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Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development

This commit is contained in:
Philip Eisenlohr 2016-04-27 09:28:51 -04:00
parent b3e9877058 02021b9bb0
commit 426658eb36
14 changed files with 145 additions and 102 deletions
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2
VERSION
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@ -1 +1 @@
v2.0.0-160-g26f437b
v2.0.0-201-gd497503

7
code/crystallite.f90
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@ -3962,7 +3962,6 @@ subroutine crystallite_orientations
use plastic_nonlocal, only: &
plastic_nonlocal_updateCompatibility
implicit none
integer(pInt) &
c, & !< counter in integration point component loop
@ -3978,16 +3977,15 @@ subroutine crystallite_orientations
! --- CALCULATE ORIENTATION AND LATTICE ROTATION ---
nonlocalPresent: if (any(plasticState%nonLocal)) then
!$OMP PARALLEL DO PRIVATE(orientation)
do e = FEsolving_execElem(1),FEsolving_execElem(2)
do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e)
do c = 1_pInt,homogenization_Ngrains(mesh_element(3,e))
! somehow this subroutine is not threadsafe, so need critical statement here; not clear, what exactly the problem is
!$OMP CRITICAL (polarDecomp)
orientation = math_RtoQ(transpose(math_rotationalPart33(crystallite_Fe(1:3,1:3,c,i,e)))) ! rotational part from polar decomposition as quaternion
orientation = math_RtoQ(transpose(math_rotationalPart33(crystallite_Fe(1:3,1:3,c,i,e))))
!$OMP END CRITICAL (polarDecomp)
crystallite_rotation(1:4,c,i,e) = lattice_qDisorientation(crystallite_orientation0(1:4,c,i,e), & ! active rotation from ori0
crystallite_rotation(1:4,c,i,e) = lattice_qDisorientation(crystallite_orientation0(1:4,c,i,e), &! active rotation from initial
orientation) ! to current orientation (with no symmetry)
crystallite_orientation(1:4,c,i,e) = orientation
enddo; enddo; enddo
@ -3997,6 +3995,7 @@ subroutine crystallite_orientations
! --- UPDATE SOME ADDITIONAL VARIABLES THAT ARE NEEDED FOR NONLOCAL MATERIAL ---
! --- we use crystallite_orientation from above, so need a separate loop
nonlocalPresent: if (any(plasticState%nonLocal)) then
!$OMP PARALLEL DO PRIVATE(myPhase,neighboring_e,neighboring_i,neighboringPhase)
do e = FEsolving_execElem(1),FEsolving_execElem(2)
do i = FEsolving_execIP(1,e),FEsolving_execIP(2,e)

