Merge branch 'development' of magit1.mpie.de:damask/DAMASK into development
This commit is contained in:
Martin Diehl
commit
aeb633a42d
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@ -9,6 +9,14 @@
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/* http://stackoverflow.com/questions/30279228/is-there-an-alternative-to-getcwd-in-fortran-2003-2008 */
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int isdirectory_c(const char *dir){
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struct stat statbuf;
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if(stat(dir, &statbuf) != 0)
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return 0;
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return S_ISDIR(statbuf.st_mode);
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}
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void getcurrentworkdir_c(char cwd[], int *stat ){
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char cwd_tmp[1024];
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if(getcwd(cwd_tmp, sizeof(cwd_tmp)) == cwd_tmp){
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@ -20,9 +28,14 @@ void getcurrentworkdir_c(char cwd[], int *stat ){
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}
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}
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int isdirectory_c(const char *dir){
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struct stat statbuf;
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if(stat(dir, &statbuf) != 0)
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return 0;
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return S_ISDIR(statbuf.st_mode);
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void gethostname_c(char hostname[], int *stat ){
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char hostname_tmp[1024];
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if(gethostname(hostname_tmp, sizeof(hostname_tmp)) == 0){
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strcpy(hostname,hostname_tmp);
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*stat = 0;
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}
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else{
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*stat = 1;
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}
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}
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@ -1568,8 +1568,6 @@ subroutine IO_error(error_ID,el,ip,g,ext_msg)
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msg = 'math_check: R*v == q*v failed'
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case (410_pInt)
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msg = 'eigenvalues computation error'
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case (450_pInt)
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msg = 'unknown symmetry type specified'
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!-------------------------------------------------------------------------------------------------
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! homogenization errors
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@ -1450,7 +1450,7 @@ pure function math_EulerToQ(eulerangles)
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cos(halfangles(1)-halfangles(3)) * s, &
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sin(halfangles(1)-halfangles(3)) * s, &
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sin(halfangles(1)+halfangles(3)) * c ]
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math_EulerToQ = math_qConj(math_EulerToQ) ! convert to passive rotation
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math_EulerToQ = math_qConj(math_EulerToQ) ! convert to passive rotation
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end function math_EulerToQ
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@ -1508,7 +1508,7 @@ pure function math_EulerAxisAngleToR(axis,omega)
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real(pReal), dimension(3), intent(in) :: axis
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real(pReal), intent(in) :: omega
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math_EulerAxisAngleToR = transpose(math_axisAngleToR(axis,omega)) ! convert to passive rotation
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math_EulerAxisAngleToR = transpose(math_axisAngleToR(axis,omega)) ! convert to passive rotation
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end function math_EulerAxisAngleToR
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@ -1527,7 +1527,7 @@ pure function math_EulerAxisAngleToQ(axis,omega)
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real(pReal), dimension(3), intent(in) :: axis
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real(pReal), intent(in) :: omega
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math_EulerAxisAngleToQ = math_qConj(math_axisAngleToQ(axis,omega)) ! convert to passive rotation
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math_EulerAxisAngleToQ = math_qConj(math_axisAngleToQ(axis,omega)) ! convert to passive rotation
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end function math_EulerAxisAngleToQ
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@ -1550,7 +1550,7 @@ pure function math_axisAngleToQ(axis,omega)
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norm = sqrt(math_mul3x3(axis,axis))
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rotation: if (norm > 1.0e-8_pReal) then
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axisNrm = axis/norm ! normalize axis to be sure
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axisNrm = axis/norm ! normalize axis to be sure
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math_axisAngleToQ = [cos(0.5_pReal*omega), sin(0.5_pReal*omega) * axisNrm(1:3)]
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else rotation
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math_axisAngleToQ = [1.0_pReal,0.0_pReal,0.0_pReal,0.0_pReal]
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@ -1864,37 +1864,29 @@ end function math_sampleGaussVar
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!--------------------------------------------------------------------------------------------------
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!> @brief symmetrically equivalent Euler angles for given sample symmetry 1:triclinic, 2:monoclinic, 4:orthotropic
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!> @brief symmetrically equivalent Euler angles for given sample symmetry
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!> @detail 1 (equivalent to != 2 and !=4):triclinic, 2:monoclinic, 4:orthotropic
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!--------------------------------------------------------------------------------------------------
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pure function math_symmetricEulers(sym,Euler)
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implicit none
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integer(pInt), intent(in) :: sym
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integer(pInt), intent(in) :: sym !< symmetry Class
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real(pReal), dimension(3), intent(in) :: Euler
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real(pReal), dimension(3,3) :: math_symmetricEulers
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integer(pInt) :: i,j
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math_symmetricEulers(1,1) = PI+Euler(1)
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math_symmetricEulers(2,1) = Euler(2)
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math_symmetricEulers(3,1) = Euler(3)
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math_symmetricEulers = transpose(reshape([PI+Euler(1), PI-Euler(1), 2.0_pReal*PI-Euler(1), &
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Euler(2), PI-Euler(2), PI -Euler(2), &
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Euler(3), PI+Euler(3), PI +Euler(3)],[3,3])) ! transpose is needed to have symbolic notation instead of column-major
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math_symmetricEulers(1,2) = PI-Euler(1)
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math_symmetricEulers(2,2) = PI-Euler(2)
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math_symmetricEulers(3,2) = PI+Euler(3)
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math_symmetricEulers(1,3) = 2.0_pReal*PI-Euler(1)
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math_symmetricEulers(2,3) = PI-Euler(2)
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math_symmetricEulers(3,3) = PI+Euler(3)
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forall (i=1_pInt:3_pInt,j=1_pInt:3_pInt) math_symmetricEulers(j,i) = modulo(math_symmetricEulers(j,i),2.0_pReal*pi)
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math_symmetricEulers = modulo(math_symmetricEulers,2.0_pReal*pi)
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select case (sym)
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case (4_pInt) ! all done
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case (4_pInt) ! orthotropic: all done
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case (2_pInt) ! return only first
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case (2_pInt) ! monoclinic: return only first
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math_symmetricEulers(1:3,2:3) = 0.0_pReal
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case default ! return blank
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case default ! triclinic: return blank
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math_symmetricEulers = 0.0_pReal
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end select
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@ -20,6 +20,7 @@ module DAMASK_interface
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geometryFile = '', & !< parameter given for geometry file
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loadCaseFile = '' !< parameter given for load case file
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character(len=1024), private :: workingDirectory !< accessed by getSolverWorkingDirectoryName for compatibility reasons
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character, private,parameter :: pathSep = '/'
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public :: &
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getSolverWorkingDirectoryName, &
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@ -31,7 +32,6 @@ module DAMASK_interface
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getLoadCaseFile, &
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rectifyPath, &
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makeRelativePath, &
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getPathSep, &
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IIO_stringValue, &
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IIO_intValue, &
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IIO_lc, &
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@ -44,6 +44,8 @@ contains
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!--------------------------------------------------------------------------------------------------
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subroutine DAMASK_interface_init()
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use, intrinsic :: iso_fortran_env ! to get compiler_version and compiler_options (at least for gfortran 4.6 at the moment)
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use system_routines, only: &
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getHostName
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implicit none
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character(len=1024) :: &
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@ -64,6 +66,7 @@ subroutine DAMASK_interface_init()
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integer, dimension(8) :: &
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dateAndTime ! type default integer
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PetscErrorCode :: ierr
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logical :: error
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external :: &
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quit,&
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MPI_Comm_rank,&
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@ -116,54 +119,52 @@ subroutine DAMASK_interface_init()
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tag = IIO_lc(IIO_stringValue(commandLine,chunkPos,i)) ! extract key
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select case(tag)
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case ('-h','--help')
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mainProcess2: if (worldrank == 0) then
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write(6,'(a)') ' #######################################################################'
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write(6,'(a)') ' DAMASK_spectral:'
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write(6,'(a)') ' The spectral method boundary value problem solver for'
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write(6,'(a)') ' the Düsseldorf Advanced Material Simulation Kit'
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write(6,'(a,/)')' #######################################################################'
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write(6,'(a,/)')' Valid command line switches:'
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write(6,'(a)') ' --geom (-g, --geometry)'
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write(6,'(a)') ' --load (-l, --loadcase)'
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write(6,'(a)') ' --workingdir (-w, --wd, --workingdirectory, -d, --directory)'
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write(6,'(a)') ' --restart (-r, --rs)'
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write(6,'(a)') ' --help (-h)'
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write(6,'(/,a)')' -----------------------------------------------------------------------'
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write(6,'(a)') ' Mandatory arguments:'
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write(6,'(/,a)')' --geom PathToGeomFile/NameOfGeom.geom'
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write(6,'(a)') ' Specifies the location of the geometry definition file,'
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write(6,'(a)') ' if no extension is given, .geom will be appended.'
