atol) and \
|
||||
_np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2]),atol=atol)):
|
||||
raise ValueError('Regular grid spacing violated.')
|
||||
if not (_np.allclose(coords[0],_np.linspace(start[0],end[0],cells[0]),atol=atol) and \
|
||||
_np.allclose(coords[1],_np.linspace(start[1],end[1],cells[1]),atol=atol) and \
|
||||
_np.allclose(coords[2],_np.linspace(start[2],end[2],cells[2]),atol=atol)):
|
||||
raise ValueError('Regular cell spacing violated.')
|
||||
|
||||
if ordered and not _np.allclose(coord0.reshape(tuple(grid)+(3,),order='F'),cell_coord0(grid,size,origin),atol=atol):
|
||||
if ordered and not _np.allclose(coordinates0.reshape(tuple(cells)+(3,),order='F'),
|
||||
coordinates0_point(cells,size,origin),atol=atol):
|
||||
raise ValueError('Input data is not ordered (x fast, z slow).')
|
||||
|
||||
return (grid,size,origin)
|
||||
return (cells,size,origin)
|
||||
|
||||
|
||||
def coord0_check(coord0):
|
||||
def coordinates0_check(coordinates0):
|
||||
"""
|
||||
Check whether coordinates lie on a regular grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
coord0 : numpy.ndarray
|
||||
array of undeformed cell coordinates.
|
||||
coordinates0 : numpy.ndarray
|
||||
Array of undeformed cell coordinates.
|
||||
|
||||
"""
|
||||
cell_coord0_gridSizeOrigin(coord0,ordered=True)
|
||||
cellsSizeOrigin_coordinates0_point(coordinates0,ordered=True)
|
||||
|
||||
|
||||
def node_coord0(grid,size,origin=_np.zeros(3)):
|
||||
def coordinates0_node(cells,size,origin=_np.zeros(3)):
|
||||
"""
|
||||
Nodal positions (undeformed).
|
||||
|
||||
Parameters
|
||||
----------
|
||||
grid : numpy.ndarray of shape (3)
|
||||
number of grid points.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Number of cells.
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
origin : numpy.ndarray of shape (3), optional
|
||||
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
"""
|
||||
return _np.stack(_np.meshgrid(_np.linspace(origin[0],size[0]+origin[0],grid[0]+1),
|
||||
_np.linspace(origin[1],size[1]+origin[1],grid[1]+1),
|
||||
_np.linspace(origin[2],size[2]+origin[2],grid[2]+1),indexing = 'ij'),
|
||||
return _np.stack(_np.meshgrid(_np.linspace(origin[0],size[0]+origin[0],cells[0]+1),
|
||||
_np.linspace(origin[1],size[1]+origin[1],cells[1]+1),
|
||||
_np.linspace(origin[2],size[2]+origin[2],cells[2]+1),indexing = 'ij'),
|
||||
axis = -1)
|
||||
|
||||
|
||||
def node_displacement_fluct(size,F):
|
||||
def displacement_fluct_node(size,F):
|
||||
"""
|
||||
Nodal displacement field from fluctuation part of the deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
return cell_2_node(cell_displacement_fluct(size,F))
|
||||
return point_to_node(displacement_fluct_point(size,F))
|
||||
|
||||
|
||||
def node_displacement_avg(size,F):
|
||||
def displacement_avg_node(size,F):
|
||||
"""
|
||||
Nodal displacement field from average part of the deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
F_avg = _np.average(F,axis=(0,1,2))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),node_coord0(F.shape[:3],size))
|
||||
return _np.einsum('ml,ijkl->ijkm',F_avg - _np.eye(3),coordinates0_node(F.shape[:3],size))
|
||||
|
||||
|
||||
def node_displacement(size,F):
|
||||
def displacement_node(size,F):
|
||||
"""
|
||||
Nodal displacement field from deformation gradient field.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
|
||||
"""
|
||||
return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
|
||||
return displacement_avg_node(size,F) + displacement_fluct_node(size,F)
|
||||
|
||||
|
||||
def node_coord(size,F,origin=_np.zeros(3)):
|
||||
def coordinates_node(size,F,origin=_np.zeros(3)):
|
||||
"""
|
||||
Nodal positions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size of the periodic field.
|
||||
Physical size of the periodic field.
|
||||
F : numpy.ndarray
|
||||
deformation gradient field.
|
||||
Deformation gradient field.
|
||||
origin : numpy.ndarray of shape (3), optional
|
||||
physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
Physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
|
||||
|
||||
"""
|
||||
return node_coord0(F.shape[:3],size,origin) + node_displacement(size,F)
|
||||
return coordinates0_node(F.shape[:3],size,origin) + displacement_node(size,F)
|
||||
|
||||
|
||||
def cell_2_node(cell_data):
|
||||
"""Interpolate periodic cell data to nodal data."""
|
||||
def point_to_node(cell_data):
|
||||
"""Interpolate periodic point data to nodal data."""
|
||||
n = ( cell_data + _np.roll(cell_data,1,(0,1,2))
|
||||
+ _np.roll(cell_data,1,(0,)) + _np.roll(cell_data,1,(1,)) + _np.roll(cell_data,1,(2,))
|
||||
+ _np.roll(cell_data,1,(0,1)) + _np.roll(cell_data,1,(1,2)) + _np.roll(cell_data,1,(2,0)))*0.125
|
||||
|
|
@ -355,8 +357,8 @@ def cell_2_node(cell_data):
|
|||
return _np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
|
||||
|
||||
|
||||
def node_2_cell(node_data):
|
||||
"""Interpolate periodic nodal data to cell data."""
|
||||
def node_2_point(node_data):
|
||||
"""Interpolate periodic nodal data to point data."""
|
||||
c = ( node_data + _np.roll(node_data,1,(0,1,2))
|
||||
+ _np.roll(node_data,1,(0,)) + _np.roll(node_data,1,(1,)) + _np.roll(node_data,1,(2,))
|
||||
+ _np.roll(node_data,1,(0,1)) + _np.roll(node_data,1,(1,2)) + _np.roll(node_data,1,(2,0)))*0.125
|
||||
|
|
@ -364,57 +366,57 @@ def node_2_cell(node_data):
|
|||
return c[1:,1:,1:]
|
||||
|
||||
|
||||
def node_coord0_gridSizeOrigin(coord0,ordered=True):
|
||||
def cellsSizeOrigin_coordinates0_node(coordinates0,ordered=True):
|
||||
"""
|
||||
Return grid 'DNA', i.e. grid, size, and origin from 1D array of nodal positions.
|
||||
Return grid 'DNA', i.e. cells, size, and origin from 1D array of nodal positions.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
coord0 : numpy.ndarray of shape (:,3)
|
||||
undeformed nodal coordinates.
|
||||
coordinates0 : numpy.ndarray of shape (:,3)
|
||||
Undeformed nodal coordinates.
|
||||
ordered : bool, optional
|
||||
expect coord0 data to be ordered (x fast, z slow).
|
||||
Expect coordinates0 data to be ordered (x fast, z slow).
|
||||
Defaults to True.
|
||||
|
||||
"""
|
||||
coords = [_np.unique(coord0[:,i]) for i in range(3)]
|
||||
coords = [_np.unique(coordinates0[:,i]) for i in range(3)]
|
||||
mincorner = _np.array(list(map(min,coords)))
|
||||
maxcorner = _np.array(list(map(max,coords)))
|
||||
grid = _np.array(list(map(len,coords)),'i') - 1
|
||||
cells = _np.array(list(map(len,coords)),'i') - 1
|
||||
size = maxcorner-mincorner
|
||||
origin = mincorner
|
||||
|
||||
if (grid+1).prod() != len(coord0):
|
||||
raise ValueError('Data count {len(coord0)} does not match grid {grid}.')