130
code/lattice.f90
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@ -17,13 +17,7 @@ module lattice
LATTICE_maxNslipFamily = 13_pInt, & !< max # of slip system families over lattice structures
LATTICE_maxNtwinFamily = 4_pInt, & !< max # of twin system families over lattice structures
LATTICE_maxNtransFamily = 2_pInt, & !< max # of transformation system families over lattice structures
LATTICE_maxNcleavageFamily = 3_pInt, & !< max # of transformation system families over lattice structures
LATTICE_maxNslip = 52_pInt, & !< max # of slip systems over lattice structures
LATTICE_maxNtwin = 24_pInt, & !< max # of twin systems over lattice structures
LATTICE_maxNinteraction = 182_pInt, & !< max # of interaction types (in hardening matrix part)
LATTICE_maxNnonSchmid = 6_pInt, & !< max # of non schmid contributions over lattice structures
LATTICE_maxNtrans = 12_pInt, & !< max # of transformations over lattice structures
LATTICE_maxNcleavage = 9_pInt !< max # of cleavage over lattice structures
LATTICE_maxNcleavageFamily = 3_pInt !< max # of transformation system families over lattice structures
integer(pInt), allocatable, dimension(:,:), protected, public :: &
lattice_NslipSystem, & !< total # of slip systems in each family
@ -80,25 +74,25 @@ module lattice
lattice_NnonSchmid !< total # of non-Schmid contributions for each structure
!--------------------------------------------------------------------------------------------------
! fcc
! face centered cubic
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
LATTICE_fcc_NslipSystem = int([12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],pInt) !< total # of slip systems per family for fcc
LATTICE_fcc_NslipSystem = int([12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],pInt) !< # of slip systems per family for fcc
integer(pInt), dimension(LATTICE_maxNtwinFamily), parameter, public :: &
LATTICE_fcc_NtwinSystem = int([12, 0, 0, 0],pInt) !< total # of twin systems per family for fcc
LATTICE_fcc_NtwinSystem = int([12, 0, 0, 0],pInt) !< # of twin systems per family for fcc
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_fcc_NtransSystem = int([12, 0],pInt) !< total # of transformation systems per family for fcc
LATTICE_fcc_NtransSystem = int([12, 0],pInt) !< # of transformation systems per family for fcc
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_fcc_NcleavageSystem = int([3, 4, 0],pInt) !< total # of cleavage systems per family for fcc
LATTICE_fcc_NcleavageSystem = int([3, 4, 0],pInt) !< # of cleavage systems per family for fcc
integer(pInt), parameter, private :: &
LATTICE_fcc_Nslip = sum(lattice_fcc_NslipSystem), & !< total # of slip systems for fcc
LATTICE_fcc_Ntwin = sum(lattice_fcc_NtwinSystem), & !< total # of twin systems for fcc
LATTICE_fcc_Nslip = 12_pInt, & !sum(lattice_fcc_NslipSystem), & !< total # of slip systems for fcc
LATTICE_fcc_Ntwin = 12_pInt, & !sum(lattice_fcc_NtwinSystem), & !< total # of twin systems for fcc
LATTICE_fcc_NnonSchmid = 0_pInt, & !< total # of non-Schmid contributions for fcc
LATTICE_fcc_Ntrans = sum(lattice_fcc_NtransSystem), & !< total # of transformation systems for fcc
LATTICE_fcc_Ncleavage = sum(lattice_fcc_NcleavageSystem) !< total # of cleavage systems for fcc
LATTICE_fcc_Ntrans = 12_pInt, & !sum(lattice_fcc_NtransSystem), & !< total # of transformation systems for fcc
LATTICE_fcc_Ncleavage = 7_pInt !sum(lattice_fcc_NcleavageSystem) !< total # of cleavage systems for fcc
real(pReal), dimension(3+3,LATTICE_fcc_Nslip), parameter, private :: &
LATTICE_fcc_systemSlip = reshape(real([&
@ -363,25 +357,25 @@ module lattice
],pReal),[ 3_pInt + 3_pInt,LATTICE_fcc_Ncleavage])
!--------------------------------------------------------------------------------------------------
! bcc
! body centered cubic
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