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write(6,'(a)') ' "PathToGeomFile" will be the working directory if not specified'
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write(6,'(a)') ' via --workingdir.'
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write(6,'(a)') ' Make sure the file "material.config" exists in the working'
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write(6,'(a)') ' directory.'
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write(6,'(a)') ' For further configuration place "numerics.config"'
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write(6,'(a)')' and "numerics.config" in that directory.'
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write(6,'(/,a)')' --load PathToLoadFile/NameOfLoadFile.load'
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write(6,'(a)') ' Specifies the location of the load case definition file,'
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write(6,'(a)') ' if no extension is given, .load will be appended.'
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write(6,'(/,a)')' -----------------------------------------------------------------------'
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write(6,'(a)') ' Optional arguments:'
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write(6,'(/,a)')' --workingdirectory PathToWorkingDirectory'
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write(6,'(a)') ' Specifies the working directory and overwrites the default'
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write(6,'(a)') ' "PathToGeomFile".'
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write(6,'(a)') ' Make sure the file "material.config" exists in the working'
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write(6,'(a)') ' directory.'
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write(6,'(a)') ' For further configuration place "numerics.config"'
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write(6,'(a)')' and "numerics.config" in that directory.'
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write(6,'(/,a)')' --restart XX'
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write(6,'(a)') ' Reads in total increment No. XX-1 and continues to'
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write(6,'(a)') ' calculate total increment No. XX.'
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write(6,'(a)') ' Appends to existing results file '
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write(6,'(a)') ' "NameOfGeom_NameOfLoadFile.spectralOut".'
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write(6,'(a)') ' Works only if the restart information for total increment'
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write(6,'(a)') ' No. XX-1 is available in the working directory.'
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write(6,'(/,a)')' -----------------------------------------------------------------------'
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write(6,'(a)') ' Help:'
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write(6,'(/,a)')' --help'
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write(6,'(a,/)')' Prints this message and exits'
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call quit(0_pInt) ! normal Termination
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endif mainProcess2
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write(6,'(a)') ' #######################################################################'
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write(6,'(a)') ' DAMASK_spectral:'
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write(6,'(a)') ' The spectral method boundary value problem solver for'
|
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write(6,'(a)') ' the Düsseldorf Advanced Material Simulation Kit'
|
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write(6,'(a,/)')' #######################################################################'
|
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write(6,'(a,/)')' Valid command line switches:'
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write(6,'(a)') ' --geom (-g, --geometry)'
|
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write(6,'(a)') ' --load (-l, --loadcase)'
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write(6,'(a)') ' --workingdir (-w, --wd, --workingdirectory, -d, --directory)'
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write(6,'(a)') ' --restart (-r, --rs)'
|
||||
write(6,'(a)') ' --help (-h)'
|
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write(6,'(/,a)')' -----------------------------------------------------------------------'
|
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write(6,'(a)') ' Mandatory arguments:'
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||||
write(6,'(/,a)')' --geom PathToGeomFile/NameOfGeom.geom'
|
||||
write(6,'(a)') ' Specifies the location of the geometry definition file,'
|
||||
write(6,'(a)') ' if no extension is given, .geom will be appended.'
|
||||
write(6,'(a)') ' "PathToGeomFile" will be the working directory if not specified'
|
||||
write(6,'(a)') ' via --workingdir.'
|
||||
write(6,'(a)') ' Make sure the file "material.config" exists in the working'
|
||||
write(6,'(a)') ' directory.'
|
||||
write(6,'(a)') ' For further configuration place "numerics.config"'
|
||||
write(6,'(a)')' and "numerics.config" in that directory.'
|
||||
write(6,'(/,a)')' --load PathToLoadFile/NameOfLoadFile.load'
|
||||
write(6,'(a)') ' Specifies the location of the load case definition file,'
|
||||
write(6,'(a)') ' if no extension is given, .load will be appended.'
|
||||
write(6,'(/,a)')' -----------------------------------------------------------------------'
|
||||
write(6,'(a)') ' Optional arguments:'
|
||||
write(6,'(/,a)')' --workingdirectory PathToWorkingDirectory'
|
||||
write(6,'(a)') ' Specifies the working directory and overwrites the default'
|
||||
write(6,'(a)') ' "PathToGeomFile".'
|
||||
write(6,'(a)') ' Make sure the file "material.config" exists in the working'
|
||||
write(6,'(a)') ' directory.'
|
||||
write(6,'(a)') ' For further configuration place "numerics.config"'
|
||||
write(6,'(a)')' and "numerics.config" in that directory.'
|
||||
write(6,'(/,a)')' --restart XX'
|
||||
write(6,'(a)') ' Reads in total increment No. XX-1 and continues to'
|
||||
write(6,'(a)') ' calculate total increment No. XX.'
|
||||
write(6,'(a)') ' Appends to existing results file '
|
||||
write(6,'(a)') ' "NameOfGeom_NameOfLoadFile.spectralOut".'
|
||||
write(6,'(a)') ' Works only if the restart information for total increment'
|
||||
write(6,'(a)') ' No. XX-1 is available in the working directory.'
|
||||
write(6,'(/,a)')' -----------------------------------------------------------------------'
|
||||
write(6,'(a)') ' Help:'
|
||||
write(6,'(/,a)')' --help'
|
||||
write(6,'(a,/)')' Prints this message and exits'
|
||||
call quit(0_pInt) ! normal Termination
|
||||
case ('-l', '--load', '--loadcase')
|
||||
loadcaseArg = IIO_stringValue(commandLine,chunkPos,i+1_pInt)
|
||||
case ('-g', '--geom', '--geometry')
|
||||
|
|
@ -185,25 +186,23 @@ subroutine DAMASK_interface_init()
|
|||
geometryFile = getGeometryFile(geometryArg)
|
||||
loadCaseFile = getLoadCaseFile(loadCaseArg)
|
||||
|
||||
call get_environment_variable('HOSTNAME',hostName)
|
||||
call get_environment_variable('USER',userName)
|
||||
mainProcess3: if (worldrank == 0) then
|
||||
write(6,'(a,a)') ' Host name: ', trim(hostName)
|
||||
write(6,'(a,a)') ' User name: ', trim(userName)
|
||||
write(6,'(a,a)') ' Path separator: ', getPathSep()
|
||||
write(6,'(a,a)') ' Command line call: ', trim(commandLine)
|
||||
if (len(trim(workingDirArg))>0) &
|
||||
write(6,'(a,a)') ' Working dir argument: ', trim(workingDirArg)
|
||||
write(6,'(a,a)') ' Geometry argument: ', trim(geometryArg)
|
||||
write(6,'(a,a)') ' Loadcase argument: ', trim(loadcaseArg)
|
||||
write(6,'(a,a)') ' Working directory: ', trim(getSolverWorkingDirectoryName())
|
||||
write(6,'(a,a)') ' Geometry file: ', trim(geometryFile)
|
||||
write(6,'(a,a)') ' Loadcase file: ', trim(loadCaseFile)
|
||||
write(6,'(a,a)') ' Solver job name: ', trim(getSolverJobName())
|
||||
if (SpectralRestartInc > 1_pInt) &
|
||||
write(6,'(a,i6.6)') ' Restart at increment: ', spectralRestartInc
|
||||
write(6,'(a,l1,/)') ' Append to result file: ', appendToOutFile
|
||||
endif mainProcess3
|
||||
error = getHostName(hostName)
|
||||
write(6,'(a,a)') ' Host name: ', trim(hostName)
|
||||
write(6,'(a,a)') ' User name: ', trim(userName)
|
||||
write(6,'(a,a)') ' Path separator: ', pathSep
|
||||
write(6,'(a,a)') ' Command line call: ', trim(commandLine)
|
||||
if (len(trim(workingDirArg))>0) &
|
||||
write(6,'(a,a)') ' Working dir argument: ', trim(workingDirArg)
|
||||
write(6,'(a,a)') ' Geometry argument: ', trim(geometryArg)
|
||||
write(6,'(a,a)') ' Loadcase argument: ', trim(loadcaseArg)
|
||||
write(6,'(a,a)') ' Working directory: ', trim(getSolverWorkingDirectoryName())
|
||||
write(6,'(a,a)') ' Geometry file: ', trim(geometryFile)
|
||||
write(6,'(a,a)') ' Loadcase file: ', trim(loadCaseFile)
|
||||
write(6,'(a,a)') ' Solver job name: ', trim(getSolverJobName())
|
||||
if (SpectralRestartInc > 1_pInt) &
|
||||
write(6,'(a,i6.6)') ' Restart at increment: ', spectralRestartInc
|
||||
write(6,'(a,l1,/)') ' Append to result file: ', appendToOutFile
|
||||
|
||||
end subroutine DAMASK_interface_init
|
||||
|
||||
|
|
@ -222,11 +221,9 @@ character(len=1024) function storeWorkingDirectory(workingDirectoryArg,geometryA
|
|||
character(len=*), intent(in) :: workingDirectoryArg !< working directory argument
|
||||
character(len=*), intent(in) :: geometryArg !< geometry argument
|
||||
character(len=1024) :: cwd
|
||||
character :: pathSep
|
||||
logical :: error
|
||||
external :: quit
|
||||
|
||||
pathSep = getPathSep()
|
||||
wdGiven: if (len(workingDirectoryArg)>0) then
|
||||
absolutePath: if (workingDirectoryArg(1:1) == pathSep) then
|
||||
storeWorkingDirectory = workingDirectoryArg
|
||||
|
|
@ -262,6 +259,7 @@ end function storeWorkingDirectory
|
|||
character(len=1024) function getSolverWorkingDirectoryName()
|
||||
|
||||
implicit none
|
||||
|
||||
getSolverWorkingDirectoryName = workingDirectory
|
||||
|
||||
end function getSolverWorkingDirectoryName
|
||||
|
|
@ -274,10 +272,8 @@ character(len=1024) function getSolverJobName()
|
|||
|
||||
implicit none
|
||||
integer :: posExt,posSep
|
||||
character :: pathSep
|
||||
character(len=1024) :: tempString
|
||||
|
||||
pathSep = getPathSep()
|
||||
|
||||
tempString = geometryFile
|
||||
posExt = scan(tempString,'.',back=.true.)