|
||||
if (cells+1).prod() != len(coordinates0):
|
||||
raise ValueError(f'Data count {len(coordinates0)} does not match cells {cells}.')
|
||||
|
||||
atol = _np.max(size)*5e-2
|
||||
if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1),atol=atol) and \
|
||||
_np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1),atol=atol) and \
|
||||
_np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1),atol=atol)):
|
||||
raise ValueError('Regular grid spacing violated.')
|
||||
if not (_np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],cells[0]+1),atol=atol) and \
|
||||
_np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],cells[1]+1),atol=atol) and \
|
||||
_np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],cells[2]+1),atol=atol)):
|
||||
raise ValueError('Regular cell spacing violated.')
|
||||
|
||||
if ordered and not _np.allclose(coord0.reshape(tuple(grid+1)+(3,),order='F'),node_coord0(grid,size,origin),atol=atol):
|
||||
if ordered and not _np.allclose(coordinates0.reshape(tuple(cells+1)+(3,),order='F'),
|
||||
coordinates0_node(cells,size,origin),atol=atol):
|
||||
raise ValueError('Input data is not ordered (x fast, z slow).')
|
||||
|
||||
return (grid,size,origin)
|
||||
return (cells,size,origin)
|
||||
|
||||
|
||||
def regrid(size,F,new_grid):
|
||||
def regrid(size,F,cells):
|
||||
"""
|
||||
Return mapping from coordinates in deformed configuration to a regular grid.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
size : numpy.ndarray of shape (3)
|
||||
physical size
|
||||
Physical size.
|
||||
F : numpy.ndarray of shape (:,:,:,3,3)
|
||||
deformation gradient field
|
||||
new_grid : numpy.ndarray of shape (3)
|
||||
new grid for undeformed coordinates
|
||||
Deformation gradient field.
|
||||
cells : numpy.ndarray of shape (3)
|
||||
Cell count along x,y,z of remapping grid.
|
||||
|
||||
"""
|
||||
c = cell_coord0(F.shape[:3],size) \
|
||||
+ cell_displacement_avg(size,F) \
|
||||
+ cell_displacement_fluct(size,F)
|
||||
c = coordinates_point(size,F)
|
||||
|
||||
outer = _np.dot(_np.average(F,axis=(0,1,2)),size)
|
||||
for d in range(3):
|
||||
|
|
@ -422,4 +424,4 @@ def regrid(size,F,new_grid):
|
|||
c[_np.where(c[:,:,:,d]>outer[d])] -= outer[d]
|
||||
|
||||
tree = _spatial.cKDTree(c.reshape(-1,3),boxsize=outer)
|
||||
return tree.query(cell_coord0(new_grid,outer))[1].flatten()
|
||||
return tree.query(coordinates0_point(cells,outer))[1].flatten()
|
||||
|
|
|
|||
|
|
@ -7,7 +7,7 @@ from . import util
|
|||
from . import grid_filters
|
||||
|
||||
|
||||
def from_random(size,N_seeds,grid=None,rng_seed=None):
|
||||
def from_random(size,N_seeds,cells=None,rng_seed=None):
|
||||
"""
|
||||
Random seeding in space.
|
||||
|
||||
|
|
@ -17,21 +17,21 @@ def from_random(size,N_seeds,grid=None,rng_seed=None):
|
|||
Physical size of the seeding domain.
|
||||
N_seeds : int
|
||||
Number of seeds.
|
||||
grid : numpy.ndarray of shape (3), optional.
|
||||
If given, ensures that all seeds initiate one grain if using a
|
||||
standard Voronoi tessellation.
|
||||
cells : numpy.ndarray of shape (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
|
||||
A seed to initialize the BitGenerator. Defaults to None.
|
||||
If None, then fresh, unpredictable entropy will be pulled from the OS.
|
||||
|
||||
"""
|
||||
rng = _np.random.default_rng(rng_seed)
|
||||
if grid is None:
|
||||
if cells is None:
|
||||
coords = rng.random((N_seeds,3)) * size
|
||||
else:
|
||||
grid_coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
|
||||
coords = grid_coords[rng.choice(_np.prod(grid),N_seeds, replace=False)] \
|
||||
+ _np.broadcast_to(size/grid,(N_seeds,3))*(rng.random((N_seeds,3))*.5-.25) # wobble without leaving grid
|
||||
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
|
||||
|
||||
return coords
|
||||
|
||||
|
|
@ -77,14 +77,14 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
|
|||
return coords
|
||||
|
||||
|
||||
def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
|
||||
def from_grid(grid,selection=None,invert=False,average=False,periodic=True):
|
||||
"""
|
||||
Create seed from existing geometry description.
|
||||
Create seed from existing grid description.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
geom : damask.Geom
|
||||
Geometry, from which the material IDs are used as seeds.
|
||||
grid : damask.Grid
|
||||
Grid, from which the material IDs are used as seeds.
|
||||
selection : iterable of integers, optional
|
||||
Material IDs to consider.
|
||||
invert : boolean, false
|
||||
|
|
@ -95,10 +95,10 @@ def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
|
|||
Center of gravity with periodic boundaries.
|
||||
|
||||
"""
|
||||
material = geom.material.reshape((-1,1),order='F')
|
||||
mask = _np.full(geom.grid.prod(),True,dtype=bool) if selection is None else \
|
||||
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()
|
||||
coords = grid_filters.cell_coord0(geom.grid,geom.size).reshape(-1,3,order='F')
|
||||
coords = grid_filters.coordinates0_point(grid.cells,grid.size).reshape(-1,3,order='F')
|
||||
|
||||
if not average:
|
||||
return (coords[mask],material[mask])
|
||||
|
|
@ -106,8 +106,8 @@ def from_geom(geom,selection=None,invert=False,average=False,periodic=True):
|
|||
materials = _np.unique(material[mask])
|
||||
coords_ = _np.zeros((materials.size,3),dtype=float)
|
||||
for i,mat in enumerate(materials):
|
||||
pc = (2*_np.pi*coords[material[:,0]==mat,:]-geom.origin)/geom.size
|
||||
coords_[i] = geom.origin + geom.size / 2 / _np.pi * (_np.pi +
|
||||
pc = (2*_np.pi*coords[material[:,0]==mat,:]-grid.origin)/grid.size
|
||||
coords_[i] = grid.origin + grid.size / 2 / _np.pi * (_np.pi +
|
||||
_np.arctan2(-_np.average(_np.sin(pc),axis=0),
|
||||
-_np.average(_np.cos(pc),axis=0))) \
|
||||
if periodic else \
|
||||
|
|
|
|||
|
|
@ -1,10 +1,10 @@
|
|||
homogenization:
|
||||
SX:
|
||||
N_constituents: 2
|
||||
mech: {type: none}
|
||||
N_constituents: 1
|
||||
mechanics: {type: none}
|
||||
Taylor:
|
||||
N_constituents: 2
|
||||
mech: {type: isostrain}
|
||||
mechanics: {type: isostrain}
|
||||
|
||||
material:
|
||||
- constituents:
|
||||
|
|
@ -34,11 +34,11 @@ material:
|
|||
phase:
|
||||
Aluminum:
|
||||
lattice: cF
|
||||
mech:
|
||||
mechanics:
|
||||
output: [F, P, F_e, F_p, L_p]
|
||||
elasticity: {C_11: 106.75e9, C_12: 60.41e9, C_44: 28.34e9, type: hooke}
|
||||
Steel:
|
||||
lattice: cI
|
||||
mech:
|
||||
mechanics:
|
||||
output: [F, P, F_e, F_p, L_p]
|
||||
elasticity: {C_11: 233.3e9, C_12: 135.5e9, C_44: 118.0e9, type: hooke}
|
||||
|
|
|
|||
|
|
@ -1,8 +1,9 @@
|
|||
import pytest
|
||||
import numpy as np
|
||||
from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
|
||||
|
||||
from damask import VTK
|
||||
from damask import Geom
|
||||
from damask import Grid
|
||||
from damask import Table
|
||||
from damask import Rotation
|
||||
from damask import util
|
||||
|
|
@ -10,9 +11,9 @@ from damask import seeds
|
|||
from damask import grid_filters
|
||||
|
||||
|
||||
def geom_equal(a,b):
|
||||
def grid_equal(a,b):
|
||||
return np.all(a.material == b.material) and \
|
||||
np.all(a.grid == b.grid) and \
|
||||
np.all(a.cells == b.cells) and \
|
||||
np.allclose(a.size, b.size) and \
|
||||
str(a.diff(b)) == str(b.diff(a))
|
||||
|
||||
|
|
@ -23,15 +24,15 @@ def default():
|
|||
np.arange(2,42),
|
||||
np.ones(40,dtype=int)*2,
|
||||
np.arange(1,41))).reshape(8,5,4,order='F')
|
||||
return Geom(x,[8e-6,5e-6,4e-6])
|
||||
return Grid(x,[8e-6,5e-6,4e-6])
|
||||
|
||||
@pytest.fixture
|
||||
def ref_path(ref_path_base):
|
||||
"""Directory containing reference results."""
