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Merge branch 'development' 

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	VERSION
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Test User 2016-04-29 08:03:07 +02:00
parent a616f06fc4 5089d86b3d
commit 054d9710b5
15 changed files with 357 additions and 310 deletions
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2
VERSION
View File

@ -1 +1 @@
v2.0.0-196-g1940b8d
v2.0.0-205-gced4d9d

130
code/lattice.f90
View File

@ -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
View File

@ -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)

8
processing/post/addCompatibilityMismatch.py
View File

@ -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 []):

23
processing/post/addDisplacement.py
View File

@ -101,7 +101,7 @@ parser.add_option('-f',
help = 'column label of deformation gradient [%default]')
parser.add_option('-p',
'--pos', '--position',
dest = 'coords',
dest = 'pos',
metavar = 'string',
help = 'label of coordinates [%default]')
parser.add_option('--nodal',
@ -110,7 +110,7 @@ parser.add_option('--nodal',
help = 'output nodal (instad of cell-centered) displacements')
parser.set_defaults(defgrad = 'f',
coords = 'pos',
pos = 'pos',
nodal = False,
)
@ -121,13 +121,14 @@ parser.set_defaults(defgrad = 'f',
if filenames == []: filenames = [None]
for name in filenames:
try: table = damask.ASCIItable(name = name,
outname = (os.path.splitext(name)[0] +
'_nodal' +
os.path.splitext(name)[1]) if (options.nodal and name) else None,
os.path.splitext(name)[1]) if (options.nodal and name) else None
try: table = damask.ASCIItable(name = name,
outname = outname,
buffered = False)
except: continue
damask.util.report(scriptName,name)
damask.util.report(scriptName,'{}{}'.format(name,' --> {}'.format(outname) if outname else ''))
# ------------------------------------------ read header ------------------------------------------
@ -141,13 +142,13 @@ for name in filenames:
if table.label_dimension(options.defgrad) != 9:
errors.append('deformation gradient "{}" is not a 3x3 tensor.'.format(options.defgrad))
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))
errors.append('coordinates "{}" need to have one, two, or three dimensions.'.format(options.pos))
elif coordDim < 3:
remarks.append('appending {} dimension{} to coordinates "{}"...'.format(3-coordDim,
's' if coordDim < 2 else '',
options.coords))
options.pos))
if remarks != []: damask.util.croak(remarks)
if errors != []:
@ -157,7 +158,7 @@ for name in filenames:
# --------------- figure out size and grid ---------------------------------------------------------
table.data_readArray([options.defgrad,options.coords])
table.data_readArray([options.defgrad,options.pos])
table.data_rewind()
if len(table.data.shape) < 2: table.data.shape += (1,) # expand to 2D shape
@ -196,8 +197,8 @@ for name in filenames:
table.info_append(scriptID + '\t' + ' '.join(sys.argv[1:]))
table.labels_append((['{}_pos' .format(i+1) for i in xrange(3)] if options.nodal else []) +
['{}_avg({}).{}' .format(i+1,options.defgrad,options.coords) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.coords) for i in xrange(3)] )
['{}_avg({}).{}' .format(i+1,options.defgrad,options.pos) for i in xrange(3)] +
['{}_fluct({}).{}'.format(i+1,options.defgrad,options.pos) for i in xrange(3)] )
table.head_write()
# ------------------------------------------ output data -------------------------------------------

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 []):