|
||||
|
|
@ -308,11 +304,9 @@ character(len=1024) function getGeometryFile(geometryParameter)
|
|||
cwd
|
||||
integer :: posExt, posSep
|
||||
logical :: error
|
||||
character :: pathSep
|
||||
external :: quit
|
||||
|
||||
getGeometryFile = geometryParameter
|
||||
pathSep = getPathSep()
|
||||
posExt = scan(getGeometryFile,'.',back=.true.)
|
||||
posSep = scan(getGeometryFile,pathSep,back=.true.)
|
||||
|
||||
|
|
@ -344,11 +338,9 @@ character(len=1024) function getLoadCaseFile(loadCaseParameter)
|
|||
cwd
|
||||
integer :: posExt, posSep
|
||||
logical :: error
|
||||
character :: pathSep
|
||||
external :: quit
|
||||
|
||||
getLoadCaseFile = loadcaseParameter
|
||||
pathSep = getPathSep()
|
||||
posExt = scan(getLoadCaseFile,'.',back=.true.)
|
||||
posSep = scan(getLoadCaseFile,pathSep,back=.true.)
|
||||
|
||||
|
|
@ -374,11 +366,8 @@ function rectifyPath(path)
|
|||
implicit none
|
||||
character(len=*) :: path
|
||||
character(len=len_trim(path)) :: rectifyPath
|
||||
character :: pathSep
|
||||
integer :: i,j,k,l ! no pInt
|
||||
|
||||
pathSep = getPathSep()
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! remove /./ from path
|
||||
l = len_trim(path)
|
||||
|
|
@ -415,10 +404,8 @@ character(len=1024) function makeRelativePath(a,b)
|
|||
|
||||
implicit none
|
||||
character (len=*) :: a,b
|
||||
character :: pathSep
|
||||
integer :: i,posLastCommonSlash,remainingSlashes !no pInt
|
||||
|
||||
pathSep = getPathSep()
|
||||
posLastCommonSlash = 0
|
||||
remainingSlashes = 0
|
||||
|
||||
|
|
@ -434,35 +421,6 @@ character(len=1024) function makeRelativePath(a,b)
|
|||
end function makeRelativePath
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief counting / and \ in $PATH System variable the character occuring more often is assumed
|
||||
! to be the path separator
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
character function getPathSep()
|
||||
|
||||
implicit none
|
||||
character(len=2048) :: &
|
||||
path
|
||||
integer(pInt) :: &
|
||||
backslash = 0_pInt, &
|
||||
slash = 0_pInt
|
||||
integer :: i
|
||||
|
||||
call get_environment_variable('PATH',path)
|
||||
do i=1, len(trim(path))
|
||||
if (path(i:i)=='/') slash = slash + 1_pInt
|
||||
if (path(i:i)=='\') backslash = backslash + 1_pInt
|
||||
enddo
|
||||
|
||||
if (backslash>slash) then
|
||||
getPathSep = '\'
|
||||
else
|
||||
getPathSep = '/'
|
||||
endif
|
||||
|
||||
end function getPathSep
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief taken from IO, check IO_stringValue for documentation
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
|
|
|
|||
|
|
@ -9,7 +9,8 @@ module system_routines
|
|||
|
||||
public :: &
|
||||
isDirectory, &
|
||||
getCWD
|
||||
getCWD, &
|
||||
getHostName
|
||||
|
||||
interface
|
||||
|
||||
|
|
@ -29,6 +30,14 @@ interface
|
|||
integer(C_INT),intent(out) :: stat
|
||||
end subroutine getCurrentWorkDir_C
|
||||
|
||||
subroutine getHostName_C(str, stat) bind(C)
|
||||
use, intrinsic :: ISO_C_Binding, only: &
|
||||
C_INT, &
|
||||
C_CHAR
|
||||
character(kind=C_CHAR), dimension(1024), intent(out) :: str ! C string is an array
|
||||
integer(C_INT),intent(out) :: stat
|
||||
end subroutine getHostName_C
|
||||
|
||||
end interface
|
||||
|
||||
|
||||
|
|
@ -85,5 +94,34 @@ logical function getCWD(str)
|
|||
|
||||
end function getCWD
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief gets the current host name
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
logical function getHostName(str)
|
||||
use, intrinsic :: ISO_C_Binding, only: &
|
||||
C_INT, &
|
||||
C_CHAR, &
|
||||
C_NULL_CHAR
|
||||
|
||||
implicit none
|
||||
character(len=*), intent(out) :: str
|
||||
character(kind=C_CHAR), dimension(1024) :: strFixedLength ! C string is an array
|
||||
integer(C_INT) :: stat
|
||||
integer :: i
|
||||
|
||||
str = repeat('',len(str))
|
||||
call getHostName_C(strFixedLength,stat)
|
||||
do i=1,1024 ! copy array components until Null string is found
|
||||
if (strFixedLength(i) /= C_NULL_CHAR) then
|
||||
str(i:i)=strFixedLength(i)
|
||||
else
|
||||
exit
|
||||
endif
|
||||
enddo
|
||||
getHostName=merge(.True.,.False.,stat /= 0_C_INT)
|
||||
|
||||
end function getHostName
|
||||
|
||||
end module system_routines
|
||||
|
||||
|
|
|
|||
|
|
@ -8,32 +8,20 @@ plasticity nonlocal
|
|||
(output) rho_edge
|
||||
(output) rho_screw
|
||||
(output) rho_sgl
|
||||
(output) rho_sgl_edge
|
||||
(output) rho_sgl_edge_pos
|
||||
(output) rho_sgl_edge_neg
|
||||
(output) rho_sgl_screw
|
||||
(output) rho_sgl_screw_pos
|
||||
(output) rho_sgl_screw_neg
|
||||
(output) rho_sgl_mobile
|
||||
(output) rho_sgl_edge_mobile
|
||||
(output) rho_sgl_edge_pos_mobile
|
||||
(output) rho_sgl_edge_neg_mobile
|
||||
(output) rho_sgl_screw_mobile
|
||||
(output) rho_sgl_screw_pos_mobile
|
||||
(output) rho_sgl_screw_neg_mobile
|
||||
(output) rho_sgl_immobile
|
||||
(output) rho_sgl_edge_immobile
|
||||
(output) rho_sgl_edge_pos_immobile
|
||||
(output) rho_sgl_edge_neg_immobile
|
||||
(output) rho_sgl_screw_immobile
|
||||
(output) rho_sgl_screw_pos_immobile
|
||||
(output) rho_sgl_screw_neg_immobile
|
||||
(output) rho_dip
|
||||
(output) rho_dip_edge
|
||||
(output) rho_dip_screw
|
||||
(output) excess_rho
|
||||
(output) excess_rho_edge
|
||||
(output) excess_rho_screw
|
||||
(output) rho_forest
|
||||
(output) delta
|
||||
(output) delta_sgl
|
||||
|
|
@ -47,10 +35,8 @@ plasticity nonlocal
|
|||
(output) rho_dot_sgl
|
||||
(output) rho_dot_sgl_mobile
|
||||
(output) rho_dot_dip