|
||||
return ref_path_base/'Geom'
|
||||
return ref_path_base/'Grid'
|
||||
|
||||
|
||||
class TestGeom:
|
||||
class TestGrid:
|
||||
|
||||
@pytest.fixture(autouse=True)
|
||||
def _patch_execution_stamp(self, patch_execution_stamp):
|
||||
|
|
@ -46,7 +47,7 @@ class TestGeom:
|
|||
|
||||
|
||||
def test_diff_not_equal(self,default):
|
||||
new = Geom(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
|
||||
new = Grid(default.material[1:,1:,1:]+1,default.size*.9,np.ones(3)-default.origin,comments=['modified'])
|
||||
assert str(default.diff(new)) != ''
|
||||
|
||||
def test_repr(self,default):
|
||||
|
|
@ -54,36 +55,44 @@ class TestGeom:
|
|||
|
||||
def test_read_write_vtr(self,default,tmp_path):
|
||||
default.save(tmp_path/'default')
|
||||
new = Geom.load(tmp_path/'default.vtr')
|
||||
assert geom_equal(new,default)
|
||||
new = Grid.load(tmp_path/'default.vtr')
|
||||
assert grid_equal(new,default)
|
||||
|
||||
def test_invalid_vtr(self,tmp_path):
|
||||
def test_invalid_no_material(self,tmp_path):
|
||||
v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
|
||||
v.save(tmp_path/'no_materialpoint.vtr',parallel=False)
|
||||
with pytest.raises(ValueError):
|
||||
Geom.load(tmp_path/'no_materialpoint.vtr')
|
||||
Grid.load(tmp_path/'no_materialpoint.vtr')
|
||||
|
||||
def test_invalid_material(self):
|
||||
def test_invalid_spacing(self,tmp_path,default):
|
||||
default.save(tmp_path/'spacing_ok.vtr')
|
||||
vtk = VTK.load(tmp_path/'spacing_ok.vtr')
|
||||
vtk.vtk_data.SetXCoordinates(np_to_vtk(np.sort(np.random.random(default.cells[0]))))
|
||||
vtk.save(tmp_path/'invalid_spacing.vtr',parallel=False)
|
||||
with pytest.raises(ValueError):
|
||||
Grid.load(tmp_path/'invalid_spacing.vtr')
|
||||
|
||||
def test_invalid_material_type(self):
|
||||
with pytest.raises(TypeError):
|
||||
Geom(np.zeros((3,3,3),dtype='complex'),np.ones(3))
|
||||
Grid(np.zeros((3,3,3),dtype='complex'),np.ones(3))
|
||||
|
||||
def test_cast_to_int(self):
|
||||
g = Geom(np.zeros((3,3,3)),np.ones(3))
|
||||
g = Grid(np.zeros((3,3,3)),np.ones(3))
|
||||
assert g.material.dtype in np.sctypes['int']
|
||||
|
||||
def test_invalid_size(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
Geom(default.material[1:,1:,1:],
|
||||
Grid(default.material[1:,1:,1:],
|
||||
size=np.ones(2))
|
||||
|
||||
def test_save_load_ASCII(self,default,tmp_path):
|
||||
default.save_ASCII(tmp_path/'ASCII')
|
||||
default.material -= 1
|
||||
assert geom_equal(Geom.load_ASCII(tmp_path/'ASCII'),default)
|
||||
assert grid_equal(Grid.load_ASCII(tmp_path/'ASCII'),default)
|
||||
|
||||
def test_invalid_origin(self,default):
|
||||
with pytest.raises(ValueError):
|
||||
Geom(default.material[1:,1:,1:],
|
||||
Grid(default.material[1:,1:,1:],
|
||||
size=np.ones(3),
|
||||
origin=np.ones(4))
|
||||
|
||||
|
|
@ -91,14 +100,14 @@ class TestGeom:
|
|||
def test_invalid_materials_shape(self,default):
|
||||
material = np.ones((3,3))
|
||||
with pytest.raises(ValueError):
|
||||
Geom(material,
|
||||
Grid(material,
|
||||
size=np.ones(3))
|
||||
|
||||
|
||||
def test_invalid_materials_type(self,default):
|
||||
material = np.random.randint(1,300,(3,4,5))==1
|
||||
with pytest.raises(TypeError):
|
||||
Geom(material)
|
||||
Grid(material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('directions,reflect',[
|
||||
|
|
@ -113,7 +122,7 @@ class TestGeom:
|
|||
tag = f'directions_{"-".join(directions)}+reflect_{reflect}'
|
||||
reference = ref_path/f'mirror_{tag}.vtr'
|
||||
if update: modified.save(reference)
|
||||
assert geom_equal(Geom.load(reference),
|
||||
assert grid_equal(Grid.load(reference),
|
||||
modified)
|
||||
|
||||
|
||||
|
|
@ -135,17 +144,17 @@ class TestGeom:
|
|||
tag = f'directions_{"-".join(directions)}'
|
||||
reference = ref_path/f'flip_{tag}.vtr'
|
||||
if update: modified.save(reference)
|
||||
assert geom_equal(Geom.load(reference),
|
||||
assert grid_equal(Grid.load(reference),
|
||||
modified)
|
||||
|
||||
|
||||
def test_flip_invariant(self,default):
|
||||
assert geom_equal(default,default.flip([]))
|
||||
assert grid_equal(default,default.flip([]))
|
||||
|
||||
|
||||
@pytest.mark.parametrize('direction',[['x'],['x','y']])
|
||||
def test_flip_double(self,default,direction):
|
||||
assert geom_equal(default,default.flip(direction).flip(direction))
|
||||
assert grid_equal(default,default.flip(direction).flip(direction))
|
||||
|
||||
|
||||
@pytest.mark.parametrize('directions',[(1,2,'y'),('a','b','x'),[1]])
|
||||
|
|
@ -162,12 +171,12 @@ class TestGeom:
|
|||
reference = ref_path/f'clean_{stencil}_{"+".join(map(str,[None] if selection is None else selection))}_{periodic}'
|
||||
if update and stencil > 1:
|
||||
current.save(reference)
|
||||
assert geom_equal(Geom.load(reference) if stencil > 1 else default,
|
||||
assert grid_equal(Grid.load(reference) if stencil > 1 else default,
|
||||
current
|
||||
)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('grid',[
|
||||
@pytest.mark.parametrize('cells',[
|
||||
(10,11,10),
|
||||
[10,13,10],
|
||||
np.array((10,10,10)),
|
||||
|
|
@ -176,12 +185,12 @@ class TestGeom:
|
|||
np.array((10,20,2))
|
||||
]
|
||||
)
|
||||
def test_scale(self,default,update,ref_path,grid):
|
||||
modified = default.scale(grid)
|
||||
tag = f'grid_{util.srepr(grid,"-")}'
|
||||
def test_scale(self,default,update,ref_path,cells):
|
||||
modified = default.scale(cells)
|
||||
tag = f'grid_{util.srepr(cells,"-")}'
|
||||
reference = ref_path/f'scale_{tag}.vtr'
|
||||
if update: modified.save(reference)
|
||||
assert geom_equal(Geom.load(reference),
|
||||
assert grid_equal(Grid.load(reference),
|
||||
modified)
|
||||
|
||||
|
||||
|
|
@ -190,21 +199,21 @@ class TestGeom:
|
|||
for m in np.unique(material):
|
||||
material[material==m] = material.max() + np.random.randint(1,30)
|
||||
default.material -= 1
|
||||
modified = Geom(material,
|
||||
modified = Grid(material,
|
||||
default.size,
|
||||
default.origin)
|
||||
assert not geom_equal(modified,default)
|
||||
assert geom_equal(default,
|
||||
assert not grid_equal(modified,default)
|
||||
assert grid_equal(default,
|
||||
modified.renumber())
|
||||
|
||||
|
||||
def test_substitute(self,default):
|
||||
offset = np.random.randint(1,500)