LATTICE_bcc_NslipSystem = int([ 12, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], pInt) !< total # of slip systems per family for bcc
LATTICE_bcc_NslipSystem = int([ 12, 12, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], pInt) !< # of slip systems per family for bcc
integer(pInt), dimension(LATTICE_maxNtwinFamily), parameter, public :: &
LATTICE_bcc_NtwinSystem = int([ 12, 0, 0, 0], pInt) !< total # of twin systems per family for bcc
LATTICE_bcc_NtwinSystem = int([ 12, 0, 0, 0], pInt) !< # of twin systems per family for bcc
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_bcc_NtransSystem = int([0,0],pInt) !< total # of transformation systems per family for bcc
LATTICE_bcc_NtransSystem = int([0,0],pInt) !< # of transformation systems per family for bcc
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_bcc_NcleavageSystem = int([3,6,0],pInt) !< total # of cleavage systems per family for bcc
LATTICE_bcc_NcleavageSystem = int([3,6,0],pInt) !< # of cleavage systems per family for bcc
integer(pInt), parameter, private :: &
LATTICE_bcc_Nslip = sum(lattice_bcc_NslipSystem), & !< total # of slip systems for bcc
LATTICE_bcc_Ntwin = sum(lattice_bcc_NtwinSystem), & !< total # of twin systems for bcc
LATTICE_bcc_Nslip = 24_pInt, & !sum(lattice_bcc_NslipSystem), & !< total # of slip systems for bcc
LATTICE_bcc_Ntwin = 12_pInt, & !sum(lattice_bcc_NtwinSystem), & !< total # of twin systems for bcc
LATTICE_bcc_NnonSchmid = 6_pInt, & !< total # of non-Schmid contributions for bcc (A. Koester, A. Ma, A. Hartmaier 2012)
LATTICE_bcc_Ntrans = sum(lattice_bcc_NtransSystem), & !< total # of transformation systems for bcc
LATTICE_bcc_Ncleavage = sum(lattice_bcc_NcleavageSystem) !< total # of cleavage systems for bcc
LATTICE_bcc_Ntrans = 0_pInt, & !sum(lattice_bcc_NtransSystem), & !< total # of transformation systems for bcc
LATTICE_bcc_Ncleavage = 9_pInt !sum(lattice_bcc_NcleavageSystem) !< total # of cleavage systems for bcc
real(pReal), dimension(3+3,LATTICE_bcc_Nslip), parameter, private :: &
LATTICE_bcc_systemSlip = reshape(real([&
@ -560,7 +554,7 @@ module lattice
],pReal),[ 3_pInt + 3_pInt,LATTICE_bcc_Ncleavage])
!--------------------------------------------------------------------------------------------------
! hex
! hexagonal
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
lattice_hex_NslipSystem = int([ 3, 3, 3, 6, 12, 6, 0, 0, 0, 0, 0, 0, 0],pInt) !< # of slip systems per family for hex
@ -568,17 +562,17 @@ module lattice
lattice_hex_NtwinSystem = int([ 6, 6, 6, 6],pInt) !< # of slip systems per family for hex
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_hex_NtransSystem = int([0,0],pInt) !< total # of transformation systems per family for hex
LATTICE_hex_NtransSystem = int([0,0],pInt) !< # of transformation systems per family for hex
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_hex_NcleavageSystem = int([3,0,0],pInt) !< total # of cleavage systems per family for hex
LATTICE_hex_NcleavageSystem = int([3,0,0],pInt) !< # of cleavage systems per family for hex
integer(pInt), parameter, private :: &
LATTICE_hex_Nslip = sum(lattice_hex_NslipSystem), & !< total # of slip systems for hex
LATTICE_hex_Ntwin = sum(lattice_hex_NtwinSystem), & !< total # of twin systems for hex
LATTICE_hex_Nslip = 33_pInt, & !sum(lattice_hex_NslipSystem), & !< total # of slip systems for hex
LATTICE_hex_Ntwin = 24_pInt, & !sum(lattice_hex_NtwinSystem), & !< total # of twin systems for hex
LATTICE_hex_NnonSchmid = 0_pInt, & !< total # of non-Schmid contributions for hex
LATTICE_hex_Ntrans = sum(lattice_hex_NtransSystem), & !< total # of transformation systems for hex
LATTICE_hex_Ncleavage = sum(lattice_hex_NcleavageSystem) !< total # of cleavage systems for hex
LATTICE_hex_Ntrans = 0_pInt, & !sum(lattice_hex_NtransSystem), & !< total # of transformation systems for hex
LATTICE_hex_Ncleavage = 3_pInt !sum(lattice_hex_NcleavageSystem) !< total # of cleavage systems for hex
