polishing
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parent
218e6a79a8
commit
1bfbd30ae2
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@ -3,6 +3,7 @@ stages:
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- prepare
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- prepare
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- python
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- python
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- compile
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- compile
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- setup
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- fortran
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- fortran
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- performance
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- performance
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- deploy
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- deploy
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@ -161,8 +162,10 @@ compile_Marc:
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- master
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- master
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- release
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- release
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###################################################################################################
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setup_grid:
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setup_grid:
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stage: compile
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stage: setup
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script:
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script:
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- module load $IntelCompiler $MPI_Intel $PETSc_Intel
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- module load $IntelCompiler $MPI_Intel $PETSc_Intel
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- BUILD_DIR=$(mktemp -d)
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- BUILD_DIR=$(mktemp -d)
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@ -174,7 +177,7 @@ setup_grid:
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- release
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- release
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setup_mesh:
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setup_mesh:
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stage: compile
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stage: setup
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script:
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script:
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- module load $IntelCompiler $MPI_Intel $PETSc_Intel
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- module load $IntelCompiler $MPI_Intel $PETSc_Intel
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- BUILD_DIR=$(mktemp -d)
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- BUILD_DIR=$(mktemp -d)
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@ -1,8 +1,8 @@
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import os
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import copy
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import copy
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import warnings
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import multiprocessing as mp
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import multiprocessing as mp
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from functools import partial
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from functools import partial
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import os
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import warnings
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import numpy as np
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import numpy as np
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import pandas as pd
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import pandas as pd
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@ -20,7 +20,7 @@ class Grid:
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Geometry definition for grid solvers.
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Geometry definition for grid solvers.
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Create and manipulate geometry definitions for storage as VTK
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Create and manipulate geometry definitions for storage as VTK
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image data files ('.vit' extension). A grid contains the
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image data files ('.vti' extension). A grid contains the
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material ID (referring to the entry in 'material.yaml') and
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material ID (referring to the entry in 'material.yaml') and
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the physical size.
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the physical size.
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"""
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"""
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@ -166,9 +166,7 @@ class Grid:
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Grid-based geometry from file.
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Grid-based geometry from file.
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"""
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"""
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if str(fname).endswith('.vtr'):
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v = VTK.load(fname if str(fname).endswith('.vti') else str(fname)+'.vti')
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warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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v = VTK.load(fname)
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comments = v.get_comments()
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comments = v.get_comments()
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cells = np.array(v.vtk_data.GetDimensions())-1
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cells = np.array(v.vtk_data.GetDimensions())-1
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
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@ -1,4 +1,5 @@
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import os
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import os
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import warnings
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import multiprocessing as mp
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import multiprocessing as mp
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from pathlib import Path
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from pathlib import Path
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@ -69,8 +70,6 @@ class VTK:
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"""
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"""
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Create VTK of type vtk.vtkRectilinearGrid.
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Create VTK of type vtk.vtkRectilinearGrid.
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This is the common type for grid solver results.
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Parameters
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Parameters
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----------
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----------
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grid : iterable of int, len (3)
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grid : iterable of int, len (3)
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@ -86,6 +85,7 @@ class VTK:
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VTK-based geometry without nodal or cell data.
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VTK-based geometry without nodal or cell data.
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"""
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"""
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warnings.warn('Support for vtr files will be removed in DAMASK 3.1.0', DeprecationWarning,2)
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vtk_data = vtk.vtkRectilinearGrid()
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vtk_data = vtk.vtkRectilinearGrid()
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vtk_data.SetDimensions(*(np.array(grid)+1))
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vtk_data.SetDimensions(*(np.array(grid)+1))
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coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
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coord = [np_to_vtk(np.linspace(origin[i],origin[i]+size[i],grid[i]+1),deep=True) for i in [0,1,2]]
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@ -179,8 +179,8 @@ class VTK:
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Parameters
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Parameters
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----------
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----------
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fname : str or pathlib.Path
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fname : str or pathlib.Path
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Filename for reading. Valid extensions are .vtr, .vtu, .vtp, and .vtk.
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Filename for reading. Valid extensions are .vti, .vtr, .vtu, .vtp, and .vtk.
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dataset_type : {'vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
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dataset_type : {'vtkImageData', ''vtkRectilinearGrid', 'vtkUnstructuredGrid', 'vtkPolyData'}, optional
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Name of the vtk.vtkDataSet subclass when opening a .vtk file.
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Name of the vtk.vtkDataSet subclass when opening a .vtk file.
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Returns
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Returns
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@ -164,9 +164,9 @@ subroutine readVTI(grid,geomSize,origin,material)
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integer, dimension(:), intent(out), allocatable :: &
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integer, dimension(:), intent(out), allocatable :: &
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material
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material
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character(len=:), allocatable :: fileContent, dataType, headerType, temp
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character(len=:), allocatable :: fileContent, dataType, headerType
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logical :: inFile,inGrid,gotCoordinates,gotCellData,compressed
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logical :: inFile,inImage,gotCellData,compressed
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integer :: fileUnit, myStat, coord
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integer :: fileUnit, myStat
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integer(pI64) :: &
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integer(pI64) :: &
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fileLength, & !< length of the geom file (in characters)
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fileLength, & !< length of the geom file (in characters)
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startPos, endPos, &
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startPos, endPos, &
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@ -186,12 +186,11 @@ subroutine readVTI(grid,geomSize,origin,material)
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close(fileUnit)
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close(fileUnit)
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inFile = .false.