|
||||
(output) rho_dot_gen
|
||||
(output) rho_dot_gen_edge
|
||||
(output) rho_dot_gen_screw
|
||||
(output) rho_dot_sgl2dip
|
||||
(output) rho_dot_sgl2dip_edge
|
||||
(output) rho_dot_sgl2dip_screw
|
||||
(output) rho_dot_ann_ath
|
||||
|
|
@ -66,24 +52,6 @@ plasticity nonlocal
|
|||
(output) velocity_edge_neg
|
||||
(output) velocity_screw_pos
|
||||
(output) velocity_screw_neg
|
||||
(output) slipdirection.x
|
||||
(output) slipdirection.y
|
||||
(output) slipdirection.z
|
||||
(output) slipnormal.x
|
||||
(output) slipnormal.y
|
||||
(output) slipnormal.z
|
||||
(output) fluxDensity_edge_pos.x
|
||||
(output) fluxDensity_edge_pos.y
|
||||
(output) fluxDensity_edge_pos.z
|
||||
(output) fluxDensity_edge_neg.x
|
||||
(output) fluxDensity_edge_neg.y
|
||||
(output) fluxDensity_edge_neg.z
|
||||
(output) fluxDensity_screw_pos.x
|
||||
(output) fluxDensity_screw_pos.y
|
||||
(output) fluxDensity_screw_pos.z
|
||||
(output) fluxDensity_screw_neg.x
|
||||
(output) fluxDensity_screw_neg.y
|
||||
(output) fluxDensity_screw_neg.z
|
||||
(output) maximumDipoleHeight_edge
|
||||
(output) maximumDipoleHeight_screw
|
||||
(output) accumulated_shear
|
||||
|
|
|
|||
|
|
@ -14,8 +14,6 @@ plasticity nonlocal
|
|||
(output) rho_dip_edge
|
||||
(output) rho_dip_screw
|
||||
(output) rho_forest
|
||||
(output) excess_rho_edge
|
||||
(output) excess_rho_screw
|
||||
(output) accumulatedshear
|
||||
(output) shearrate
|
||||
(output) resolvedstress
|
||||
|
|
@ -30,24 +28,6 @@ plasticity nonlocal
|
|||
(output) rho_dot_edgejogs
|
||||
(output) rho_dot_flux_edge
|
||||
(output) rho_dot_flux_screw
|
||||
(output) slipdirection.x
|
||||
(output) slipdirection.y
|
||||
(output) slipdirection.z
|
||||
(output) slipnormal.x
|
||||
(output) slipnormal.y
|
||||
(output) slipnormal.z
|
||||
(output) fluxdensity_edge_pos.x
|
||||
(output) fluxdensity_edge_pos.y
|
||||
(output) fluxdensity_edge_pos.z
|
||||
(output) fluxdensity_edge_neg.x
|
||||
(output) fluxdensity_edge_neg.y
|
||||
(output) fluxdensity_edge_neg.z
|
||||
(output) fluxdensity_screw_pos.x
|
||||
(output) fluxdensity_screw_pos.y
|
||||
(output) fluxdensity_screw_pos.z
|
||||
(output) fluxdensity_screw_neg.x
|
||||
(output) fluxdensity_screw_neg.y
|
||||
(output) fluxdensity_screw_neg.z
|
||||
|
||||
lattice_structure fcc
|
||||
Nslip 12 # number of slip systems per family
|
||||
|
|
|
|||
|
|
@ -7,11 +7,6 @@ plasticity phenopowerlaw
|
|||
(output) resolvedstress_slip
|
||||
(output) accumulated_shear_slip
|
||||
(output) totalshear
|
||||
(output) resistance_twin
|
||||
(output) shearrate_twin
|
||||
(output) resolvedstress_twin
|
||||
(output) accumulated_shear_twin
|
||||
(output) totalvolfrac_twin
|
||||
|
||||
lattice_structure fcc
|
||||
Nslip 12 # per family
|
||||
|
|
@ -26,19 +21,6 @@ n_slip 20
|
|||
tau0_slip 31e6 # per family
|
||||
tausat_slip 63e6 # per family
|
||||
a_slip 2.25
|
||||
gdot0_twin 0.001
|
||||
n_twin 20
|
||||
tau0_twin 31e6 # per family
|
||||
s_pr 0 # push-up factor for slip saturation due to twinning
|
||||
twin_b 0
|
||||
twin_c 0
|
||||
twin_d 0
|
||||
twin_e 0
|
||||
h0_slipslip 75e6
|
||||
h0_twinslip 0
|
||||
h0_twintwin 0
|
||||
interaction_slipslip 1 1 1.4 1.4 1.4 1.4
|
||||
interaction_sliptwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
||||
interaction_twinslip 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
||||
interaction_twintwin 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
|
||||
atol_resistance 1
|
||||
|
|
|
|||
|
|
@ -995,11 +995,17 @@ class Orientation:
|
|||
relationModel,
|
||||
direction,
|
||||
targetSymmetry = None):
|
||||
"""
|
||||
orientation relationship
|
||||
|
||||
positive number: fcc --> bcc
|
||||
negative number: bcc --> fcc
|
||||
"""
|
||||
if relationModel not in ['KS','GT','GTdash','NW','Pitsch','Bain']: return None
|
||||
if int(direction) == 0: return None
|
||||
|
||||
# KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592 DOES THIS PAPER EXISTS?
|
||||
# KS from S. Morito et al./Journal of Alloys and Compounds 5775 (2013) S587-S592
|
||||
# for KS rotation matrices also check K. Kitahara et al./Acta Materialia 54 (2006) 1279-1288
|
||||
# GT from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
|
||||
# GT' from Y. He et al./Journal of Applied Crystallography (2006). 39, 72-81
|
||||
# NW from H. Kitahara et al./Materials Characterization 54 (2005) 378-386
|
||||
|
|
@ -1226,14 +1232,14 @@ class Orientation:
|
|||
myPlane /= np.linalg.norm(myPlane)
|
||||
myNormal = [float(i) for i in normals[relationModel][variant,me]] # map(float, planes[...]) does not work in python 3
|
||||
myNormal /= np.linalg.norm(myNormal)
|
||||
myMatrix = np.array([myPlane,myNormal,np.cross(myPlane,myNormal)])
|
||||
myMatrix = np.array([myNormal,np.cross(myPlane,myNormal),myPlane]).T
|
||||
|
||||
otherPlane = [float(i) for i in planes[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
|
||||
otherPlane /= np.linalg.norm(otherPlane)
|
||||
otherNormal = [float(i) for i in normals[relationModel][variant,other]] # map(float, planes[...]) does not work in python 3
|
||||
otherNormal /= np.linalg.norm(otherNormal)
|
||||
otherMatrix = np.array([otherPlane,otherNormal,np.cross(otherPlane,otherNormal)])
|
||||
otherMatrix = np.array([otherNormal,np.cross(otherPlane,otherNormal),otherPlane]).T
|
||||
|
||||
rot=np.dot(otherMatrix.T,myMatrix)
|
||||
rot=np.dot(otherMatrix,myMatrix.T)
|
||||
|
||||
return Orientation(matrix=np.dot(rot,self.asMatrix())) # no symmetry information ??