real(pReal), dimension(4+4,LATTICE_hex_Nslip), parameter, private :: &
LATTICE_hex_systemSlip = reshape(real([&
@ -842,25 +836,25 @@ module lattice
!--------------------------------------------------------------------------------------------------
! bct
! body centered tetragonal
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
LATTICE_bct_NslipSystem = int([2, 2, 2, 4, 2, 4, 2, 2, 4, 8, 4, 8, 8 ],pInt) !< # of slip systems per family for bct (Sn) Bieler J. Electr Mater 2009
integer(pInt), dimension(LATTICE_maxNtwinFamily), parameter, public :: &
LATTICE_bct_NtwinSystem = int([0, 0, 0, 0], pInt) !< total # of twin systems per family for bct-example
LATTICE_bct_NtwinSystem = int([0, 0, 0, 0], pInt) !< # of twin systems per family for bct
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_bct_NtransSystem = int([0,0],pInt) !< total # of transformation systems per family for bct
LATTICE_bct_NtransSystem = int([0,0],pInt) !< # of transformation systems per family for bct
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_bct_NcleavageSystem = int([0,0,0],pInt) !< total # of cleavage systems per family for bct
LATTICE_bct_NcleavageSystem = int([0,0,0],pInt) !< # of cleavage systems per family for bct
integer(pInt), parameter, private :: &
LATTICE_bct_Nslip = sum(lattice_bct_NslipSystem), & !< total # of slip systems for bct
LATTICE_bct_Ntwin = sum(lattice_bct_NtwinSystem), & !< total # of twin systems for bct
LATTICE_bct_Nslip = 52_pInt, & !sum(lattice_bct_NslipSystem), & !< total # of slip systems for bct
LATTICE_bct_Ntwin = 0_pInt, & !sum(lattice_bct_NtwinSystem), & !< total # of twin systems for bct
LATTICE_bct_NnonSchmid = 0_pInt, & !< total # of non-Schmid contributions for bct
LATTICE_bct_Ntrans = sum(lattice_bct_NtransSystem), & !< total # of transformation systems for bct
LATTICE_bct_Ncleavage = sum(lattice_bct_NcleavageSystem) !< total # of cleavage systems for bct
LATTICE_bct_Ntrans = 0_pInt, & !sum(lattice_bct_NtransSystem), & !< total # of transformation systems for bct
LATTICE_bct_Ncleavage = 0_pInt !sum(lattice_bct_NcleavageSystem) !< total # of cleavage systems for bct
real(pReal), dimension(3+3,LATTICE_bct_Nslip), parameter, private :: &
LATTICE_bct_systemSlip = reshape(real([&
@ -1003,11 +997,24 @@ module lattice
!--------------------------------------------------------------------------------------------------
! isotropic
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
LATTICE_iso_NslipSystem = int([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ],pInt) !< # of slip systems per family for iso
integer(pInt), dimension(LATTICE_maxNtwinFamily), parameter, public :: &
LATTICE_iso_NtwinSystem = int([0, 0, 0, 0], pInt) !< # of twin systems per family for iso
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_iso_NtransSystem = int([0, 0],pInt) !< # of transformation systems per family for iso
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_iso_NcleavageSystem = int([3,0,0],pInt) !< total # of cleavage systems per family for iso
LATTICE_iso_NcleavageSystem = int([3,0,0],pInt) !< # of cleavage systems per family for iso
integer(pInt), parameter, private :: &
LATTICE_iso_Ncleavage = sum(LATTICE_iso_NcleavageSystem) !< total # of cleavage systems for iso
LATTICE_iso_Nslip = 0_pInt, & !sum(lattice_iso_NslipSystem), & !< total # of slip systems for iso
LATTICE_iso_Ntwin = 0_pInt, & !sum(lattice_iso_NtwinSystem), & !< total # of twin systems for iso
LATTICE_iso_NnonSchmid = 0_pInt, & !< total # of non-Schmid contributions for iso
LATTICE_iso_Ntrans = 0_pInt, & !sum(lattice_iso_NtransSystem), & !< total # of transformation systems for iso
LATTICE_iso_Ncleavage = 3_pInt !sum(lattice_iso_NcleavageSystem) !< total # of cleavage systems for iso
real(pReal), dimension(3+3,LATTICE_iso_Ncleavage), parameter, private :: &