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inFile = .false.
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inGrid = .false.
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inImage = .false.
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gotCoordinates = .false.
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gotCelldata = .false.
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gotCelldata = .false.
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!--------------------------------------------------------------------------------------------------
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!--------------------------------------------------------------------------------------------------
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! interpret XML file
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! parse XML file
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startPos = 1_pI64
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startPos = 1_pI64
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do while (startPos < len(fileContent,kind=pI64))
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do while (startPos < len(fileContent,kind=pI64))
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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endPos = startPos + index(fileContent(startPos:),IO_EOL,kind=pI64) - 2_pI64
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@ -205,11 +204,10 @@ subroutine readVTI(grid,geomSize,origin,material)
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compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
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compressed = getXMLValue(fileContent(startPos:endPos),'compressor') == 'vtkZLibDataCompressor'
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endif
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endif
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else
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else
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if (.not. inGrid) then
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if (.not. inImage) then
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if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
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if (index(fileContent(startPos:endPos),'<ImageData',kind=pI64) /= 0_pI64) then
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inGrid = .true.
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inImage = .true.
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print*, 'x'
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call cellsSizeOrigin(grid,geomSize,origin,fileContent(startPos:endPos))
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call cellsSizeOrigin(fileContent(startPos:endPos))
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endif
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endif
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else
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else
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if (index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
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if (index(fileContent(startPos:endPos),'<CellData>',kind=pI64) /= 0_pI64) then
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@ -235,7 +233,7 @@ subroutine readVTI(grid,geomSize,origin,material)
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endif
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endif
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endif
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endif
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if(gotCellData .and. gotCoordinates) exit
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if (gotCellData) exit
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startPos = endPos + 2_pI64
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startPos = endPos + 2_pI64
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end do
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end do
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@ -245,19 +243,21 @@ subroutine readVTI(grid,geomSize,origin,material)
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if(any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
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if(any(geomSize<=0)) call IO_error(error_ID = 844, ext_msg='size')
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if(any(grid<1)) call IO_error(error_ID = 844, ext_msg='grid')
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if(any(grid<1)) call IO_error(error_ID = 844, ext_msg='grid')
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material = material + 1
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material = material + 1
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if(any(material<0)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
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if(any(material<1)) call IO_error(error_ID = 844, ext_msg='material ID < 0')
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contains
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contains
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!------------------------------------------------------------------------------------------------
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!------------------------------------------------------------------------------------------------
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!> @brief determine size and origin from coordinates
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!> @brief determine size and origin from coordinates
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!------------------------------------------------------------------------------------------------
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!------------------------------------------------------------------------------------------------
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subroutine cellsSizeOrigin(header)
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subroutine cellsSizeOrigin(c,s,o,header)
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integer, dimension(3), intent(out) :: c
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real(pReal), dimension(3), intent(out) :: s,o
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character(len=*), intent(in) :: header
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character(len=*), intent(in) :: header
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character(len=:), allocatable :: temp
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character(len=:), allocatable :: temp
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real(pReal), dimension(:), allocatable :: coords,delta,origin
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real(pReal), dimension(:), allocatable :: delta
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integer, dimension(:), allocatable :: stringPos
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integer, dimension(:), allocatable :: stringPos
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integer :: i
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integer :: i
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@ -265,15 +265,17 @@ subroutine readVTI(grid,geomSize,origin,material)
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if (getXMLValue(header,'Direction') /= '1 0 0 0 1 0 0 0 1') &
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if (getXMLValue(header,'Direction') /= '1 0 0 0 1 0 0 0 1') &
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call IO_error(error_ID = 844, ext_msg = 'coordinate order')
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call IO_error(error_ID = 844, ext_msg = 'coordinate order')
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temp = getXMLValue(header,'Origin')
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temp = getXMLValue(header,'WholeExtent')
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origin = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
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if (any([(IO_floatValue(temp,IO_stringPos(temp),i),i=1,5,2)] /= 0)) &
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call IO_error(error_ID = 844, ext_msg = 'coordinate start')
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c = [(IO_floatValue(temp,IO_stringPos(temp),i),i=2,6,2)]
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temp = getXMLValue(header,'Spacing')
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temp = getXMLValue(header,'Spacing')
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delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
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delta = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
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temp = getXMLValue(header,'WholeExtent')
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s = delta * real(c,pReal)
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grid = [(IO_floatValue(temp,IO_stringPos(temp),i),i=2,6,2)]
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temp = getXMLValue(header,'Origin')
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geomSize = delta * real(grid,pReal)
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o = [(IO_floatValue(temp,IO_stringPos(temp),i),i=1,3)]
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end subroutine
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end subroutine
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