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DAMASK_EICMD
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This commit is contained in:
Martin Diehl 2021-06-15 19:38:01 +02:00
parent 218e6a79a8
commit 1bfbd30ae2
4 changed files with 41 additions and 38 deletions
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7
.gitlab-ci.yml
View File

@ -3,6 +3,7 @@ stages:
- prepare
- python
- compile
- setup
- fortran
- performance
- deploy
@ -161,8 +162,10 @@ compile_Marc:
- master
- release
###################################################################################################
setup_grid:
stage: compile
stage: setup
script:
- module load $IntelCompiler $MPI_Intel $PETSc_Intel
- BUILD_DIR=$(mktemp -d)
@ -174,7 +177,7 @@ setup_grid:
- release
setup_mesh:
stage: compile
stage: setup
script:
- module load $IntelCompiler $MPI_Intel $PETSc_Intel
- BUILD_DIR=$(mktemp -d)

10
python/damask/_grid.py
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@ -1,8 +1,8 @@
import os
import copy
import warnings
import multiprocessing as mp
from functools import partial
import os
import warnings
import numpy as np
import pandas as pd
@ -20,7 +20,7 @@ class Grid:
Geometry definition for grid solvers.
Create and manipulate geometry definitions for storage as VTK
image data files ('.vit' extension). A grid contains the
image data files ('.vti' extension). A grid contains the
material ID (referring to the entry in 'material.yaml') and
the physical size.
"""
@ -166,9 +166,7 @@ class Grid:
Grid-based geometry from file.
"""
if str(fname).endswith('.vtr'):
warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2)
v = VTK.load(fname)
v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
comments = v.get_comments()
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T

8
python/damask/_vtk.py
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@ -1,4 +1,5 @@
import os
import warnings
import multiprocessing as mp
from pathlib import Path
@ -69,8 +70,6 @@ class VTK:
"""
Create VTK of type vtk.vtkRectilinearGrid.
This is the common type for grid solver results.
Parameters
----------
grid : iterable of int, len (3)
@ -86,6 +85,7 @@ class VTK:
VTK-based geometry without nodal or cell data.
"""
warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2)
vtk_data = vtk.vtkRectilinearGrid()
vtk_data.SetDimensions(*(np.array(grid)+1))
coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
@ -179,8 +179,8 @@ class VTK:
Parameters
----------
fname : str or pathlib.Path
Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
dataset_type : {'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
Name of the vtk.vtkDataSet subclass when opening a .vtk file.
Returns

52
src/grid/discretization_grid.f90
View File

@ -164,9 +164,9 @@ subroutine readVTI(grid,geomSize,origin,material)
integer, dimension(:), intent(out), allocatable :: &
material
character(len=:), allocatable :: fileContent, dataType, headerType, temp
logical :: inFile,inGrid,gotCoordinates,gotCellData,compressed
integer :: fileUnit, myStat, coord
character(len=:), allocatable :: fileContent, dataType, headerType
logical :: inFile,inImage,gotCellData,compressed
integer :: fileUnit, myStat
integer(pI64) :: &
fileLength, & !< length of the geom file (in characters)
startPos, endPos, &
@ -186,39 +186,37 @@ subroutine readVTI(grid,geomSize,origin,material)
close(fileUnit)
inFile = .false.
inGrid = .false.
gotCoordinates = .false.
inImage = .false.
gotCelldata = .false.
!--------------------------------------------------------------------------------------------------
! interpret XML file
! parse XML file
startPos = 1_pI64
do while (startPos < len(fileContent,kind=pI64))
endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
if (endPos < startPos) endPos = len(fileContent,kind=pI64) ! end of file without new line
if(.not. inFile) then
if (.not. inFile) then
if(index(fileContent(startPos:endPos),'<VTKFile',kind=pI64) /= 0_pI64) then
inFile = .true.
if(.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
if (.not. fileFormatOk(fileContent(startPos:endPos))) call IO_error(error_ID = 844, ext_msg='file format')
headerType = merge('UInt64','UInt32',getXMLValue(fileContent(startPos:endPos),'header_type')=='UInt64')
compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
endif
else
if (.not. inGrid) then
if (.not. inImage) then
if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
inGrid = .true.
print*, 'x'
call cellsSizeOrigin(fileContent(startPos:endPos))
inImage = .true.
call cellsSizeOrigin(grid,geomSize,origin,fileContent(startPos:endPos))
endif
else
if(index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
if (index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
gotCellData = .true.
do while (index(fileContent(startPos:endPos),'</CellData>',kind=pI64) == 0_pI64)
if(index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
if (index(fileContent(startPos:endPos),'<DataArray',kind=pI64) /= 0_pI64 .and. &
getXMLValue(fileContent(startPos:endPos),'Name') == 'material' ) then
if(getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
if (getXMLValue(fileContent(startPos:endPos),'format') /= 'binary') &
call IO_error(error_ID = 844, ext_msg='format (material)')
dataType = getXMLValue(fileContent(startPos:endPos),'type')
@ -235,7 +233,7 @@ subroutine readVTI(grid,geomSize,origin,material)
endif
endif
if(gotCellData .and. gotCoordinates) exit
if (gotCellData) exit
startPos = endPos + 2_pI64
end do
@ -245,19 +243,21 @@ subroutine readVTI(grid,geomSize,origin,material)
if(any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
if(any(grid<1)) call IO_error(error_ID = 844, ext_msg='grid')
material = material + 1
if(any(material<0)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
if(any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
contains
!------------------------------------------------------------------------------------------------
!> @brief determine size and origin from coordinates
!------------------------------------------------------------------------------------------------
subroutine cellsSizeOrigin(header)
subroutine cellsSizeOrigin(c,s,o,header)
integer, dimension(3), intent(out) :: c
real(pReal), dimension(3), intent(out) :: s,o
character(len=*), intent(in) :: header
character(len=:), allocatable :: temp
real(pReal), dimension(:), allocatable :: coords,delta,origin
real(pReal), dimension(:), allocatable :: delta
integer, dimension(:), allocatable :: stringPos
integer :: i
@ -265,15 +265,17 @@ subroutine readVTI(grid,geomSize,origin,material)
if (getXMLValue(header,'Direction') /= '1 0 0 0 1 0 0 0 1') &
call IO_error(error_ID = 844, ext_msg = 'coordinate order')
temp = getXMLValue(header,'Origin')
origin = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
temp = getXMLValue(header,'WholeExtent')
if (any([(IO_floatValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
call IO_error(error_ID = 844, ext_msg = 'coordinate start')
c = [(IO_floatValue(temp,IO_stringPos(temp),i),i=2,6,2)]
temp = getXMLValue(header,'Spacing')
delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
temp = getXMLValue(header,'WholeExtent')
grid = [(IO_floatValue(temp,IO_stringPos(temp),i),i=2,6,2)]
s = delta * real(c,pReal)
geomSize = delta * real(grid,pReal)
temp = getXMLValue(header,'Origin')
o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
end subroutine