|
||||
modified = Geom(default.material + offset,
|
||||
modified = Grid(default.material + offset,
|
||||
default.size,
|
||||
default.origin)
|
||||
assert not geom_equal(modified,default)
|
||||
assert geom_equal(default,
|
||||
assert not grid_equal(modified,default)
|
||||
assert grid_equal(default,
|
||||
modified.substitute(np.arange(default.material.max())+1+offset,
|
||||
np.arange(default.material.max())+1))
|
||||
|
||||
|
|
@ -212,12 +221,12 @@ class TestGeom:
|
|||
f = np.unique(default.material.flatten())[:np.random.randint(1,default.material.max())]
|
||||
t = np.random.permutation(f)
|
||||
modified = default.substitute(f,t)
|
||||
assert np.array_equiv(t,f) or (not geom_equal(modified,default))
|
||||
assert geom_equal(default, modified.substitute(t,f))
|
||||
assert np.array_equiv(t,f) or (not grid_equal(modified,default))
|
||||
assert grid_equal(default, modified.substitute(t,f))
|
||||
|
||||
def test_sort(self):
|
||||
grid = np.random.randint(5,20,3)
|
||||
m = Geom(np.random.randint(1,20,grid)*3,np.ones(3)).sort().material.flatten(order='F')
|
||||
cells = np.random.randint(5,20,3)
|
||||
m = Grid(np.random.randint(1,20,cells)*3,np.ones(3)).sort().material.flatten(order='F')
|
||||
for i,v in enumerate(m):
|
||||
assert i==0 or v > m[:i].max() or v in m[:i]
|
||||
|
||||
|
|
@ -227,7 +236,7 @@ class TestGeom:
|
|||
modified = default.copy()
|
||||
for i in range(np.rint(360/axis_angle[3]).astype(int)):
|
||||
modified.rotate(Rotation.from_axis_angle(axis_angle,degrees=True))
|
||||
assert geom_equal(default,modified)
|
||||
assert grid_equal(default,modified)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('Eulers',[[32.0,68.0,21.0],
|
||||
|
|
@ -237,15 +246,15 @@ class TestGeom:
|
|||
tag = f'Eulers_{util.srepr(Eulers,"-")}'
|
||||
reference = ref_path/f'rotate_{tag}.vtr'
|
||||
if update: modified.save(reference)
|
||||
assert geom_equal(Geom.load(reference),
|
||||
assert grid_equal(Grid.load(reference),
|
||||
modified)
|
||||
|
||||
|
||||
def test_canvas(self,default):
|
||||
grid = default.grid
|
||||
cells = default.cells
|
||||
grid_add = np.random.randint(0,30,(3))
|
||||
modified = default.canvas(grid + grid_add)
|
||||
assert np.all(modified.material[:grid[0],:grid[1],:grid[2]] == default.material)
|
||||
modified = default.canvas(cells + grid_add)
|
||||
assert np.all(modified.material[:cells[0],:cells[1],:cells[2]] == default.material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('center1,center2',[(np.random.random(3)*.5,np.random.random()*8),
|
||||
|
|
@ -263,8 +272,8 @@ class TestGeom:
|
|||
o = np.random.random(3)-.5
|
||||
g = np.random.randint(8,32,(3))
|
||||
s = np.random.random(3)+.5
|
||||
G_1 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
|
||||
G_2 = Geom(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
|
||||
G_1 = Grid(np.ones(g,'i'),s,o).add_primitive(diameter,center1,exponent)
|
||||
G_2 = Grid(np.ones(g,'i'),s,o).add_primitive(diameter,center2,exponent)
|
||||
assert np.count_nonzero(G_1.material!=2) == np.count_nonzero(G_2.material!=2)
|
||||
|
||||
|
||||
|
|
@ -279,9 +288,9 @@ class TestGeom:
|
|||
g = np.random.randint(8,32,(3))
|
||||
s = np.random.random(3)+.5
|
||||
fill = np.random.randint(10)+2
|
||||
G_1 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
|
||||
G_2 = Geom(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
|
||||
assert geom_equal(G_1,G_2)
|
||||
G_1 = Grid(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,inverse=inverse,periodic=periodic)
|
||||
G_2 = Grid(np.ones(g,'i'),s).add_primitive(.3,center,1,fill,Rotation.from_random(),inverse,periodic=periodic)
|
||||
assert grid_equal(G_1,G_2)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('trigger',[[1],[]])
|
||||
|
|
@ -300,9 +309,9 @@ class TestGeom:
|
|||
if len(trigger) > 0:
|
||||
m2[m==1] = 1
|
||||
|
||||
geom = Geom(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
|
||||
grid = Grid(m,np.random.rand(3)).vicinity_offset(vicinity,offset,trigger=trigger)
|
||||
|
||||
assert np.all(m2==geom.material)
|
||||
assert np.all(m2==grid.material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
|
|
@ -314,39 +323,39 @@ class TestGeom:
|
|||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
def test_tessellation_approaches(self,periodic):
|
||||
grid = np.random.randint(10,20,3)
|
||||
cells = np.random.randint(10,20,3)
|
||||
size = np.random.random(3) + 1.0
|
||||
N_seeds= np.random.randint(10,30)
|
||||
seeds = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
|
||||
Voronoi = Geom.from_Voronoi_tessellation( grid,size,seeds, np.arange(N_seeds)+5,periodic)
|
||||
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(N_seeds),np.arange(N_seeds)+5,periodic)
|
||||
assert geom_equal(Laguerre,Voronoi)
|
||||
Voronoi = Grid.from_Voronoi_tessellation( cells,size,seeds, np.arange(N_seeds)+5,periodic)
|
||||
Laguerre = Grid.from_Laguerre_tessellation(cells,size,seeds,np.ones(N_seeds),np.arange(N_seeds)+5,periodic)
|
||||
assert grid_equal(Laguerre,Voronoi)
|
||||
|
||||
|
||||
def test_Laguerre_weights(self):
|
||||
grid = np.random.randint(10,20,3)
|
||||
cells = np.random.randint(10,20,3)
|
||||
size = np.random.random(3) + 1.0
|
||||
N_seeds= np.random.randint(10,30)
|
||||
seeds = np.random.rand(N_seeds,3) * np.broadcast_to(size,(N_seeds,3))
|
||||
weights= np.full((N_seeds),-np.inf)
|
||||
ms = np.random.randint(N_seeds)
|
||||
weights[ms] = np.random.random()
|
||||
Laguerre = Geom.from_Laguerre_tessellation(grid,size,seeds,weights,periodic=np.random.random()>0.5)
|
||||
Laguerre = Grid.from_Laguerre_tessellation(cells,size,seeds,weights,periodic=np.random.random()>0.5)
|
||||
assert np.all(Laguerre.material == ms)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('approach',['Laguerre','Voronoi'])
|
||||
def test_tessellate_bicrystal(self,approach):
|
||||
grid = np.random.randint(5,10,3)*2
|
||||
size = grid.astype(np.float)
|
||||
cells = np.random.randint(5,10,3)*2
|
||||
size = cells.astype(np.float)
|
||||
seeds = np.vstack((size*np.array([0.5,0.25,0.5]),size*np.array([0.5,0.75,0.5])))
|
||||
material = np.zeros(grid)
|
||||
material[:,grid[1]//2:,:] = 1
|
||||
material = np.zeros(cells)
|
||||
material[:,cells[1]//2:,:] = 1
|
||||