LATTICE_iso_systemCleavage = reshape(real([&
@ -1019,11 +1026,24 @@ module lattice
!--------------------------------------------------------------------------------------------------
! orthorhombic
integer(pInt), dimension(LATTICE_maxNslipFamily), parameter, public :: &
LATTICE_ortho_NslipSystem = int([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0 ],pInt) !< # of slip systems per family for ortho
integer(pInt), dimension(LATTICE_maxNtwinFamily), parameter, public :: &
LATTICE_ortho_NtwinSystem = int([0, 0, 0, 0], pInt) !< # of twin systems per family for ortho
integer(pInt), dimension(LATTICE_maxNtransFamily), parameter, public :: &
LATTICE_ortho_NtransSystem = int([0, 0],pInt) !< # of transformation systems per family for ortho
integer(pInt), dimension(LATTICE_maxNcleavageFamily), parameter, public :: &
LATTICE_ortho_NcleavageSystem = int([1,1,1],pInt) !< total # of cleavage systems per family for ortho
LATTICE_ortho_NcleavageSystem = int([1,1,1],pInt) !< # of cleavage systems per family for ortho
integer(pInt), parameter, private :: &
LATTICE_ortho_Ncleavage = sum(LATTICE_ortho_NcleavageSystem) !< total # of cleavage systems for ortho
LATTICE_ortho_Nslip = 0_pInt, & !sum(lattice_ortho_NslipSystem), & !< total # of slip systems for ortho
LATTICE_ortho_Ntwin = 0_pInt, & !sum(lattice_ortho_NtwinSystem), & !< total # of twin systems for ortho
LATTICE_ortho_NnonSchmid = 0_pInt, & !< total # of non-Schmid contributions for ortho
LATTICE_ortho_Ntrans = 0_pInt, & !sum(lattice_ortho_NtransSystem), & !< total # of transformation systems for ortho
LATTICE_ortho_Ncleavage = 3_pInt !sum(lattice_ortho_NcleavageSystem) !< total # of cleavage systems for ortho
real(pReal), dimension(3+3,LATTICE_ortho_Ncleavage), parameter, private :: &
LATTICE_ortho_systemCleavage = reshape(real([&
@ -1033,6 +1053,26 @@ module lattice
1, 0, 0, 0, 0, 1 &
],pReal),[ 3_pInt + 3_pInt,LATTICE_ortho_Ncleavage])
integer(pInt), parameter, public :: &
LATTICE_maxNslip = 52_pInt, &
!LATTICE_maxNslip = maxval([LATTICE_fcc_Nslip,LATTICE_bcc_Nslip,LATTICE_hex_Nslip,\
! LATTICE_bct_Nslip,LATTICE_iso_Nslip,LATTICE_ortho_Nslip]), & !< max # of slip systems over lattice structures
LATTICE_maxNtwin = 24_pInt, &
!LATTICE_maxNtwin = maxval([LATTICE_fcc_Ntwin,LATTICE_bcc_Ntwin,LATTICE_hex_Ntwin,\
! LATTICE_bct_Ntwin,LATTICE_iso_Ntwin,LATTICE_ortho_Ntwin]), & !< max # of twin systems over lattice structures
LATTICE_maxNnonSchmid = 6_pInt, &
!LATTICE_maxNtwin = maxval([LATTICE_fcc_NnonSchmid,LATTICE_bcc_NnonSchmid,\
! LATTICE_hex_NnonSchmid,LATTICE_bct_NnonSchmid,\
! LATTICE_iso_NnonSchmid,LATTICE_ortho_NnonSchmid]), & !< max # of non-Schmid contributions over lattice structures
LATTICE_maxNtrans = 12_pInt, &
!LATTICE_maxNtrans = maxval([LATTICE_fcc_Ntrans,LATTICE_bcc_Ntrans,LATTICE_hex_Ntrans,\
! LATTICE_bct_Ntrans,LATTICE_iso_Ntrans,LATTICE_ortho_Ntrans]),&!< max # of transformation systems over lattice structures
LATTICE_maxNcleavage = 9_pInt, &
!LATTICE_maxNcleavage = maxval([LATTICE_fcc_Ncleavage,LATTICE_bcc_Ncleavage,\
! LATTICE_hex_Ncleavage,LATTICE_bct_Ncleavage,\
! LATTICE_iso_Ncleavage,LATTICE_ortho_Ncleavage]) !< max # of cleavage systems over lattice structures
LATTICE_maxNinteraction = 182_pInt !< max # of interaction types (in hardening matrix part)
real(pReal), dimension(:,:,:), allocatable, public, protected :: &
lattice_C66, lattice_trans_C66
real(pReal), dimension(:,:,:,:,:), allocatable, public, protected :: &
@ -1250,7 +1290,7 @@ subroutine lattice_init
endif mainProcess
!--------------------------------------------------------------------------------------------------
! consistency checks
! consistency checks (required since ifort 15.0 does not support sum/maxval in parameter definition)
if (LATTICE_maxNslip /= maxval([LATTICE_fcc_Nslip,LATTICE_bcc_Nslip,LATTICE_hex_Nslip,LATTICE_bct_Nslip])) &
call IO_error(0_pInt,ext_msg = 'LATTICE_maxNslip')

