Merge branch 'misc-improvements' into 'development'

polishing

See merge request damask/DAMASK!497
This commit is contained in:
Franz Roters 2022-01-11 15:45:09 +00:00
commit 76fe2d2b36
11 changed files with 139 additions and 110 deletions

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@ -45,7 +45,7 @@ variables:
MPI_INTEL: "MPI/Intel/2022.0.1/IntelMPI/2021.5.0" MPI_INTEL: "MPI/Intel/2022.0.1/IntelMPI/2021.5.0"
# ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # ++++++++++++ PETSc ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1" PETSC_GNU: "Libraries/PETSc/3.16.1/GNU-10-OpenMPI-4.1.1"
PETSC_INTELLLVM: "Libraries/PETSc/3.16.2/oneAPI-2022.0.1-IntelMPI-2021.5.0" PETSC_INTELLLVM: "Libraries/PETSc/3.16.3/oneAPI-2022.0.1-IntelMPI-2021.5.0"
PETSC_INTEL: "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0" PETSC_INTEL: "Libraries/PETSc/3.16.2/Intel-2022.0.1-IntelMPI-2021.5.0"
# ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ # ++++++++++++ MSC Marc +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
MSC: "FEM/MSC/2021.3.1" MSC: "FEM/MSC/2021.3.1"

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@ -10,7 +10,7 @@ endif()
# Dummy project to determine compiler names and version # Dummy project to determine compiler names and version
project(Prerequisites LANGUAGES) project(Prerequisites LANGUAGES)
set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig") set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig")
pkg_check_modules(PETSC REQUIRED PETSc>=3.12.0 PETSc<3.17.0) pkg_search_module(PETSC REQUIRED PETSc>=3.12.0 PETSc<3.17.0)
pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler) pkg_get_variable(CMAKE_Fortran_COMPILER PETSc fcompiler)
pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler) pkg_get_variable(CMAKE_C_COMPILER PETSc ccompiler)
@ -88,16 +88,12 @@ else()
message(FATAL_ERROR "Compiler type(CMAKE_Fortran_COMPILER_ID) not recognized") message(FATAL_ERROR "Compiler type(CMAKE_Fortran_COMPILER_ID) not recognized")
endif() endif()
file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_EXTERNAL_LIB REGEX "PETSC_WITH_EXTERNAL_LIB = .*$?") file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_EXTERNAL_LIB REGEX "PETSC_EXTERNAL_LIB_BASIC = .*$?")
string(REGEX MATCHALL "-[lLW]([^\" ]+)" PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}") string(REPLACE "PETSC_EXTERNAL_LIB_BASIC = " "" PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}")
list(REMOVE_DUPLICATES PETSC_EXTERNAL_LIB)
string(REPLACE ";" " " PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB}")
message("PETSC_EXTERNAL_LIB:\n${PETSC_EXTERNAL_LIB}\n") message("PETSC_EXTERNAL_LIB:\n${PETSC_EXTERNAL_LIB}\n")
file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_INCLUDES REGEX "PETSC_FC_INCLUDES = .*$?") file(STRINGS "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/petsc/conf/petscvariables" PETSC_INCLUDES REGEX "PETSC_FC_INCLUDES = .*$?")
string(REGEX MATCHALL "-I([^\" ]+)" PETSC_INCLUDES "${PETSC_INCLUDES}") string(REPLACE "PETSC_FC_INCLUDES = " "" PETSC_INCLUDES "${PETSC_INCLUDES}")
list(REMOVE_DUPLICATES PETSC_INCLUDES)
string(REPLACE ";" " " PETSC_INCLUDES "${PETSC_INCLUDES}")
message("PETSC_INCLUDES:\n${PETSC_INCLUDES}\n") message("PETSC_INCLUDES:\n${PETSC_INCLUDES}\n")
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${BUILDCMD_PRE} ${OPENMP_FLAGS} ${STANDARD_CHECK} ${OPTIMIZATION_FLAGS} ${COMPILE_FLAGS} ${PRECISION_FLAGS}") set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${BUILDCMD_PRE} ${OPENMP_FLAGS} ${STANDARD_CHECK} ${OPTIMIZATION_FLAGS} ${COMPILE_FLAGS} ${PRECISION_FLAGS}")
@ -109,7 +105,7 @@ if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
endif() endif()
set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}") set(CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE} "${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}} ${PETSC_INCLUDES} ${BUILDCMD_POST}")
set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> ${PETSC_EXTERNAL_LIB} -lz ${BUILDCMD_POST}") set(CMAKE_Fortran_LINK_EXECUTABLE "${CMAKE_Fortran_LINK_EXECUTABLE} <OBJECTS> -o <TARGET> <LINK_LIBRARIES> -L${PETSC_LIBRARY_DIRS} -lpetsc ${PETSC_EXTERNAL_LIB} -lz ${BUILDCMD_POST}")
message("Fortran Compiler Flags:\n${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}}\n") message("Fortran Compiler Flags:\n${CMAKE_Fortran_FLAGS_${CMAKE_BUILD_TYPE}}\n")
message("C Compiler Flags:\n${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}\n") message("C Compiler Flags:\n${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}\n")