if approach == 'Laguerre':
|
||||
geom = Geom.from_Laguerre_tessellation(grid,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
|
||||
grid = Grid.from_Laguerre_tessellation(cells,size,seeds,np.ones(2),periodic=np.random.random()>0.5)
|
||||
elif approach == 'Voronoi':
|
||||
geom = Geom.from_Voronoi_tessellation(grid,size,seeds, periodic=np.random.random()>0.5)
|
||||
assert np.all(geom.material == material)
|
||||
grid = Grid.from_Voronoi_tessellation(cells,size,seeds, periodic=np.random.random()>0.5)
|
||||
assert np.all(grid.material == material)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('surface',['Schwarz P',
|
||||
|
|
@ -363,14 +372,14 @@ class TestGeom:
|
|||
'Fisher-Koch S',
|
||||
])
|
||||
def test_minimal_surface_basic_properties(self,surface):
|
||||
grid = np.random.randint(60,100,3)
|
||||
size = np.ones(3)+np.random.rand(3)
|
||||
cells = np.random.randint(60,100,3)
|
||||
size = np.ones(3)+np.random.rand(3)
|
||||
threshold = 2*np.random.rand()-1.
|
||||
periods = np.random.randint(2)+1
|
||||
materials = np.random.randint(0,40,2)
|
||||
geom = Geom.from_minimal_surface(grid,size,surface,threshold,periods,materials)
|
||||
assert set(geom.material.flatten()) | set(materials) == set(materials) \
|
||||
and (geom.size == size).all() and (geom.grid == grid).all()
|
||||
grid = Grid.from_minimal_surface(cells,size,surface,threshold,periods,materials)
|
||||
assert set(grid.material.flatten()) | set(materials) == set(materials) \
|
||||
and (grid.size == size).all() and (grid.cells == cells).all()
|
||||
|
||||
@pytest.mark.parametrize('surface,threshold',[('Schwarz P',0),
|
||||
('Double Primitive',-1./6.),
|
||||
|
|
@ -386,36 +395,36 @@ class TestGeom:
|
|||
('Fisher-Koch S',0),
|
||||
])
|
||||
def test_minimal_surface_volume(self,surface,threshold):
|
||||
grid = np.ones(3,dtype=int)*64
|
||||
geom = Geom.from_minimal_surface(grid,np.ones(3),surface,threshold)
|
||||
assert np.isclose(np.count_nonzero(geom.material==1)/np.prod(geom.grid),.5,rtol=1e-3)
|
||||
cells = np.ones(3,dtype=int)*64
|
||||
grid = Grid.from_minimal_surface(cells,np.ones(3),surface,threshold)
|
||||
assert np.isclose(np.count_nonzero(grid.material==1)/np.prod(grid.cells),.5,rtol=1e-3)
|
||||
|
||||
|
||||
def test_from_table(self):
|
||||
grid = np.random.randint(60,100,3)
|
||||
cells = np.random.randint(60,100,3)
|
||||
size = np.ones(3)+np.random.rand(3)
|
||||
coords = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
|
||||
z=np.ones(grid.prod())
|
||||
z[grid[:2].prod()*int(grid[2]/2):]=0
|
||||
coords = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
|
||||
z=np.ones(cells.prod())
|
||||
z[cells[:2].prod()*int(cells[2]/2):]=0
|
||||
t = Table(np.column_stack((coords,z)),{'coords':3,'z':1})
|
||||
g = Geom.from_table(t,'coords',['1_coords','z'])
|
||||
assert g.N_materials == g.grid[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == grid[0]).all()
|
||||
g = Grid.from_table(t,'coords',['1_coords','z'])
|
||||
assert g.N_materials == g.cells[0]*2 and (g.material[:,:,-1]-g.material[:,:,0] == cells[0]).all()
|
||||
|
||||
|
||||
def test_from_table_recover(self,tmp_path):
|
||||
grid = np.random.randint(60,100,3)
|
||||
cells = np.random.randint(60,100,3)
|
||||
size = np.ones(3)+np.random.rand(3)
|
||||
s = seeds.from_random(size,np.random.randint(60,100))
|
||||
geom = Geom.from_Voronoi_tessellation(grid,size,s)
|
||||
coords = grid_filters.cell_coord0(grid,size)
|
||||
t = Table(np.column_stack((coords.reshape(-1,3,order='F'),geom.material.flatten(order='F'))),{'c':3,'m':1})
|
||||
assert geom_equal(geom.sort().renumber(),Geom.from_table(t,'c',['m']))
|
||||
grid = Grid.from_Voronoi_tessellation(cells,size,s)
|
||||
coords = grid_filters.coordinates0_point(cells,size)
|
||||
t = Table(np.column_stack((coords.reshape(-1,3,order='F'),grid.material.flatten(order='F'))),{'c':3,'m':1})
|
||||
assert grid_equal(grid.sort().renumber(),Grid.from_table(t,'c',['m']))
|
||||
|
||||
@pytest.mark.parametrize('periodic',[True,False])
|
||||
@pytest.mark.parametrize('direction',['x','y','z',['x','y'],'zy','xz',['x','y','z']])
|
||||
def test_get_grain_boundaries(self,update,ref_path,periodic,direction):
|
||||
geom=Geom.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current=geom.get_grain_boundaries(periodic,direction)
|
||||
grid=Grid.load(ref_path/'get_grain_boundaries_8g12x15x20.vtr')
|
||||
current=grid.get_grain_boundaries(periodic,direction)
|
||||
if update:
|
||||
current.save(ref_path/f'get_grain_boundaries_8g12x15x20_{direction}_{periodic}.vtu',parallel=False)
|
||||
reference=VTK.load(ref_path/f'get_grain_boundaries_8g12x15x20_{"".join(direction)}_{periodic}.vtu')
|
||||
|
|
@ -169,7 +169,7 @@ class TestResult:
|
|||
|
||||
@pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]])
|
||||
def test_add_IPF_color(self,default,d):
|
||||
default.add_IPF_color('O',np.array(d))
|
||||
default.add_IPF_color(d,'O')
|
||||
loc = {'O': default.get_dataset_location('O'),
|
||||
'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
|
||||
qu = default.read_dataset(loc['O']).view(np.double).squeeze()
|
||||
|
|
@ -356,11 +356,11 @@ class TestResult:
|
|||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
def test_coordinates(self,default,mode):
|
||||
if mode == 'cell':
|
||||
a = grid_filters.cell_coord0(default.grid,default.size,default.origin)
|
||||
b = default.cell_coordinates.reshape(tuple(default.grid)+(3,),order='F')
|
||||
a = grid_filters.coordinates0_point(default.cells,default.size,default.origin)
|
||||
b = default.coordinates0_point.reshape(tuple(default.cells)+(3,),order='F')
|
||||
elif mode == 'node':
|
||||
a = grid_filters.node_coord0(default.grid,default.size,default.origin)
|
||||
b = default.node_coordinates.reshape(tuple(default.grid+1)+(3,),order='F')
|
||||
a = grid_filters.coordinates0_node(default.cells,default.size,default.origin)
|
||||
b = default.coordinates0_node.reshape(tuple(default.cells+1)+(3,),order='F')
|
||||
assert np.allclose(a,b)
|
||||
|
||||
@pytest.mark.parametrize('output',['F',[],['F','P']])
|
||||
|
|
|
|||
|
|
@ -800,6 +800,14 @@ class TestRotation:
|
|||
print(f'append 2x {shape} --> {s.shape}')
|
||||
assert s[0,...] == r[0,...] and s[-1,...] == p[-1,...]