|
||||
|
|
|
|||
|
|
@ -23,6 +23,8 @@ class Test():
|
|||
'keep': False,
|
||||
'accept': False,
|
||||
'updateRequest': False,
|
||||
'show': False,
|
||||
'select': None,
|
||||
}
|
||||
for arg in defaults.keys():
|
||||
setattr(self,arg,kwargs.get(arg) if kwargs.get(arg) else defaults[arg])
|
||||
|
|
@ -58,10 +60,18 @@ class Test():
|
|||
action = "store_true",
|
||||
dest = "accept",
|
||||
help = "calculate results but always consider test as successfull")
|
||||
|
||||
self.parser.add_option("-l", "--list",
|
||||
action = "store_true",
|
||||
dest = "show",
|
||||
help = "show all test variants and do no calculation")
|
||||
self.parser.add_option("-s", "--select",
|
||||
dest = "select",
|
||||
help = "run test of given name only")
|
||||
self.parser.set_defaults(keep = self.keep,
|
||||
accept = self.accept,
|
||||
update = self.updateRequest,
|
||||
show = self.show,
|
||||
select = self.select,
|
||||
)
|
||||
|
||||
|
||||
|
|
@ -73,21 +83,26 @@ class Test():
|
|||
self.prepareAll()
|
||||
|
||||
for variant,name in enumerate(self.variants):
|
||||
try:
|
||||
if not self.options.keep:
|
||||
self.prepare(variant)
|
||||
self.run(variant)
|
||||
if self.options.show:
|
||||
logging.critical('{}: {}'.format(variant,name))
|
||||
elif self.options.select is not None and name != self.options.select:
|
||||
pass
|
||||
else:
|
||||
try:
|
||||
if not self.options.keep:
|
||||
self.prepare(variant)
|
||||
self.run(variant)
|
||||
|
||||
self.postprocess(variant)
|
||||
self.postprocess(variant)
|
||||
|
||||
if self.options.update:
|
||||
if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))
|
||||
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
|
||||
return variant+1 # return culprit
|
||||
if self.options.update:
|
||||
if self.update(variant) != 0: logging.critical('update for "{}" failed.'.format(name))
|
||||
elif not (self.options.accept or self.compare(variant)): # no update, do comparison
|
||||
return variant+1 # return culprit
|
||||
|
||||
except Exception as e :
|
||||
logging.critical('exception during variant execution: {}'.format(e))
|
||||
return variant+1 # return culprit
|
||||
except Exception as e :
|
||||
logging.critical('exception during variant execution: {}'.format(e))
|
||||
return variant+1 # return culprit
|
||||
return 0
|
||||
|
||||
def feasible(self):
|
||||
|
|
|
|||
|
|
@ -0,0 +1,74 @@
|
|||
#!/usr/bin/env python2.7
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,h5py
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog [geomfile[s]]', description = """
|
||||
Convert DREAM3D file to ASCIItable
|
||||
|
||||
""", version = scriptID)
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
rootDir ='DataContainers/ImageDataContainer'
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: parser.error('no input file specified.')
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(outname = os.path.splitext(name)[0]+'.txt',
|
||||
buffered = False
|
||||
)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
inFile = h5py.File(name, 'r')
|
||||
|
||||
grid = inFile[rootDir+'/_SIMPL_GEOMETRY/DIMENSIONS'][...]
|
||||
|
||||
|
||||
# --- read comments --------------------------------------------------------------------------------
|
||||
|
||||
coords = (np.mgrid[0:grid[2], 0:grid[1], 0: grid[0]]).reshape(3, -1).T
|
||||
coords = (np.fliplr(coords)*inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...] \
|
||||
+ inFile[rootDir+'/_SIMPL_GEOMETRY/ORIGIN'][...] \
|
||||
+ inFile[rootDir+'/_SIMPL_GEOMETRY/SPACING'][...]*0.5)
|
||||
|
||||
table.data = np.hstack( (coords,
|
||||
inFile[rootDir+'/CellData/EulerAngles'][...].reshape(grid.prod(),3),
|
||||
inFile[rootDir+'/CellData/Phases'][...].reshape(grid.prod(),1),
|
||||
inFile[rootDir+'/CellData/Confidence Index'][...].reshape(grid.prod(),1),
|
||||
inFile[rootDir+'/CellData/Fit'][...].reshape(grid.prod(),1),
|
||||
inFile[rootDir+'/CellData/Image Quality'][...].reshape(grid.prod(),1)))
|
||||
|
||||
|
||||
labels = ['1_pos','2_pos','3_pos',
|
||||
'1_Euler','2_Euler','3_Euler',
|
||||
'PhaseID','CI','Fit','IQ']
|
||||
try:
|
||||
table.data = np.hstack((table.data, inFile[rootDir+'/CellData/FeatureIds'][...].reshape(grid.prod(),1)))
|
||||
labels.append(['FeatureID'])
|
||||
except Exception:
|
||||
pass
|
||||
|
||||
# ------------------------------------------ assemble header ---------------------------------------
|
||||
table.labels_clear()
|
||||
table.labels_append(labels,reset = True)
|
||||
table.head_write()
|
||||
|
||||
# ------------------------------------------ finalize output ---------------------------------------
|
||||
table.data_writeArray() #(fmt='%e2.2')
|
||||
table.close()
|
||||
|
|
@ -11,7 +11,7 @@ do
|
|||
< $geom \
|
||||
| \
|
||||
vtk_addRectilinearGridData \
|
||||
--scalar microstructure \
|
||||
--data microstructure \
|
||||
--inplace \
|
||||
--vtk ${geom%.*}.vtk
|
||||
rm ${geom%.*}.vtk
|
||||
|
|
|
|||
|
|
@ -89,9 +89,9 @@ for name in filenames:
|
|||
|
||||
# Calculates gaussian weights for simulating 3d diffusion
|
||||
gauss = np.exp(-(X*X + Y*Y + Z*Z)/(2.0*options.d*options.d))/math.pow(2.0*np.pi*options.d*options.d,1.5)
|
||||
gauss[:,:,grid[2]/2::] = gauss[:,:,round(grid[2]/2.)-1::-1] # trying to cope with uneven (odd) grid size
|
||||
gauss[:,grid[1]/2::,:] = gauss[:,round(grid[1]/2.)-1::-1,:]
|
||||
gauss[grid[0]/2::,:,:] = gauss[round(grid[0]/2.)-1::-1,:,:]
|
||||
gauss[:,:,grid[2]/2::] = gauss[:,:,int(round(grid[2]/2.))-1::-1] # trying to cope with uneven (odd) grid size
|
||||
gauss[:,grid[1]/2::,:] = gauss[:,int(round(grid[1]/2.))-1::-1,:]
|
||||
gauss[grid[0]/2::,:,:] = gauss[int(round(grid[0]/2.))-1::-1,:,:]
|
||||
gauss = np.fft.rfftn(gauss)
|
||||
|
||||
interfacialEnergy = lambda A,B: (A*B != 0)*(A != B)*1.0 #1.0 if A & B are distinct & nonzero, 0.0 otherwise
|
||||
|
|
|
|||
|
|
@ -0,0 +1,117 @@
|
|||
#!/usr/bin/env python2.7
|
||||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import os,sys,math
|
||||
import numpy as np
|
||||
import damask
|
||||
from optparse import OptionParser
|
||||
|
||||
scriptName = os.path.splitext(os.path.basename(__file__))[0]
|
||||
scriptID = ' '.join([scriptName,damask.version])
|
||||
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
# MAIN
|
||||
#--------------------------------------------------------------------------------------------------
|
||||
|
||||
validDirections = ['x','y','z']
|
||||
parser = OptionParser(option_class=damask.extendableOption, usage='%prog options [geomfile(s)]', description = """
|
||||
Mirrors spectral geometry description along given directions.
|
||||
|
||||
""", version=scriptID)
|
||||
|
||||
parser.add_option('-d','--direction',
|
||||
dest = 'directions',
|
||||
action = 'extend', metavar = '<string LIST>',
|
||||
help = "directions in which to mirror {'x','y','z'}")
|
||||
|
||||
(options, filenames) = parser.parse_args()
|
||||
|
||||
if options.directions is None:
|
||||
parser.error('no direction given.')