42
processing/post/addEuclideanDistance.py
View File

@ -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,
@ -151,15 +151,17 @@ 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)
if remarks != []: damask.util.croak(remarks)
if remarks != []:
damask.util.croak(remarks)
remarks = []
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
@ -184,6 +186,8 @@ for name in filenames:
N = grid.prod()
if N != len(table.data): errors.append('data count {} does not match grid {}.'.format(N,'x'.join(map(str,grid))))
else: remarks.append('grid: {}x{}x{}'.format(*grid))
if remarks != []: damask.util.croak(remarks)
if errors != []:
damask.util.croak(errors)
table.close(dismiss = True)
@ -194,8 +198,8 @@ for name in filenames:
stack = [table.data]
neighborhood = neighborhoods[options.neighborhood]
convoluted = np.empty([len(neighborhood)]+list(grid+2),'i')
microstructure = periodic_3Dpad(np.array(table.data[:,idCol].reshape(grid),'i'))
diffToNeighbor = np.empty(list(grid+2)+[len(neighborhood)],'i')
microstructure = periodic_3Dpad(table.data[:,idCol].astype('i').reshape(grid,order='F'))
for i,p in enumerate(neighborhood):
stencil = np.zeros((3,3,3),'i')
@ -203,24 +207,28 @@ for name in filenames:
stencil[p[0]+1,
p[1]+1,
p[2]+1] = 1
convoluted[i,:,:,:] = ndimage.convolve(microstructure,stencil)
diffToNeighbor[:,:,:,i] = ndimage.convolve(microstructure,stencil) # compare ID at each point...
# ...to every one in the specified neighborhood
# for same IDs at both locations ==> 0
distance = np.ones((len(feature_list),grid[0],grid[1],grid[2]),'d')
convoluted = np.sort(convoluted,axis = 0)
uniques = np.where(convoluted[0,1:-1,1:-1,1:-1] != 0, 1,0) # initialize unique value counter (exclude myself [= 0])
diffToNeighbor = np.sort(diffToNeighbor) # sort diff such that number of changes in diff (steps)...
# ...reflects number of unique neighbors
uniques = np.where(diffToNeighbor[1:-1,1:-1,1:-1,0] != 0, 1,0) # initialize unique value counter (exclude myself [= 0])
for i in xrange(1,len(neighborhood)): # check remaining points in neighborhood
uniques += np.where(np.logical_and(
convoluted[i,1:-1,1:-1,1:-1] != convoluted[i-1,1:-1,1:-1,1:-1], # flip of ID difference detected?
convoluted[i,1:-1,1:-1,1:-1] != 0), # not myself?
1,0) # count flip
diffToNeighbor[1:-1,1:-1,1:-1,i] != 0, # not myself?
diffToNeighbor[1:-1,1:-1,1:-1,i] != diffToNeighbor[1:-1,1:-1,1:-1,i-1],
), # flip of ID difference detected?
1,0) # count that flip
distance = np.ones((len(feature_list),grid[0],grid[1],grid[2]),'d')
for i,feature_id in enumerate(feature_list):
distance[i,:,:,:] = np.where(uniques >= features[feature_id]['aliens'],0.0,1.0) # seed with 0.0 when enough unique neighbor IDs are present
distance[i,:,:,:] = ndimage.morphology.distance_transform_edt(distance[i,:,:,:])*[options.scale]*3
distance.shape = ([len(feature_list),grid.prod(),1])
distance = distance.reshape([len(feature_list),grid.prod(),1],order='F')
for i in xrange(len(feature_list)):
stack.append(distance[i,:])

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)]

23
processing/post/sortTable.py
View File

@ -14,7 +14,7 @@ scriptID = ' '.join([scriptName,damask.version])
# --------------------------------------------------------------------
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [file[s]]', description = """
Sort rows by given column label(s).
Sort rows by given (or all) column label(s).
Examples:
With coordinates in columns "x", "y", and "z"; sorting with x slowest and z fastest varying index: --label x,y,z.
@ -30,24 +30,18 @@ parser.add_option('-r','--reverse',
action = 'store_true',
help = 'sort in reverse')
parser.set_defaults(key = [],
reverse = False,
parser.set_defaults(reverse = False,
)
(options,filenames) = parser.parse_args()
if options.keys is None:
parser.error('No sorting column(s) specified.')
options.keys.reverse() # numpy sorts with most significant column as last
# --- loop over input files -------------------------------------------------------------------------
if filenames == []: filenames = [None]
for name in filenames:
try:
table = damask.ASCIItable(name = name,
try: table = damask.ASCIItable(name = name,
buffered = False)
except: continue
damask.util.report(scriptName,name)
@ -61,13 +55,14 @@ for name in filenames:
# ------------------------------------------ process data ---------------------------------------
table.data_readArray()
keys = table.labels[::-1] if options.keys is None else options.keys[::-1] # numpy sorts with most significant column as last
cols = []
remarks = []
for i,column in enumerate(table.label_index(options.keys)):
if column < 0:
remarks.append("label {0} not present.".format(options.keys[i]))
else:
cols += [table.data[:,column]]
for i,column in enumerate(table.label_index(keys)):
if column < 0: remarks.append('label "{}" not present...'.format(keys[i]))
else: cols += [table.data[:,column]]
if remarks != []: damask.util.croak(remarks)
ind = np.lexsort(cols) if cols != [] else np.arange(table.data.shape[0])

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 []))