|
||||
|
||||
@pytest.mark.parametrize('shape',[None,1,(1,),(4,2),(3,3,2)])
|
||||
def test_append_list(self,shape):
|
||||
r = Rotation.from_random(shape=shape)
|
||||
p = Rotation.from_random(shape=shape)
|
||||
s = r.append([r,p])
|
||||
print(f'append 3x {shape} --> {s.shape}')
|
||||
assert s[0,...] == r[0,...] and s[-1,...] == p[-1,...]
|
||||
|
||||
@pytest.mark.parametrize('quat,standardized',[
|
||||
([-1,0,0,0],[1,0,0,0]),
|
||||
([-0.5,-0.5,-0.5,-0.5],[0.5,0.5,0.5,0.5]),
|
||||
|
|
@ -1022,7 +1030,7 @@ class TestRotation:
|
|||
rng = tuple(zip(np.zeros(3),limits))
|
||||
|
||||
weights = Table.load(ref_path/'ODF_experimental_cell.txt').get('intensity').flatten()
|
||||
Eulers = grid_filters.cell_coord0(steps,limits)
|
||||
Eulers = grid_filters.coordinates0_point(steps,limits)
|
||||
Eulers = np.radians(Eulers) if not degrees else Eulers
|
||||
|
||||
Eulers_r = Rotation.from_ODF(weights,Eulers.reshape(-1,3,order='F'),N,degrees,fractions).as_Euler_angles(True)
|
||||
|
|
@ -1040,7 +1048,7 @@ class TestRotation:
|
|||
weights = Table.load(ref_path/'ODF_experimental.txt').get('intensity')
|
||||
weights = weights.reshape(steps+1,order='F')[:-1,:-1,:-1].reshape(-1,order='F')
|
||||
|
||||
Eulers = grid_filters.node_coord0(steps,limits)[:-1,:-1,:-1]
|
||||
Eulers = grid_filters.coordinates0_node(steps,limits)[:-1,:-1,:-1]
|
||||
Eulers = np.radians(Eulers) if not degrees else Eulers
|
||||
|
||||
Eulers_r = Rotation.from_ODF(weights,Eulers.reshape(-1,3,order='F'),N,degrees).as_Euler_angles(True)
|
||||
|
|
|
|||
|
|
@ -8,7 +8,7 @@ from damask import Table
|
|||
def default():
|
||||
"""Simple Table."""
|
||||
x = np.ones((5,13),dtype=float)
|
||||
return Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['test data','contains only ones'])
|
||||
return Table(x,{'F':(3,3),'v':(3,),'s':(1,)},['test data','contains five rows of only ones'])
|
||||
|
||||
@pytest.fixture
|
||||
def ref_path(ref_path_base):
|
||||
|
|
@ -20,8 +20,9 @@ class TestTable:
|
|||
def test_repr(self,default):
|
||||
print(default)
|
||||
|
||||
def test_len(self):
|
||||
len(Table(np.random.rand(7,3),{'X':3})) == 7
|
||||
@pytest.mark.parametrize('N',[10,40])
|
||||
def test_len(self,N):
|
||||
assert len(Table(np.random.rand(N,3),{'X':3})) == N
|
||||
|
||||
def test_get_scalar(self,default):
|
||||
d = default.get('s')
|
||||
|
|
@ -39,6 +40,10 @@ class TestTable:
|
|||
d = default.get('5_F')
|
||||
assert np.allclose(d,1.0) and d.shape[1:] == (1,)
|
||||
|
||||
@pytest.mark.parametrize('N',[10,40])
|
||||
def test_getitem(self,N):
|
||||
assert len(Table(np.random.rand(N,1),{'X':1})[:N//2]) == N//2
|
||||
|
||||
@pytest.mark.parametrize('mode',['str','path'])
|
||||
def test_write_read(self,default,tmp_path,mode):
|
||||
default.save(tmp_path/'default.txt')
|
||||
|
|
|
|||
|
|
@ -16,9 +16,9 @@ def ref_path(ref_path_base):
|
|||
@pytest.fixture
|
||||
def default():
|
||||
"""Simple VTK."""
|
||||
grid = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
return VTK.from_rectilinear_grid(grid,size)
|
||||
cells = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
return VTK.from_rectilinear_grid(cells,size)
|
||||
|
||||
class TestVTK:
|
||||
|
||||
|
|
@ -27,10 +27,10 @@ class TestVTK:
|
|||
print('patched damask.util.execution_stamp')
|
||||
|
||||
def test_rectilinearGrid(self,tmp_path):
|
||||
grid = np.random.randint(5,10,3)*2
|
||||
cells = np.random.randint(5,10,3)*2
|
||||
size = np.random.random(3) + 1.0
|
||||
origin = np.random.random(3)
|
||||
v = VTK.from_rectilinear_grid(grid,size,origin)
|
||||
v = VTK.from_rectilinear_grid(cells,size,origin)
|
||||
string = v.__repr__()
|
||||
v.save(tmp_path/'rectilinearGrid',False)
|
||||
vtr = VTK.load(tmp_path/'rectilinearGrid.vtr')
|
||||
|
|
@ -152,11 +152,11 @@ class TestVTK:
|
|||
np.allclose(polyData.get('coordinates'),points)
|
||||
|
||||
def test_compare_reference_rectilinearGrid(self,update,ref_path,tmp_path):
|
||||
grid = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
rectilinearGrid = VTK.from_rectilinear_grid(grid,size)
|
||||
c = grid_filters.cell_coord0(grid,size).reshape(-1,3,order='F')
|
||||
n = grid_filters.node_coord0(grid,size).reshape(-1,3,order='F')
|
||||
cells = np.array([5,6,7],int)
|
||||
size = np.array([.6,1.,.5])
|
||||
rectilinearGrid = VTK.from_rectilinear_grid(cells,size)
|
||||
c = grid_filters.coordinates0_point(cells,size).reshape(-1,3,order='F')
|
||||
n = grid_filters.coordinates0_node(cells,size).reshape(-1,3,order='F')
|
||||
rectilinearGrid.add(c,'cell')
|
||||
rectilinearGrid.add(n,'node')
|
||||
if update:
|
||||
|
|
|
|||
|
|
@ -5,124 +5,124 @@ from damask import grid_filters
|
|||
|
||||
class TestGridFilters:
|
||||
|
||||
def test_cell_coord0(self):
|
||||
def test_coordinates0_point(self):
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.cell_coord0(grid,size)
|
||||
assert np.allclose(coord[0,0,0],size/grid*.5) and coord.shape == tuple(grid) + (3,)
|
||||
cells = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.coordinates0_point(cells,size)
|
||||
assert np.allclose(coord[0,0,0],size/cells*.5) and coord.shape == tuple(cells) + (3,)
|
||||
|
||||
def test_node_coord0(self):
|
||||
def test_coordinates0_node(self):
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.node_coord0(grid,size)
|
||||
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(grid+1) + (3,)
|
||||
cells = np.random.randint(8,32,(3))
|
||||
coord = grid_filters.coordinates0_node(cells,size)
|
||||
assert np.allclose(coord[-1,-1,-1],size) and coord.shape == tuple(cells+1) + (3,)
|
||||
|
||||
def test_coord0(self):
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
c = grid_filters.cell_coord0(grid+1,size+size/grid)
|
||||
n = grid_filters.node_coord0(grid,size) + size/grid*.5
|
||||
cells = np.random.randint(8,32,(3))
|
||||
c = grid_filters.coordinates0_point(cells+1,size+size/cells)
|
||||
n = grid_filters.coordinates0_node(cells,size) + size/cells*.5
|
||||
assert np.allclose(c,n)
|
||||
|
||||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
@pytest.mark.parametrize('mode',['point','node'])
|
||||
def test_grid_DNA(self,mode):
|
||||
"""Ensure that xx_coord0_gridSizeOrigin is the inverse of xx_coord0."""