|
||||
if not set(options.directions).issubset(validDirections):
|
||||
invalidDirections = [str(e) for e in set(options.directions).difference(validDirections)]
|
||||
parser.error('invalid directions {}. '.format(*invalidDirections))
|
||||
|
||||
# --- loop over input files -------------------------------------------------------------------------
|
||||
|
||||
if filenames == []: filenames = [None]
|
||||
|
||||
for name in filenames:
|
||||
try:
|
||||
table = damask.ASCIItable(name = name,
|
||||
buffered = False, labeled = False)
|
||||
except: continue
|
||||
damask.util.report(scriptName,name)
|
||||
|
||||
# --- interpret header ----------------------------------------------------------------------------
|
||||
|
||||
table.head_read()
|
||||
info,extra_header = table.head_getGeom()
|
||||
|
||||
damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
|
||||
'size x y z: %s'%(' x '.join(map(str,info['size']))),
|
||||
'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
|
||||
'homogenization: %i'%info['homogenization'],
|
||||
'microstructures: %i'%info['microstructures'],
|
||||
])
|
||||
|
||||
errors = []
|
||||
if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
|
||||
if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
|
||||
if errors != []:
|
||||
damask.util.croak(errors)
|
||||
table.close(dismiss = True)
|
||||
continue
|
||||
|
||||
# --- read data ------------------------------------------------------------------------------------
|
||||
|
||||
microstructure = table.microstructure_read(info['grid']).reshape(info['grid'],order='F') # read microstructure
|
||||
|
||||
if 'z' in options.directions:
|
||||
microstructure = np.concatenate([microstructure,microstructure[:,:,::-1]],2)
|
||||
if 'y' in options.directions:
|
||||
microstructure = np.concatenate([microstructure,microstructure[:,::-1,:]],1)
|
||||
if 'x' in options.directions:
|
||||
microstructure = np.concatenate([microstructure,microstructure[::-1,:,:]],0)
|
||||
|
||||
# --- do work ------------------------------------------------------------------------------------
|
||||
|
||||
newInfo = {
|
||||
'size': microstructure.shape*info['size']/info['grid'],
|
||||
'grid': microstructure.shape,
|
||||
}
|
||||
|
||||
|
||||
# --- report ---------------------------------------------------------------------------------------
|
||||
|
||||
remarks = []
|
||||
if (any(newInfo['grid'] != info['grid'])):
|
||||
remarks.append('--> grid a b c: %s'%(' x '.join(map(str,newInfo['grid']))))
|
||||
if (any(newInfo['size'] != info['size'])):
|
||||
remarks.append('--> size x y z: %s'%(' x '.join(map(str,newInfo['size']))))
|
||||
if remarks != []: damask.util.croak(remarks)
|
||||
|
||||
# --- write header ---------------------------------------------------------------------------------
|
||||
|
||||
table.labels_clear()
|
||||
table.info_clear()
|
||||
table.info_append([
|
||||
scriptID + ' ' + ' '.join(sys.argv[1:]),
|
||||
"grid\ta {grid[0]}\tb {grid[1]}\tc {grid[2]}".format(grid=newInfo['grid']),
|
||||
"size\tx {size[0]}\ty {size[1]}\tz {size[2]}".format(size=newInfo['size']),
|
||||
"origin\tx {origin[0]}\ty {origin[1]}\tz {origin[2]}".format(origin=info['origin']),
|
||||
"homogenization\t{homog}".format(homog=info['homogenization']),
|
||||
"microstructures\t{microstructures}".format(microstructures=info['microstructures']),
|
||||
extra_header
|
||||
])
|
||||
table.head_write()
|
||||
|
||||
# --- write microstructure information ------------------------------------------------------------
|
||||
|
||||
formatwidth = int(math.floor(math.log10(microstructure.max())+1))
|
||||
table.data = microstructure.reshape((newInfo['grid'][0],np.prod(newInfo['grid'][1:])),order='F').transpose()
|
||||
table.data_writeArray('%%%ii'%(formatwidth),delimiter = ' ')
|
||||
|
||||
# --- output finalization --------------------------------------------------------------------------
|
||||
|
||||
table.close() # close ASCII table
|
||||
|
|
@ -2,6 +2,7 @@
|
|||
# -*- coding: UTF-8 no BOM -*-
|
||||
|
||||
import sys,os,math,re
|
||||
import numpy as np
|
||||
from optparse import OptionParser
|
||||
import damask
|
||||
|
||||
|
|
@ -63,9 +64,8 @@ def rcbOrientationParser(content,idcolumn):
|
|||
|
||||
grains = []
|
||||
myOrientation = [0.0,0.0,0.0]
|
||||
for line in content:
|
||||
m = re.match(r'\s*(#|$)',line)
|
||||
if m: continue # skip comments and blank lines
|
||||
for j,line in enumerate(content):
|
||||
if re.match(r'^\s*(#|$)',line): continue # skip comments and blank lines
|
||||
for grain in range(2):
|
||||
myID = int(line.split()[idcolumn+grain]) # get grain id
|
||||
myOrientation = map(float,line.split())[3*grain:3+3*grain] # get orientation
|
||||
|
|
@ -75,8 +75,8 @@ def rcbOrientationParser(content,idcolumn):
|
|||
try:
|
||||
grains[myID-1] = myOrientation # store Euler angles
|
||||
except IndexError:
|
||||
message = 'You might not have chosen the correct column for the grain IDs! Please check the "--id" option.'
|
||||
print '\033[1;31m'+message+'\033[0m\n'
|
||||
damask.util.croak('You might not have chosen the correct column for the grain IDs! '+
|
||||
'Please check the "--id" option.')
|
||||
raise
|
||||
except:
|
||||
raise
|
||||
|
|
@ -91,13 +91,13 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
x = [0.,0.]
|
||||
y = [0.,0.]
|
||||
for line in content:
|
||||
m = re.match(r'\s*(#|$)',line)
|
||||
m = re.match(r'^\s*(#|$)',line)
|
||||
if m: continue # skip comments and blank lines
|
||||
try:
|
||||
(x[0],y[0],x[1],y[1]) = map(float,line.split())[segmentcolumn:segmentcolumn+4] # get start and end coordinates of each segment.
|
||||
except IndexError:
|
||||
message = 'You might not have chosen the correct column for the segment end points! Please check the "--segment" option.'
|
||||
print '\033[1;31m'+message+'\033[0m\n'
|
||||
damask.util.croak('You might not have chosen the correct column for the segment end points! '+
|
||||
'Please check the "--segment" option.')
|
||||
raise
|
||||
except:
|
||||
raise
|
||||
|
|
@ -110,6 +110,9 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
dX = boxX[1]-boxX[0]
|
||||
dY = boxY[1]-boxY[0]
|
||||
|
||||
damask.util.croak(' bounding box {},{} -- {},{}'.format(boxX[0],boxY[0],boxX[1],boxY[1]))
|
||||
damask.util.croak(' dimension {} x {}'.format(dX,dY))
|
||||
|
||||
if size > 0.0: scalePatch = size/dX
|
||||
else: scalePatch = 1.0
|
||||
|
||||
|
|
@ -122,8 +125,7 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
grainNeighbors = []
|
||||
|
||||
for line in content:
|
||||
m = re.match(r'\s*(#|$)',line)
|
||||
if m: continue # skip comments and blank lines
|
||||
if re.match(r'^\s*(#|$)',line): continue # skip comments and blank lines
|
||||
(x[0],y[0],x[1],y[1]) = map(float,line.split())[segmentcolumn:segmentcolumn+4] # get start and end coordinates of each segment.
|
||||
(x[0],y[0]) = (M[0]*x[0]+M[1]*y[0],M[2]*x[0]+M[3]*y[0]) # apply transformation to coordinates
|
||||
(x[1],y[1]) = (M[0]*x[1]+M[1]*y[1],M[2]*x[1]+M[3]*y[1]) # to get rcb --> Euler system
|
||||
|
|
@ -133,8 +135,8 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
y[0] -= boxY[0]
|
||||
y[1] -= boxY[0]
|
||||
grainNeighbors.append(map(int,line.split()[idcolumn:idcolumn+2])) # remember right and left grain per segment
|
||||
for i in range(2): # store segment to both points
|
||||
match = False # check whether point is already known (within a small range)
|
||||
for i in range(2): # store segment to both points
|
||||
match = False # check whether point is already known (within a small range)
|
||||
for posX in connectivityXY.keys():
|
||||
if (abs(float(posX)-x[i])<dX*tolerance):
|
||||
for posY in connectivityXY[posX].keys():
|
||||
|
|
@ -144,7 +146,7 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
match = True
|
||||
break
|
||||
break
|
||||
# force to boundary if inside tolerance to it
|
||||
# force onto boundary if inside tolerance to it
|
||||
if (not match):
|
||||
if (abs(x[i])<dX*tolerance):
|
||||
x[i] = 0
|
||||
|
|
@ -168,7 +170,6 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
connectivityYX[keyY][keyX].append(segment)
|
||||
segment += 1
|
||||
|
||||
|
||||
# top border
|
||||
keyId = "0"
|
||||
boundary = connectivityYX[keyId].keys()
|
||||
|
|
@ -225,17 +226,36 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
for keyY in allkeysY:
|
||||
points.append({'coords': [float(keyX)*scalePatch,float(keyY)*scalePatch], 'segments': connectivityXY[keyX][keyY]})
|
||||
for segment in connectivityXY[keyX][keyY]:
|
||||
if (segments[segment] is None):
|
||||
segments[segment] = pointId
|
||||
else:
|
||||
segments[segment].append(pointId)
|
||||
segments[segment].append(pointId)
|
||||
pointId += 1
|
||||
|
||||
dupSegments = []
|
||||
for pointId,point in enumerate(points):
|
||||
ends = []
|
||||
goners = []
|
||||
for segment in point['segments']:
|
||||
end = segments[segment][1 if segments[segment][0] == pointId else 0]
|
||||
if end in ends:
|
||||
goners.append(segment)
|
||||
dupSegments.append(segment)
|
||||
else:
|
||||
ends.append(end)
|
||||
|
||||
for item in goners:
|
||||
point['segments'].remove(item)
|
||||
|
||||
if len(dupSegments) > 0:
|
||||
damask.util.croak(' culling {} duplicate segments...'.format(len(dupSegments)))
|
||||
for rm in dupSegments:
|
||||
segments[rm] = None
|
||||
|
||||
crappyData = False
|
||||
for pointId,point in enumerate(points):
|
||||
if len(point['segments']) < 2: # point marks a dead end!