3
code/math.f90
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@ -839,6 +839,9 @@ subroutine math_invert(myDim,A, InvA, error)
real(pReal), dimension(myDim,myDim), intent(out) :: invA
logical, intent(out) :: error
external :: &
dgetrf, &
dgetri
invA = A
call dgetrf(myDim,myDim,invA,myDim,ipiv,ierr)

1
examples/.gitignore vendored Normal file
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@ -0,0 +1 @@
postProc

8
processing/post/addCompatibilityMismatch.py
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@ -21,7 +21,7 @@ Operates on periodic three-dimensional x,y,z-ordered data sets.
parser.add_option('-c','--coordinates',
dest = 'coords',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'column heading of coordinates [%default]')
parser.add_option('-f','--defgrad',
@ -36,7 +36,7 @@ parser.add_option('--no-volume','-v',
dest = 'volume',
action = 'store_false',
help = 'omit volume mismatch')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
defgrad = 'f',
shape = True,
volume = True,
@ -64,8 +64,8 @@ for name in filenames:
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
if table.label_dimension(options.defgrad) != 9: errors.append('deformation gradient {} is not a tensor.'.format(options.defgrad))
else: colF = table.label_index(options.defgrad)

8
processing/post/addCurl.py
View File

@ -71,7 +71,7 @@ Deals with both vector- and tensor fields.
""", version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
@ -83,7 +83,7 @@ parser.add_option('-t','--tensor',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
@ -114,8 +114,8 @@ for name in filenames:
remarks = []
column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):

8
processing/post/addDivergence.py
View File

@ -57,7 +57,7 @@ Deals with both vector- and tensor-valued fields.
""", version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
@ -69,7 +69,7 @@ parser.add_option('-t','--tensor',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of tensor field values')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
@ -100,8 +100,8 @@ for name in filenames:
remarks = []
column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):

10
processing/post/addEuclideanDistance.py
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@ -90,7 +90,7 @@ Add column(s) containing Euclidean distance to grain structural features: bounda
parser.add_option('-p',
'--pos', '--position',
dest = 'coords', metavar = 'string',
dest = 'pos', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-i',
'--id', '--identifier',
@ -109,7 +109,7 @@ parser.add_option('-s',
dest = 'scale', type = 'float', metavar = 'float',
help = 'voxel size [%default]')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
id = 'texture',
neighborhood = 'neumann',
scale = 1.0,
@ -151,10 +151,10 @@ for name in filenames:
remarks = []
column = {}
coordDim = table.label_dimension(options.coords)
coordDim = table.label_dimension(options.pos)
if not 3 >= coordDim >= 1:
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.coords))
else: coordCol = table.label_index(options.coords)
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
else: coordCol = table.label_index(options.pos)
if table.label_dimension(options.id) != 1: errors.append('grain identifier {} not found.'.format(options.id))
else: idCol = table.label_index(options.id)

8
processing/post/addGradient.py
View File

@ -61,7 +61,7 @@ Deals with both vector- and scalar fields.
""", version = scriptID)
parser.add_option('-p','--pos','--periodiccellcenter',
dest = 'coords',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('-v','--vector',
@ -73,7 +73,7 @@ parser.add_option('-s','--scalar',
action = 'extend', metavar = '<string LIST>',
help = 'label(s) of scalar field values')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
)
(options,filenames) = parser.parse_args()
@ -104,8 +104,8 @@ for name in filenames:
remarks = []
column = {}
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
for type, data in items.iteritems():
for what in (data['labels'] if data['labels'] is not None else []):

8
processing/post/averageDown.py
View File

@ -20,7 +20,7 @@ Average each data block of size 'packing' into single values thus reducing the f
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'coords',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
@ -39,7 +39,7 @@ parser.add_option('-s', '--size',
dest = 'size',
type = 'float', nargs = 3, metavar = 'float float float',
help = 'size in x,y,z [autodetect]')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
shift = (0,0,0),
grid = (0,0,0),
@ -75,8 +75,8 @@ for name in filenames:
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
if remarks != []: damask.util.croak(remarks)
if errors != []:

10
processing/post/blowUp.py
View File

@ -20,7 +20,7 @@ to resolution*packing.
""", version = scriptID)
parser.add_option('-c','--coordinates',
dest = 'coords', metavar = 'string',
dest = 'pos', metavar = 'string',
help = 'column label of coordinates [%default]')
parser.add_option('-p','--packing',
dest = 'packing', type = 'int', nargs = 3, metavar = 'int int int',
@ -31,7 +31,7 @@ parser.add_option('-g','--grid',
parser.add_option('-s','--size',
dest = 'dimension', type = 'float', nargs = 3, metavar = 'int int int',
help = 'dimension in x,y,z [autodetect]')
parser.set_defaults(coords = 'pos',
parser.set_defaults(pos = 'pos',
packing = (2,2,2),
grid = (0,0,0),
size = (0.0,0.0,0.0),
@ -63,8 +63,8 @@ for name in filenames:
errors = []
remarks = []
if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
else: colCoord = table.label_index(options.coords)
if table.label_dimension(options.pos) != 3: errors.append('coordinates {} are not a vector.'.format(options.pos))
else: colCoord = table.label_index(options.pos)
colElem = table.label_index('elem')
@ -76,7 +76,7 @@ for name in filenames:
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray(options.coords)
table.data_readArray(options.pos)
table.data_rewind()
coords = [np.unique(table.data[:,i]) for i in xrange(3)]

10
processing/post/stddevDown.py
View File

@ -19,7 +19,7 @@ to resolution/packing.
""", version = scriptID)
parser.add_option('-c','--coordinates', dest='coords', type='string',\
parser.add_option('-c','--coordinates', dest='pos', type='string',\
help='column heading for coordinates [%default]')
parser.add_option('-p','--packing', dest='packing', type='int', nargs=3, \
help='dimension of packed group %default')
@ -29,7 +29,7 @@ parser.add_option('-r','--resolution', dest='resolution', type='int', nargs=3,
help='resolution in x,y,z [autodetect]')
parser.add_option('-d','--dimension', dest='dimension', type='float', nargs=3, \
help='dimension in x,y,z [autodetect]')
parser.set_defaults(coords = 'ipinitialcoord')
parser.set_defaults(coords = 'pos')
parser.set_defaults(packing = [2,2,2])
parser.set_defaults(shift = [0,0,0])
parser.set_defaults(resolution = [0,0,0])
@ -75,12 +75,12 @@ for file in files:
# --------------- figure out size and grid ---------------------------------------------------------
try:
locationCol = table.labels.index('1_%s'%options.coords) # columns containing location data
locationCol = table.labels.index('1_%s'%options.pos) # columns containing location data
except ValueError:
try:
locationCol = table.labels.index('%s.x'%options.coords) # columns containing location data (legacy naming scheme)
locationCol = table.labels.index('%s.x'%options.pos) # columns containing location data (legacy naming scheme)
except ValueError:
file['croak'].write('no coordinate data (1_%s/%s.x) found...\n'%(options.coords,options.coords))
file['croak'].write('no coordinate data (1_%s/%s.x) found...\n'%(options.pos,options.pos))
continue
if (any(options.resolution)==0 or any(options.dimension)==0.0):

8
processing/pre/geom_fromTable.py
View File

@ -21,7 +21,7 @@ Generate geometry description and material configuration from position, phase, a
""", version = scriptID)
parser.add_option('--coordinates',
dest = 'coordinates',
dest = 'pos',
type = 'string', metavar = 'string',
help = 'coordinates label')
parser.add_option('--phase',
@ -135,11 +135,11 @@ for name in filenames:
# ------------------------------------------ sanity checks ---------------------------------------
coordDim = table.label_dimension(options.coordinates)
coordDim = table.label_dimension(options.pos)
errors = []
if not 3 >= coordDim >= 2:
errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.coordinates))
errors.append('coordinates "{}" need to have two or three dimensions.'.format(options.pos))
if not np.all(table.label_dimension(label) == dim):
errors.append('input "{}" needs to have dimension {}.'.format(label,dim))
if options.phase and table.label_dimension(options.phase) != 1:
@ -150,7 +150,7 @@ for name in filenames:
table.close(dismiss = True)
continue
table.data_readArray([options.coordinates] \
table.data_readArray([options.pos] \
+ ([label] if isinstance(label, types.StringTypes) else label) \
+ ([options.phase] if options.phase else []))