|
||||
grid = np.random.randint(8,32,(3))
|
||||
"""Ensure that cellsSizeOrigin_coordinates0_xx is the inverse of coordinates0_xx."""
|
||||
cells = np.random.randint(8,32,(3))
|
||||
size = np.random.random(3)
|
||||
origin = np.random.random(3)
|
||||
coord0 = eval(f'grid_filters.{mode}_coord0(grid,size,origin)') # noqa
|
||||
_grid,_size,_origin = eval(f'grid_filters.{mode}_coord0_gridSizeOrigin(coord0.reshape(-1,3,order="F"))')
|
||||
assert np.allclose(grid,_grid) and np.allclose(size,_size) and np.allclose(origin,_origin)
|
||||
coord0 = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)') # noqa
|
||||
_cells,_size,_origin = eval(f'grid_filters.cellsSizeOrigin_coordinates0_{mode}(coord0.reshape(-1,3,order="F"))')
|
||||
assert np.allclose(cells,_cells) and np.allclose(size,_size) and np.allclose(origin,_origin)
|
||||
|
||||
def test_displacement_fluct_equivalence(self):
|
||||
"""Ensure that fluctuations are periodic."""
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(grid)+(3,3))
|
||||
assert np.allclose(grid_filters.node_displacement_fluct(size,F),
|
||||
grid_filters.cell_2_node(grid_filters.cell_displacement_fluct(size,F)))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(cells)+(3,3))
|
||||
assert np.allclose(grid_filters.displacement_fluct_node(size,F),
|
||||
grid_filters.point_to_node(grid_filters.displacement_fluct_point(size,F)))
|
||||
|
||||
def test_interpolation_to_node(self):
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(grid)+(3,3))
|
||||
assert np.allclose(grid_filters.node_coord(size,F) [1:-1,1:-1,1:-1],
|
||||
grid_filters.cell_2_node(grid_filters.cell_coord(size,F))[1:-1,1:-1,1:-1])
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(cells)+(3,3))
|
||||
assert np.allclose(grid_filters.coordinates_node(size,F) [1:-1,1:-1,1:-1],
|
||||
grid_filters.point_to_node(grid_filters.coordinates_point(size,F))[1:-1,1:-1,1:-1])
|
||||
|
||||
def test_interpolation_to_cell(self):
|
||||
grid = np.random.randint(1,30,(3))
|
||||
cells = np.random.randint(1,30,(3))
|
||||
|
||||
node_coord_x = np.linspace(0,np.pi*2,num=grid[0]+1)
|
||||
node_field_x = np.cos(node_coord_x)
|
||||
node_field = np.broadcast_to(node_field_x.reshape(-1,1,1),grid+1)
|
||||
coordinates_node_x = np.linspace(0,np.pi*2,num=cells[0]+1)
|
||||
node_field_x = np.cos(coordinates_node_x)
|
||||
node_field = np.broadcast_to(node_field_x.reshape(-1,1,1),cells+1)
|
||||
|
||||
cell_coord_x = node_coord_x[:-1]+node_coord_x[1]*.5
|
||||
cell_field_x = np.interp(cell_coord_x,node_coord_x,node_field_x,period=np.pi*2.)
|
||||
cell_field = np.broadcast_to(cell_field_x.reshape(-1,1,1),grid)
|
||||
coordinates0_point_x = coordinates_node_x[:-1]+coordinates_node_x[1]*.5
|
||||
cell_field_x = np.interp(coordinates0_point_x,coordinates_node_x,node_field_x,period=np.pi*2.)
|
||||
cell_field = np.broadcast_to(cell_field_x.reshape(-1,1,1),cells)
|
||||
|
||||
assert np.allclose(cell_field,grid_filters.node_2_cell(node_field))
|
||||
assert np.allclose(cell_field,grid_filters.node_2_point(node_field))
|
||||
|
||||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
def test_coord0_origin(self,mode):
|
||||
@pytest.mark.parametrize('mode',['point','node'])
|
||||
def test_coordinates0_origin(self,mode):
|
||||
origin= np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
grid = np.random.randint(8,32,(3))
|
||||
shifted = eval(f'grid_filters.{mode}_coord0(grid,size,origin)')
|
||||
unshifted = eval(f'grid_filters.{mode}_coord0(grid,size)')
|
||||
cells = np.random.randint(8,32,(3))
|
||||
shifted = eval(f'grid_filters.coordinates0_{mode}(cells,size,origin)')
|
||||
unshifted = eval(f'grid_filters.coordinates0_{mode}(cells,size)')
|
||||
if mode == 'cell':
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid) +(3,)))
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(cells) +(3,)))
|
||||
elif mode == 'node':
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid+1)+(3,)))
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(cells+1)+(3,)))
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.cell_displacement_avg,
|
||||
grid_filters.node_displacement_avg])
|
||||
@pytest.mark.parametrize('function',[grid_filters.displacement_avg_point,
|
||||
grid_filters.displacement_avg_node])
|
||||
def test_displacement_avg_vanishes(self,function):
|
||||
"""Ensure that random fluctuations in F do not result in average displacement."""
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(grid)+(3,3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(cells)+(3,3))
|
||||
F += np.eye(3) - np.average(F,axis=(0,1,2))
|
||||
assert np.allclose(function(size,F),0.0)
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.cell_displacement_fluct,
|
||||
grid_filters.node_displacement_fluct])
|
||||
@pytest.mark.parametrize('function',[grid_filters.displacement_fluct_point,
|
||||
grid_filters.displacement_fluct_node])
|
||||
def test_displacement_fluct_vanishes(self,function):
|
||||
"""Ensure that constant F does not result in fluctuating displacement."""
