From 33b8360ebb5997d92179b2175bae2bf86420fb6c Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 26 Apr 2016 08:11:55 +0200 Subject: [PATCH 01/11] ifort 15.0 is not capable of simple definition --- code/lattice.f90 | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/code/lattice.f90 b/code/lattice.f90 index d08d42c06..580368457 100644 --- a/code/lattice.f90 +++ b/code/lattice.f90 @@ -94,11 +94,11 @@ module lattice LATTICE_fcc_NcleavageSystem = int([3, 4, 0],pInt) !< total # 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([& @@ -377,11 +377,11 @@ module lattice LATTICE_bcc_NcleavageSystem = int([3,6,0],pInt) !< total # 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([& @@ -574,11 +574,11 @@ module lattice LATTICE_hex_NcleavageSystem = int([3,0,0],pInt) !< total # 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([& @@ -856,11 +856,11 @@ module lattice LATTICE_bct_NcleavageSystem = int([0,0,0],pInt) !< total # 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([& From f8e50cc304207d2cbbb9d960ec3021c3d6fe5f75 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 26 Apr 2016 09:35:42 +0200 Subject: [PATCH 02/11] fixed some missing "sum" initialisers, prepared more self consistent variable definitions for future use (ifort > 15.0) --- code/lattice.f90 | 106 ++++++++++++++++++++++++++++++++--------------- 1 file changed, 73 insertions(+), 33 deletions(-) diff --git a/code/lattice.f90 b/code/lattice.f90 index 580368457..bf1f53658 100644 --- a/code/lattice.f90 +++ b/code/lattice.f90 @@ -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 @@ -80,18 +74,18 @@ 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 = 12_pInt, & !sum(lattice_fcc_NslipSystem), & !< total # of slip systems for fcc @@ -312,8 +306,8 @@ module lattice 0.0, 0.0, 1.0, 45.0 & ],[ 4_pInt,LATTICE_fcc_Ntrans]) - real(pReal), dimension(LATTICE_fcc_Ntrans,LATTICE_fcc_Ntrans), parameter, private :: & ! Matrix for projection of shear from slip system to fault-band (twin) systems - LATTICE_fccTobcc_projectionTrans = reshape(real([& ! For ns = nt = nr + real(pReal), dimension(LATTICE_fcc_Ntrans,LATTICE_fcc_Ntrans), parameter, private :: & ! Matrix for projection of shear from slip system to fault-band (twin) systems + LATTICE_fccTobcc_projectionTrans = reshape(real([& ! For ns = nt = nr 0, 1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, & -1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, & 1,-1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, & @@ -363,18 +357,18 @@ 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 = 24_pInt, & !sum(lattice_bcc_NslipSystem), & !< total # of slip systems for bcc @@ -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 @@ -568,10 +562,10 @@ 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 = 33_pInt, & !sum(lattice_hex_NslipSystem), & !< total # of slip systems for hex @@ -842,18 +836,18 @@ 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 = 52_pInt, & !sum(lattice_bct_NslipSystem), & !< total # of slip systems for bct @@ -1003,12 +997,25 @@ 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([& ! Cleavage direction Plane normal @@ -1019,12 +1026,25 @@ 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([& ! Cleavage direction Plane normal @@ -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') From aae41e04795c6418fdb647ee3c5595acf47670a6 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 26 Apr 2016 09:36:27 +0200 Subject: [PATCH 03/11] external lapack functions marked as external --- code/math.f90 | 3 +++ 1 file changed, 3 insertions(+) diff --git a/code/math.f90 b/code/math.f90 index 624990ac4..9ad98df9e 100644 --- a/code/math.f90 +++ b/code/math.f90 @@ -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) From e06b9e778c460680f59d4592beb3414a873f981e Mon Sep 17 00:00:00 2001 From: Test User Date: Tue, 26 Apr 2016 16:13:28 +0200 Subject: [PATCH 04/11] updated version information after successful test of v2.0.0-199-gaae41e0 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index 73bccb41d..d0ea2c5ae 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.0-194-g137a5d1 +v2.0.0-199-gaae41e0 From d49750341146252917a93a5996553d7e82cc4562 Mon Sep 17 00:00:00 2001 From: Martin Diehl Date: Tue, 26 Apr 2016 22:49:58 +0200 Subject: [PATCH 05/11] renamed options.coords/options.coordinates consistently to options.pos --- processing/post/addCompatibilityMismatch.py | 14 +++++++------- processing/post/addCurl.py | 8 ++++---- processing/post/addDisplacement.py | 16 ++++++++-------- processing/post/addDivergence.py | 8 ++++---- processing/post/addEuclideanDistance.py | 10 +++++----- processing/post/addGradient.py | 8 ++++---- processing/post/averageDown.py | 8 ++++---- processing/post/blowUp.py | 10 +++++----- processing/post/stddevDown.py | 10 +++++----- processing/pre/geom_fromTable.py | 8 ++++---- 10 files changed, 50 insertions(+), 50 deletions(-) diff --git a/processing/post/addCompatibilityMismatch.py b/processing/post/addCompatibilityMismatch.py index 884702b93..3a73859e1 100755 --- a/processing/post/addCompatibilityMismatch.py +++ b/processing/post/addCompatibilityMismatch.py @@ -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', @@ -36,10 +36,10 @@ parser.add_option('--no-volume','-v', dest = 'volume', action = 'store_false', help = 'omit volume mismatch') -parser.set_defaults(coords = 'pos', - defgrad = 'f', - shape = True, - volume = True, +parser.set_defaults(pos = 'pos', + defgrad = 'f', + shape = True, + volume = True, ) (options,filenames) = parser.parse_args() @@ -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) diff --git a/processing/post/addCurl.py b/processing/post/addCurl.py index e368dc482..5c9a4b411 100755 --- a/processing/post/addCurl.py +++ b/processing/post/addCurl.py @@ -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 = '', 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 []): diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 0bafdb6cc..f52c8b19b 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -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, ) @@ -141,13 +141,13 @@ 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 +157,7 @@ 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 +196,8 @@ 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 ------------------------------------------- diff --git a/processing/post/addDivergence.py b/processing/post/addDivergence.py index d62c02fda..f13cb3a89 100755 --- a/processing/post/addDivergence.py +++ b/processing/post/addDivergence.py @@ -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 = '', 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 []): diff --git a/processing/post/addEuclideanDistance.py b/processing/post/addEuclideanDistance.py index 16c8e5234..9181e3785 100755 --- a/processing/post/addEuclideanDistance.py +++ b/processing/post/addEuclideanDistance.py @@ -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) diff --git a/processing/post/addGradient.py b/processing/post/addGradient.py index b2d004bd2..12ecf218d 100755 --- a/processing/post/addGradient.py +++ b/processing/post/addGradient.py @@ -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 = '', 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 []): diff --git a/processing/post/averageDown.py b/processing/post/averageDown.py index 0af56e176..808ed28bb 100755 --- a/processing/post/averageDown.py +++ b/processing/post/averageDown.py @@ -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 != []: diff --git a/processing/post/blowUp.py b/processing/post/blowUp.py index 7e6266837..6a73fe15a 100755 --- a/processing/post/blowUp.py +++ b/processing/post/blowUp.py @@ -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)] diff --git a/processing/post/stddevDown.py b/processing/post/stddevDown.py index e14ee0058..f4fdf5a90 100755 --- a/processing/post/stddevDown.py +++ b/processing/post/stddevDown.py @@ -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): diff --git a/processing/pre/geom_fromTable.py b/processing/pre/geom_fromTable.py index 53281c5df..5466236e8 100755 --- a/processing/pre/geom_fromTable.py +++ b/processing/pre/geom_fromTable.py @@ -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 [])) From 02021b9bb0f1d7e7d270750c38706aa08511cddb Mon Sep 17 00:00:00 2001 From: Test User Date: Wed, 27 Apr 2016 04:13:14 +0200 Subject: [PATCH 06/11] updated version information after successful test of v2.0.0-201-gd497503 --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index d0ea2c5ae..aeeddb7fb 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.0-199-gaae41e0 +v2.0.0-201-gd497503 From b3e987705805e9cb9d30cfde97c9cb510fc329f1 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Wed, 27 Apr 2016 09:28:43 -0400 Subject: [PATCH 07/11] changed from "coords" to "pos" remind user about (creating a new) nodal output file --- processing/post/addDisplacement.py | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/processing/post/addDisplacement.py b/processing/post/addDisplacement.py index 0bafdb6cc..782a7c24b 100755 --- a/processing/post/addDisplacement.py +++ b/processing/post/addDisplacement.py @@ -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: + outname = (os.path.splitext(name)[0] + + '_nodal' + + os.path.splitext(name)[1]) if (options.nodal and name) else None 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, + 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 ------------------------------------------- From ced4d9d393b6a826dc91b1ef37e7e80c37f9a447 Mon Sep 17 00:00:00 2001 From: Test User Date: Thu, 28 Apr 2016 04:14:08 +0200 Subject: [PATCH 08/11] updated version information after successful test of v2.0.0-204-g426658e --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index aeeddb7fb..f68d35f60 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.0-201-gd497503 +v2.0.0-204-g426658e From b9021f3b3f61425040bb4026fc97d9a8d214c74b Mon Sep 17 00:00:00 2001 From: Test User Date: Thu, 28 Apr 2016 16:13:52 +0200 Subject: [PATCH 09/11] updated version information after successful test of v2.0.0-205-gced4d9d --- VERSION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/VERSION b/VERSION index f68d35f60..7e9361c34 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -v2.0.0-204-g426658e +v2.0.0-205-gced4d9d From d3a7ceff15236172ba65bae10a679f3bd222e9b0 Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 28 Apr 2016 13:24:08 -0400 Subject: [PATCH 10/11] fixed serious bug regarding wrong reshaping order (was 'C' now 'F') of 3dim to 1dim and back. --- processing/post/addEuclideanDistance.py | 34 +++++++++++++++---------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/processing/post/addEuclideanDistance.py b/processing/post/addEuclideanDistance.py index 9181e3785..4b3f518d5 100755 --- a/processing/post/addEuclideanDistance.py +++ b/processing/post/addEuclideanDistance.py @@ -159,7 +159,9 @@ for name in filenames: 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) @@ -194,33 +198,37 @@ 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') stencil[1,1,1] = -1 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,:]) From 5089d86b3d3f205e902979122d1165e51de35d9d Mon Sep 17 00:00:00 2001 From: Philip Eisenlohr Date: Thu, 28 Apr 2016 20:28:45 -0400 Subject: [PATCH 11/11] sorting labels are now optional. uses existing labels (from left to right) for sorting if none specified. --- processing/post/sortTable.py | 27 +++++++++++---------------- 1 file changed, 11 insertions(+), 16 deletions(-) diff --git a/processing/post/sortTable.py b/processing/post/sortTable.py index 92fe221ee..e4f3c8dd0 100755 --- a/processing/post/sortTable.py +++ b/processing/post/sortTable.py @@ -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. @@ -30,25 +30,19 @@ 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, - buffered = False) + try: table = damask.ASCIItable(name = name, + buffered = False) except: continue damask.util.report(scriptName,name) @@ -61,15 +55,16 @@ 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]) if options.reverse: ind = ind[::-1]