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

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

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

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@ -114,12 +114,13 @@ class Crystal():
def __repr__(self): def __repr__(self):
"""Represent.""" """Represent."""
return '\n'.join([f'Crystal family {self.family}'] family = f'Crystal family: {self.family}'
+ ([] if self.lattice is None else [f'Bravais lattice {self.lattice}']+ return family if self.lattice is None else \
list(map(lambda x:f'{x[0]}: {x[1]:.5g}', '\n'.join([family,
zip(['a','b','c','α','β','γ',], f'Bravais lattice: {self.lattice}',
self.parameters)))) 'a={:.5g}m, b={:.5g}m, c={:.5g}m'.format(*self.parameters[:3]),
) 'α={:.5g}°, β={:.5g}°, γ={:.5g}°'.format(*np.degrees(self.parameters[3:]))])
def __eq__(self,other): def __eq__(self,other):
""" """
@ -543,6 +544,73 @@ class Crystal():
[ 1,-2, 1,-3, 1,-2, 1, 2], [ 1,-2, 1,-3, 1,-2, 1, 2],
[ 2,-1,-1,-3, 2,-1,-1, 2]])] [ 2,-1,-1,-3, 2,-1,-1, 2]])]
}, },
'tI': {
'slip': [np.array([
[+0,+0,+1, +1,+0,+0],
[+0,+0,+1, +0,+1,+0]]),
np.array([
[+0,+0,+1, +1,+1,+0],
[+0,+0,+1, -1,+1,+0]]),
np.array([
[+0,+1,+0, +1,+0,+0],
[+1,+0,+0, +0,+1,+0]]),
np.array([
[+1,-1,+1, +1,+1,+0],
[+1,-1,-1, +1,+1,+0],
[-1,-1,-1, -1,+1,+0],
[-1,-1,+1, -1,+1,+0]]),
np.array([
[+1,-1,+0, +1,+1,+0],
[+1,+1,+0, +1,-1,+0]]),
np.array([
[+0,+1,+1, +1,+0,+0],
[+0,-1,+1, +1,+0,+0],
[-1,+0,+1, +0,+1,+0],
[+1,+0,+1, +0,+1,+0]]),
np.array([
[+0,+1,+0, +0,+0,+1],
[+1,+0,+0, +0,+0,+1]]),
np.array([
[+1,+1,+0, +0,+0,+1],
[-1,+1,+0, +0,+0,+1]]),
np.array([
[+0,+1,-1, +0,+1,+1],
[+0,-1,-1, +0,-1,+1],
[-1,+0,-1, -1,+0,+1],
[+1,+0,-1, +1,+0,+1]]),
np.array([
[+1,-1,+1, +0,+1,+1],
[+1,+1,-1, +0,+1,+1],
[+1,+1,+1, +0,+1,-1],
[-1,+1,+1, +0,+1,-1],
[+1,-1,-1, +1,+0,+1],
[-1,-1,+1, +1,+0,+1],
[+1,+1,+1, +1,+0,-1],
[+1,-1,+1, +1,+0,-1]]),
np.array([
[+1,+0,+0, +0,+1,+1],
[+1,+0,+0, +0,+1,-1],
[+0,+1,+0, +1,+0,+1],
[+0,+1,+0, +1,+0,-1]]),
np.array([
[+0,+1,-1, +2,+1,+1],
[+0,-1,-1, +2,-1,+1],
[+1,+0,-1, +1,+2,+1],
[-1,+0,-1, -1,+2,+1],
[+0,+1,-1, -2,+1,+1],
[+0,-1,-1, -2,-1,+1],
[-1,+0,-1, -1,-2,+1],
[+1,+0,-1, +1,-2,+1]]),
np.array([
[-1,+1,+1, +2,+1,+1],
[-1,-1,+1, +2,-1,+1],
[+1,-1,+1, +1,+2,+1],
[-1,-1,+1, -1,+2,+1],
[+1,+1,+1, -2,+1,+1],
[+1,-1,+1, -2,-1,+1],
[-1,+1,+1, -1,-2,+1],
[+1,+1,+1, +1,-2,+1]])]
}
} }
master = _kinematics[self.lattice][mode] master = _kinematics[self.lattice][mode]
if self.lattice == 'hP': if self.lattice == 'hP':

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@ -514,6 +514,17 @@ class Orientation(Rotation,Crystal):
[ 0.07359167 -0.36505797 0.92807163]] [ 0.07359167 -0.36505797 0.92807163]]
Bunge Eulers / deg: (11.40, 21.86, 0.60) Bunge Eulers / deg: (11.40, 21.86, 0.60)
Plot a sample from the Mackenzie distribution.
>>> import matplotlib.pyplot as plt
>>> import damask
>>> N = 10000
>>> a = damask.Orientation.from_random(shape=N,family='cubic')
>>> b = damask.Orientation.from_random(shape=N,family='cubic')
>>> d = a.disorientation(b).as_axis_angle(degrees=True,pair=True)[1]
>>> plt.hist(d,25)
>>> plt.show()
""" """
if self.family != other.family: if self.family != other.family:
raise NotImplementedError('disorientation between different crystal families') raise NotImplementedError('disorientation between different crystal families')

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

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

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@ -30,7 +30,7 @@ module subroutine elastic_init(phases)
phase, & phase, &
mech, & mech, &
elastic elastic
logical :: thermal_active
print'(/,1x,a)', '<<<+- phase:mechanical:elastic init -+>>>' print'(/,1x,a)', '<<<+- phase:mechanical:elastic init -+>>>'
print'(/,1x,a)', '<<<+- phase:mechanical:elastic:Hooke init -+>>>' print'(/,1x,a)', '<<<+- phase:mechanical:elastic:Hooke init -+>>>'

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