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.random.random((3,3)), tuple(cells)+(3,3))
|
||||
assert np.allclose(function(size,F),0.0)
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.coord0_check,
|
||||
grid_filters.node_coord0_gridSizeOrigin,
|
||||
grid_filters.cell_coord0_gridSizeOrigin])
|
||||
@pytest.mark.parametrize('function',[grid_filters.coordinates0_check,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_node,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_point])
|
||||
def test_invalid_coordinates(self,function):
|
||||
invalid_coordinates = np.random.random((np.random.randint(12,52),3))
|
||||
with pytest.raises(ValueError):
|
||||
function(invalid_coordinates)
|
||||
|
||||
@pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin,
|
||||
grid_filters.cell_coord0_gridSizeOrigin])
|
||||
@pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_node,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_point])
|
||||
def test_uneven_spaced_coordinates(self,function):
|
||||
start = np.random.random(3)
|
||||
end = np.random.random(3)*10. + start
|
||||
grid = np.random.randint(8,32,(3))
|
||||
uneven = np.stack(np.meshgrid(np.logspace(start[0],end[0],grid[0]),
|
||||
np.logspace(start[1],end[1],grid[1]),
|
||||
np.logspace(start[2],end[2],grid[2]),indexing = 'ij'),
|
||||
axis = -1).reshape((grid.prod(),3),order='F')
|
||||
cells = np.random.randint(8,32,(3))
|
||||
uneven = np.stack(np.meshgrid(np.logspace(start[0],end[0],cells[0]),
|
||||
np.logspace(start[1],end[1],cells[1]),
|
||||
np.logspace(start[2],end[2],cells[2]),indexing = 'ij'),
|
||||
axis = -1).reshape((cells.prod(),3),order='F')
|
||||
with pytest.raises(ValueError):
|
||||
function(uneven)
|
||||
|
||||
|
||||
@pytest.mark.parametrize('mode',[True,False])
|
||||
@pytest.mark.parametrize('function',[grid_filters.node_coord0_gridSizeOrigin,
|
||||
grid_filters.cell_coord0_gridSizeOrigin])
|
||||
@pytest.mark.parametrize('function',[grid_filters.cellsSizeOrigin_coordinates0_node,
|
||||
grid_filters.cellsSizeOrigin_coordinates0_point])
|
||||
def test_unordered_coordinates(self,function,mode):
|
||||
origin = np.random.random(3)
|
||||
size = np.random.random(3)*10.+origin
|
||||
grid = np.random.randint(8,32,(3))
|
||||
unordered = grid_filters.node_coord0(grid,size,origin).reshape(-1,3)
|
||||
cells = np.random.randint(8,32,(3))
|
||||
unordered = grid_filters.coordinates0_node(cells,size,origin).reshape(-1,3)
|
||||
if mode:
|
||||
with pytest.raises(ValueError):
|
||||
function(unordered,mode)
|
||||
|
|
@ -131,9 +131,9 @@ class TestGridFilters:
|
|||
|
||||
def test_regrid(self):
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.eye(3), tuple(grid)+(3,3))
|
||||
assert all(grid_filters.regrid(size,F,grid) == np.arange(grid.prod()))
|
||||
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()))
|
||||
|
||||
|
||||
@pytest.mark.parametrize('differential_operator',[grid_filters.curl,
|
||||
|
|
@ -141,14 +141,14 @@ class TestGridFilters:
|
|||
grid_filters.gradient])
|
||||
def test_differential_operator_constant(self,differential_operator):
|
||||
size = np.random.random(3)+1.0
|
||||
grid = np.random.randint(8,32,(3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
shapes = {
|
||||
grid_filters.curl: [(3,),(3,3)],
|
||||
grid_filters.divergence:[(3,),(3,3)],
|
||||
grid_filters.gradient: [(1,),(3,)]
|
||||
}
|
||||
for shape in shapes[differential_operator]:
|
||||
field = np.ones(tuple(grid)+shape)*np.random.random()*1.0e5
|
||||
field = np.ones(tuple(cells)+shape)*np.random.random()*1.0e5
|
||||
assert np.allclose(differential_operator(size,field),0.0)
|
||||
|
||||
|
||||
|
|
@ -190,15 +190,15 @@ class TestGridFilters:
|
|||
@pytest.mark.parametrize('field_def,grad_def',grad_test_data)
|
||||
def test_grad(self,field_def,grad_def):
|
||||
size = np.random.random(3)+1.0
|
||||
grid = np.random.randint(8,32,(3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
|
||||
nodes = grid_filters.cell_coord0(grid,size)
|
||||
nodes = grid_filters.coordinates0_point(cells,size)
|
||||
my_locals = locals() # needed for list comprehension
|
||||
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),grid) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(grid) + ((3,) if len(field_def)==3 else (1,)))
|
||||
grad = np.stack([np.broadcast_to(eval(c,globals(),my_locals),grid) for c in grad_def], axis=-1)
|
||||
grad = grad.reshape(tuple(grid) + ((3,3) if len(grad_def)==9 else (3,)))
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),cells) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(cells) + ((3,) if len(field_def)==3 else (1,)))
|
||||
grad = np.stack([np.broadcast_to(eval(c,globals(),my_locals),cells) for c in grad_def], axis=-1)
|
||||
grad = grad.reshape(tuple(cells) + ((3,3) if len(grad_def)==9 else (3,)))
|
||||
|
||||
assert np.allclose(grad,grid_filters.gradient(size,field))
|
||||
|
||||
|
|
@ -250,15 +250,15 @@ class TestGridFilters:
|
|||
@pytest.mark.parametrize('field_def,curl_def',curl_test_data)
|
||||
def test_curl(self,field_def,curl_def):
|
||||
size = np.random.random(3)+1.0
|
||||
grid = np.random.randint(8,32,(3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
|
||||
nodes = grid_filters.cell_coord0(grid,size)
|
||||
nodes = grid_filters.coordinates0_point(cells,size)
|
||||
my_locals = locals() # needed for list comprehension
|
||||
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),grid) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(grid) + ((3,3) if len(field_def)==9 else (3,)))
|
||||
curl = np.stack([np.broadcast_to(eval(c,globals(),my_locals),grid) for c in curl_def], axis=-1)
|
||||
curl = curl.reshape(tuple(grid) + ((3,3) if len(curl_def)==9 else (3,)))
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),cells) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(cells) + ((3,3) if len(field_def)==9 else (3,)))
|
||||
curl = np.stack([np.broadcast_to(eval(c,globals(),my_locals),cells) for c in curl_def], axis=-1)
|
||||
curl = curl.reshape(tuple(cells) + ((3,3) if len(curl_def)==9 else (3,)))
|
||||
|
||||
assert np.allclose(curl,grid_filters.curl(size,field))
|
||||
|
||||
|
|
@ -303,17 +303,17 @@ class TestGridFilters:
|
|||
|
||||
def test_div(self,field_def,div_def):
|
||||
size = np.random.random(3)+1.0
|
||||
grid = np.random.randint(8,32,(3))
|
||||
cells = np.random.randint(8,32,(3))
|
||||
|
||||
nodes = grid_filters.cell_coord0(grid,size)
|
||||
nodes = grid_filters.coordinates0_point(cells,size)
|
||||
my_locals = locals() # needed for list comprehension
|
||||
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),grid) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(grid) + ((3,3) if len(field_def)==9 else (3,)))
|
||||
div = np.stack([np.broadcast_to(eval(c,globals(),my_locals),grid) for c in div_def], axis=-1)
|
||||
field = np.stack([np.broadcast_to(eval(f,globals(),my_locals),cells) for f in field_def],axis=-1)
|
||||
field = field.reshape(tuple(cells) + ((3,3) if len(field_def)==9 else (3,)))
|
||||
div = np.stack([np.broadcast_to(eval(c,globals(),my_locals),cells) for c in div_def], axis=-1)
|
||||
if len(div_def)==3:
|
||||
div = div.reshape(tuple(grid) + ((3,)))
|
||||
div = div.reshape(tuple(cells) + ((3,)))
|
||||
else:
|
||||
div=div.reshape(tuple(grid))
|
||||
div=div.reshape(tuple(cells))
|
||||
|
||||
assert np.allclose(div,grid_filters.divergence(size,field))
|
||||
|
|
|
|||
Some files were not shown because too many files have changed in this diff Show More
Loading…
Reference in New Issue