|
||||
print "Dead end at segment %i (%f,%f)"\
|
||||
%(1+point['segments'][0],boxX[0]+point['coords'][0]/scalePatch,boxY[0]+point['coords'][1]/scalePatch,)
|
||||
damask.util.croak('dead end at segment {} for point {} ({},{}).'
|
||||
.format(point['segments'][0],
|
||||
pointId,
|
||||
boxX[0]+point['coords'][0]/scalePatch,boxY[0]+point['coords'][1]/scalePatch,))
|
||||
crappyData = True
|
||||
|
||||
grains = {'draw': [], 'legs': []}
|
||||
|
|
@ -249,58 +269,69 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
innerAngleSum = 0.0
|
||||
myWalk = point['segments'].pop()
|
||||
grainLegs = [myWalk]
|
||||
if segments[myWalk][0] == myStart:
|
||||
myEnd = segments[myWalk][1]
|
||||
else:
|
||||
myEnd = segments[myWalk][0]
|
||||
|
||||
myEnd = segments[myWalk][1 if segments[myWalk][0] == myStart else 0]
|
||||
while (myEnd != pointId):
|
||||
myV = [points[myEnd]['coords'][0]-points[myStart]['coords'][0],\
|
||||
points[myEnd]['coords'][1]-points[myStart]['coords'][1]]
|
||||
myV = [points[myEnd]['coords'][0]-points[myStart]['coords'][0],
|
||||
points[myEnd]['coords'][1]-points[myStart]['coords'][1]]
|
||||
myLen = math.sqrt(myV[0]**2+myV[1]**2)
|
||||
if myLen == 0.0: damask.util.croak('mylen is zero: point {} --> {}'.format(myStart,myEnd))
|
||||
best = {'product': -2.0, 'peek': -1, 'len': -1, 'point': -1}
|
||||
for peek in points[myEnd]['segments']: # trying in turn all segments emanating from current end
|
||||
if peek == myWalk:
|
||||
continue
|
||||
peekEnd = segments[peek][1] if segments[peek][0] == myEnd else segments[peek][0]
|
||||
peekV = [points[myEnd]['coords'][0]-points[peekEnd]['coords'][0],
|
||||
points[myEnd]['coords'][1]-points[peekEnd]['coords'][1]]
|
||||
continue # do not go back same path
|
||||
peekEnd = segments[peek][1 if segments[peek][0] == myEnd else 0]
|
||||
peekV = [points[peekEnd]['coords'][0]-points[myEnd]['coords'][0],
|
||||
points[peekEnd]['coords'][1]-points[myEnd]['coords'][1]]
|
||||
peekLen = math.sqrt(peekV[0]**2+peekV[1]**2)
|
||||
crossproduct = (myV[0]*peekV[1]-myV[1]*peekV[0])/myLen/peekLen
|
||||
dotproduct = (myV[0]*peekV[0]+myV[1]*peekV[1])/myLen/peekLen
|
||||
if crossproduct*(dotproduct+1.0) >= best['product']:
|
||||
best['product'] = crossproduct*(dotproduct+1.0)
|
||||
if peekLen == 0.0: damask.util.croak('peeklen is zero: peek point {}'.format(peek))
|
||||
crossproduct = (myV[0]*peekV[1] - myV[1]*peekV[0])/myLen/peekLen
|
||||
dotproduct = (myV[0]*peekV[0] + myV[1]*peekV[1])/myLen/peekLen
|
||||
innerAngle = math.copysign(1.0,crossproduct)*(dotproduct-1.0)
|
||||
if innerAngle >= best['product']: # takes sharpest left turn
|
||||
best['product'] = innerAngle
|
||||
best['peek'] = peek
|
||||
best['point'] = peekEnd
|
||||
|
||||
innerAngleSum += best['product']
|
||||
myWalk = best['peek']
|
||||
myStart = myEnd
|
||||
myEnd = best['point']
|
||||
|
||||
if myWalk in points[myStart]['segments']:
|
||||
points[myStart]['segments'].remove(myWalk)
|
||||
else:
|
||||
sys.stderr.write(str(myWalk)+' not in segments of point '+str(myStart)+'\n')
|
||||
damask.util.croak('{} not in segments of point {}'.format(myWalk,myStart))
|
||||
grainDraw.append(points[myStart]['coords'])
|
||||
grainLegs.append(myWalk)
|
||||
|
||||
if innerAngleSum > 0.0:
|
||||
grains['draw'].append(grainDraw)
|
||||
grains['legs'].append(grainLegs)
|
||||
else:
|
||||
grains['box'] = grainLegs
|
||||
|
||||
|
||||
# build overall data structure
|
||||
|
||||
rcData = {'dimension':[dX,dY], 'point': [],'segment': [], 'grain': [], 'grainMapping': []}
|
||||
print " dimension %g x %g"%(dX,dY)
|
||||
rcData = {'dimension':[dX,dY],
|
||||
'bounds': [[boxX[0],boxY[0]],[boxX[1],boxY[1]]],
|
||||
'scale': scalePatch,
|
||||
'point': [],
|
||||
'segment': [],
|
||||
'neighbors': [],
|
||||
'grain': [],
|
||||
'grainMapping': [],
|
||||
}
|
||||
|
||||
for point in points:
|
||||
rcData['point'].append(point['coords'])
|
||||
print " found %i points"%(len(rcData['point']))
|
||||
damask.util.croak(' found {} points'.format(len(rcData['point'])))
|
||||
|
||||
for segment in segments:
|
||||
rcData['segment'].append(segment)
|
||||
print " built %i segments"%(len(rcData['segment']))
|
||||
damask.util.croak(' built {} segments'.format(len(rcData['segment'])))
|
||||
|
||||
for neighbors in grainNeighbors:
|
||||
rcData['neighbors'].append(neighbors)
|
||||
|
||||
for legs in grains['legs']: # loop over grains
|
||||
rcData['grain'].append(legs) # store list of boundary segments
|
||||
|
|
@ -314,12 +345,11 @@ def rcbParser(content,M,size,tolerance,idcolumn,segmentcolumn):
|
|||
myNeighbors[grainNeighbors[leg][side]] = 1
|
||||
if myNeighbors: # do I have any neighbors (i.e., non-bounding box segment)
|
||||
candidateGrains = sorted(myNeighbors.iteritems(), key=lambda (k,v): (v,k), reverse=True) # sort grain counting
|
||||
if candidateGrains[0][0] not in rcData['grainMapping']: # most frequent one not yet seen?
|
||||
rcData['grainMapping'].append(candidateGrains[0][0]) # must be me then
|
||||
else:
|
||||
rcData['grainMapping'].append(candidateGrains[1][0]) # special case of bi-crystal situation...
|
||||
# most frequent one not yet seen?
|
||||
rcData['grainMapping'].append(candidateGrains[0 if candidateGrains[0][0] not in rcData['grainMapping'] else 1][0]) # must be me then
|
||||
# special case of bi-crystal situation...
|
||||
|
||||
print " found %i grains\n"%(len(rcData['grain']))
|
||||
damask.util.croak(' found {} grains'.format(len(rcData['grain'])))
|
||||
|
||||
rcData['box'] = grains['box'] if 'box' in grains else []
|
||||
|
||||
|
|
@ -670,9 +700,10 @@ def image(name,imgsize,marginX,marginY,rcData):
|
|||
draw.text([offsetX+point[0]*scaleImg,sizeY-(offsetY+point[1]*scaleImg)],"%i"%id,fill=(0,0,0))
|
||||
|
||||
for id,vertex in enumerate(rcData['segment']):
|
||||
if vertex:
|
||||
start = rcData['point'][vertex[0]]
|
||||
end = rcData['point'][vertex[1]]
|
||||
draw.text([offsetX+(start[0]+end[0])/2.0*scaleImg,sizeY-(offsetY+(start[1]+end[1])/2.0*scaleImg)],"%i"%id,fill=(0,0,128))
|
||||
draw.text([offsetX+(start[0]+end[0])/2.0*scaleImg,sizeY-(offsetY+(start[1]+end[1])/2.0*scaleImg)],"%i"%id,fill=(255,0,128))
|
||||
draw.line([offsetX+start[0]*scaleImg,sizeY-(offsetY+start[1]*scaleImg),
|
||||
offsetX+ end[0]*scaleImg,sizeY-(offsetY+ end[1]*scaleImg)],width=1,fill=(128,128,128))
|
||||
|
||||
|
|
@ -739,8 +770,8 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):
|
|||
'dimension':(xsize,ysize,zsize)}
|
||||
|
||||
frameindex=len(rcData['grain'])+1 # calculate frame index as largest grain index plus one
|
||||
dx = xsize/(xres+1) # calculate step sizes
|
||||
dy = ysize/(yres+1)
|
||||
dx = xsize/(xres) # calculate step sizes
|
||||
dy = ysize/(yres)
|
||||
|
||||
grainpoints = []
|
||||
for segments in rcData['grain']: # get segments of each grain
|
||||
|
|
@ -755,11 +786,10 @@ def fftbuild(rcData,height,xframe,yframe,resolution,extrusion):
|
|||
grainpoints.append([]) # start out blank for current grain
|
||||
for p in sorted(points, key=points.get): # loop thru set of sorted points
|
||||
grainpoints[-1].append([rcData['point'][p][0],rcData['point'][p][1]]) # append x,y of point
|
||||
|
||||
bestGuess = 0 # assume grain 0 as best guess
|
||||
for i in range(int(xres*yres)): # walk through all points in xy plane
|
||||
xtest = -xframe+((i%xres)+0.5)*dx # calculate coordinates
|
||||
ytest = -yframe+(int(i/xres)+0.5)*dy
|
||||
ytest = -yframe+((i//xres)+0.5)*dy
|
||||
if(xtest < 0 or xtest > maxX): # check wether part of frame
|
||||
if( ytest < 0 or ytest > maxY): # part of edges
|
||||
fftdata['fftpoints'].append(frameindex+2) # append frameindex to result array
|
||||
|
|
@ -789,7 +819,7 @@ reconstructed boundary file
|
|||
|
||||
meshes=['dt_planar_trimesh','af_planar_trimesh','af_planar_quadmesh']
|
||||
parser.add_option('-o', '--output', action='extend', dest='output', metavar = '<string LIST>',
|
||||
help='types of output {image, mentat, procedure, spectral}')
|
||||
help='types of output {rcb, image, mentat, procedure, spectral}')
|
||||
parser.add_option('-p', '--port', type='int', metavar = 'int',
|
||||
dest='port', help='Mentat connection port [%default]')
|
||||
parser.add_option('-2', '--twodimensional', action='store_true',
|
||||
|
|
@ -847,16 +877,15 @@ parser.set_defaults(output = [],
|
|||
|
||||
(options, args) = parser.parse_args()
|
||||
|
||||
print '\033[1m'+scriptName+'\033[0m\n'
|
||||
if not len(args):
|
||||
parser.error('no boundary file specified')
|
||||
parser.error('no boundary file specified.')
|
||||
|
||||
try:
|
||||
boundaryFile = open(args[0])
|
||||
boundarySegments = boundaryFile.readlines()
|
||||
boundaryFile.close()
|
||||
except:
|
||||
print 'unable to read boundary file "%s"'%args[0]
|
||||
damask.util.croak('unable to read boundary file "{}".'.format(args[0]))
|
||||
raise
|
||||
|
||||
options.output = [s.lower() for s in options.output] # lower case
|
||||
|
|
@ -864,18 +893,46 @@ options.idcolumn -= 1 # py
|
|||
options.segmentcolumn -= 1 # python indexing starts with 0
|
||||
|
||||
myName = os.path.splitext(args[0])[0]
|
||||
print "%s\n"%myName
|
||||
damask.util.report(scriptName,myName)
|
||||
|
||||
orientationData = rcbOrientationParser(boundarySegments,options.idcolumn)
|
||||
rcData = rcbParser(boundarySegments,options.M,options.size,options.tolerance,options.idcolumn,options.segmentcolumn)
|
||||
|
||||
# ----- write corrected RCB -----
|
||||
|
||||
Minv = np.linalg.inv(np.array(options.M).reshape(2,2))
|
||||
|
||||
if 'rcb' in options.output:
|
||||
print """# Header:
|
||||
#
|
||||
# Column 1-3: right hand average orientation (phi1, PHI, phi2 in radians)
|
||||
# Column 4-6: left hand average orientation (phi1, PHI, phi2 in radians)
|
||||
# Column 7: length (in microns)
|
||||
# Column 8: trace angle (in degrees)
|
||||
# Column 9-12: x,y coordinates of endpoints (in microns)
|
||||
# Column 13-14: IDs of right hand and left hand grains"""
|
||||
for i,(left,right) in enumerate(rcData['neighbors']):
|
||||
if rcData['segment'][i]:
|
||||
first = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][0]][0]/rcData['scale'],
|
||||
rcData['bounds'][0][1]+rcData['point'][rcData['segment'][i][0]][1]/rcData['scale'],
|
||||
]))
|
||||
second = np.dot(Minv,np.array([rcData['bounds'][0][0]+rcData['point'][rcData['segment'][i][1]][0]/rcData['scale'],
|
||||
rcData['bounds'][0][1]+rcData['point'][rcData['segment'][i][1]][1]/rcData['scale'],
|
||||
]))
|
||||
print ' '.join(map(str,orientationData[left-1]+orientationData[right-1])),
|
||||
print np.linalg.norm(first-second),
|
||||
print '0',
|
||||
print ' '.join(map(str,first)),
|
||||
print ' '.join(map(str,second)),
|
||||
print ' '.join(map(str,[left,right]))
|
||||
|
||||
# ----- write image -----
|
||||
|
||||
if 'image' in options.output and options.imgsize > 0:
|
||||
if ImageCapability:
|
||||
image(myName,options.imgsize,options.xmargin,options.ymargin,rcData)
|
||||
else:
|
||||
print '...no image drawing possible (PIL missing)...'
|
||||
damask.util.croak('...no image drawing possible (PIL missing)...')
|
||||
|
||||
# ----- write spectral geom -----
|
||||
|
||||
|
|
@ -884,8 +941,8 @@ if 'spectral' in options.output:
|
|||
|
||||
geomFile = open(myName+'_'+str(int(fftdata['resolution'][0]))+'.geom','w') # open geom file for writing
|
||||
geomFile.write('3\theader\n') # write header info
|
||||
geomFile.write('resolution a %i b %i c %i\n'%(fftdata['resolution'])) # resolution
|
||||
geomFile.write('dimension x %f y %f z %f\n'%(fftdata['dimension'])) # size
|
||||
geomFile.write('grid a %i b %i c %i\n'%(fftdata['resolution'])) # grid resolution
|
||||
geomFile.write('size x %f y %f z %f\n'%(fftdata['dimension'])) # size
|
||||
geomFile.write('homogenization 1\n') # homogenization
|
||||
for z in xrange(fftdata['resolution'][2]): # z repetions
|
||||
for y in xrange(fftdata['resolution'][1]): # each x-row separately
|
||||
|
|
@ -893,8 +950,9 @@ if 'spectral' in options.output:
|
|||
(y+1)*fftdata['resolution'][0]]))+'\n') # grain indexes, x-row per line
|
||||
geomFile.close() # close geom file
|
||||
|
||||
print('assigned %i out of %i (2D) Fourier points.'\
|
||||
%(len(fftdata['fftpoints']), int(fftdata['resolution'][0])*int(fftdata['resolution'][1])))
|
||||
damask.util.croak('assigned {} out of {} (2D) Fourier points...'
|
||||
.format(len(fftdata['fftpoints']),
|
||||
int(fftdata['resolution'][0])*int(fftdata['resolution'][1])))
|
||||
|
||||
|
||||
# ----- write Mentat procedure -----
|
||||
|
|
@ -936,7 +994,7 @@ if 'mentat' in options.output:
|
|||
if 'procedure' in options.output:
|
||||
output(outputLocals['log'],outputLocals,'Stdout')
|
||||
else:
|
||||
print '...no interaction with Mentat possible...'
|
||||
damask.util.croak('...no interaction with Mentat possible...')
|
||||
|
||||
|
||||
# ----- write config data to file -----
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@ do
|
|||
vtk_pointcloud $seeds
|
||||
|
||||
vtk_addPointcloudData $seeds \
|
||||
--scalar microstructure,weight \
|
||||
--data microstructure,weight \
|
||||
--inplace \
|
||||
--vtk ${seeds%.*}.vtp \
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue