Merge branch 'vtr-to-vti' into 'development'

VTK image data is the appropriate type, not VTK rectilinear grid

See merge request damask/DAMASK!399
This commit is contained in:
Sharan Roongta 2021-06-16 19:02:20 +00:00
commit dee255ae71
111 changed files with 955 additions and 1617 deletions

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@ -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)

@ -1 +1 @@
Subproject commit 4e63593fa25bbb296fc734c82aff3353190565f7
Subproject commit 73f69c191ab7910d938b98daae0925f636b9cb57

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@ -1,6 +1,6 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 16 0 16 0 16">
<VTKFile type="ImageData" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<ImageData WholeExtent="0 16 0 16 0 16" Origin="0 0 0" Spacing="0.0625 0.0625 0.0625" Direction="1 0 0 0 1 0 0 0 1">
<FieldData>
<Array type="String" Name="comments" NumberOfTuples="2" format="binary">
AQAAAACAAAAkAAAALAAAAA==eF7LzUwuyi8uKSpNLiktSi1WMDJgyMjPzU9PzcusSizJzM/jNGQAAASkDSY=
@ -14,17 +14,6 @@
AQAAAACAAAAAAAAADwYAAA==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
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="1">
AQAAAACAAACIAAAAOAAAAA==eF5jYEAGG+wh9AEofQJKX4DSV6D0DSh9B0o/gNKPoPQTKP0MSr+A0q+g9Bso/Q5Kf7AHAB2kEak=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</ImageData>
</VTKFile>

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@ -0,0 +1,37 @@
solver: {mechanical: spectral_basic}
loadstep:
- boundary_conditions:
mechanical:
P:
- [x, x, x]
- [x, 0, x]
- [x, x, 0]
dot_F:
- [0.001, 0, 0]
- [0, x, 0]
- [0, 0, x]
discretization: {t: 10.0, N: 40}
f_out: 4
- boundary_conditions:
mechanical:
dot_P:
- [0, x, x]
- [x, x, x]
- [x, x, x]
dot_F:
- [x, 0, 0]
- [0, 0, 0]
- [0, 0, 0]
discretization: {t: 10.0, N: 20}
- boundary_conditions:
mechanical:
P:
- [0, x, x]
- [x, 0, x]
- [x, x, 0]
dot_F:
- [x, 0, 0]
- [0, x, 0]
- [0, 0, x]
discretization: {t: 10.0, N: 20}

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@ -1,14 +1,13 @@
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
import h5py
from scipy import ndimage, spatial
from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
from . import VTK
from . import util
@ -21,7 +20,7 @@ class Grid:
Geometry definition for grid solvers.
Create and manipulate geometry definitions for storage as VTK
rectiliear grid files ('.vtr' 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.
"""
@ -153,12 +152,12 @@ class Grid:
@staticmethod
def load(fname):
"""
Load from VTK rectilinear grid file.
Load from VTK image data file.
Parameters
----------
fname : str or or pathlib.Path
Grid file to read. Valid extension is .vtr, which will be appended
Grid file to read. Valid extension is .vti, which will be appended
if not given.
Returns
@ -167,15 +166,11 @@ class Grid:
Grid-based geometry from file.
"""
v = VTK.load(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr')
v = VTK.load(fname if str(fname).endswith(('.vti','.vtr')) else str(fname)+'.vti') # compatibility hack
comments = v.get_comments()
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
for i,c in enumerate([v.vtk_data.GetXCoordinates(),v.vtk_data.GetYCoordinates(),v.vtk_data.GetZCoordinates()]):
if not np.allclose(vtk_to_np(c),np.linspace(bbox[0][i],bbox[1][i],cells[i]+1)):
raise ValueError('regular grid spacing violated')
return Grid(material = v.get('material').reshape(cells,order='F'),
size = bbox[1] - bbox[0],
origin = bbox[0],
@ -254,6 +249,30 @@ class Grid:
return Grid(material.reshape(cells,order='F'),size,origin,comments)
@staticmethod
def load_Neper(fname):
"""
Load from Neper VTK file.
Parameters
----------
fname : str, pathlib.Path, or file handle
Geometry file to read.
Returns
-------
loaded : damask.Grid
Grid-based geometry from file.
"""
v = VTK.load(fname,'vtkImageData')
cells = np.array(v.vtk_data.GetDimensions())-1
bbox = np.array(v.vtk_data.GetBounds()).reshape(3,2).T
return Grid(v.get('MaterialId').reshape(cells,order='F') - 1, bbox[1] - bbox[0], bbox[0],
util.execution_stamp('Grid','load_Neper'))
@staticmethod
def load_DREAM3D(fname,
feature_IDs=None,cell_data=None,
@ -320,7 +339,7 @@ class Grid:
@staticmethod
def from_table(table,coordinates,labels):
"""
Generate grid from ASCII table.
Create grid from ASCII table.
Parameters
----------
@ -357,7 +376,7 @@ class Grid:
@staticmethod
def from_Laguerre_tessellation(cells,size,seeds,weights,material=None,periodic=True):
"""
Generate grid from Laguerre tessellation.
Create grid from Laguerre tessellation.
Parameters
----------
@ -413,7 +432,7 @@ class Grid:
@staticmethod
def from_Voronoi_tessellation(cells,size,seeds,material=None,periodic=True):
"""
Generate grid from Voronoi tessellation.
Create grid from Voronoi tessellation.
Parameters
----------
@ -494,7 +513,7 @@ class Grid:
@staticmethod
def from_minimal_surface(cells,size,surface,threshold=0.0,periods=1,materials=(0,1)):
"""
Generate grid from definition of triply periodic minimal surface.
Create grid from definition of triply periodic minimal surface.
Parameters
----------
@ -556,21 +575,21 @@ class Grid:
def save(self,fname,compress=True):
"""
Save as VTK rectilinear grid file.
Save as VTK image data file.
Parameters
----------
fname : str or pathlib.Path
Filename to write. Valid extension is .vtr, it will be appended if not given.
Filename to write. Valid extension is .vti, it will be appended if not given.
compress : bool, optional
Compress with zlib algorithm. Defaults to True.
"""
v = VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
v = VTK.from_image_data(self.cells,self.size,self.origin)
v.add(self.material.flatten(order='F'),'material')
v.add_comments(self.comments)
v.save(fname if str(fname).endswith('.vtr') else str(fname)+'.vtr',parallel=False,compress=compress)
v.save(fname if str(fname).endswith('.vti') else str(fname)+'.vti',parallel=False,compress=compress)
def save_ASCII(self,fname):

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@ -527,7 +527,7 @@ class Result:
def geometry0(self):
"""Initial/undeformed geometry."""
if self.structured:
return VTK.from_rectilinear_grid(self.cells,self.size,self.origin)
return VTK.from_image_data(self.cells,self.size,self.origin)
else:
with h5py.File(self.fname,'r') as f:
return VTK.from_unstructured_grid(f['/geometry/x_n'][()],
@ -1516,7 +1516,7 @@ class Result:
Export to VTK cell/point data.
One VTK file per visible increment is created.
For cell data, the VTK format is a rectilinear grid (.vtr) for
For cell data, the VTK format is a image data (.vti) for
grid-based simulations and an unstructured grid (.vtu) for
mesh-baed simulations. For point data, the VTK format is poly
data (.vtp).

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@ -1,4 +1,5 @@
import os
import warnings
import multiprocessing as mp
from pathlib import Path
@ -34,13 +35,41 @@ class VTK:
self.vtk_data = vtk_data
@staticmethod
def from_image_data(cells,size,origin=np.zeros(3)):
"""
Create VTK of type vtk.vtkImageData.
This is the common type for grid solver results.
Parameters
----------
cells : iterable of int, len (3)
Number of cells along each dimension.
size : iterable of float, len (3)
Physical length along each dimension.
origin : iterable of float, len (3), optional
Coordinates of grid origin.
Returns
-------
new : damask.VTK
VTK-based geometry without nodal or cell data.
"""
vtk_data = vtk.vtkImageData()
vtk_data.SetDimensions(*(np.array(cells)+1))
vtk_data.SetOrigin(*(np.array(origin)))
vtk_data.SetSpacing(*(size/cells))
return VTK(vtk_data)
@staticmethod
def from_rectilinear_grid(grid,size,origin=np.zeros(3)):
"""
Create VTK of type vtk.vtkRectilinearGrid.
This is the common type for grid solver results.
Parameters
----------
grid : iterable of int, len (3)
@ -56,6 +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]]
@ -149,8 +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
@ -167,6 +197,9 @@ class VTK:
reader.SetFileName(str(fname))
if dataset_type is None:
raise TypeError('Dataset type for *.vtk file not given.')
elif dataset_type.lower().endswith(('imagedata','image_data')):
reader.Update()
vtk_data = reader.GetStructuredPointsOutput()
elif dataset_type.lower().endswith(('rectilineargrid','rectilinear_grid')):
reader.Update()
vtk_data = reader.GetRectilinearGridOutput()
@ -179,7 +212,9 @@ class VTK:
else:
raise TypeError(f'Unknown dataset type {dataset_type} for vtk file')
else:
if ext == '.vtr':
if ext == '.vti':
reader = vtk.vtkXMLImageDataReader()
elif ext == '.vtr':
reader = vtk.vtkXMLRectilinearGridReader()
elif ext == '.vtu':
reader = vtk.vtkXMLUnstructuredGridReader()
@ -213,7 +248,9 @@ class VTK:
Compress with zlib algorithm. Defaults to True.
"""
if isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
if isinstance(self.vtk_data,vtk.vtkImageData):
writer = vtk.vtkXMLImageDataWriter()
elif isinstance(self.vtk_data,vtk.vtkRectilinearGrid):
writer = vtk.vtkXMLRectilinearGridWriter()
elif isinstance(self.vtk_data,vtk.vtkUnstructuredGrid):
writer = vtk.vtkXMLUnstructuredGridWriter()

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@ -9,7 +9,7 @@ from . import grid_filters as _grid_filters
def from_random(size,N_seeds,cells=None,rng_seed=None):
"""
Random seeding in space.
Place seeds randomly in space.
Parameters
----------
@ -43,7 +43,7 @@ def from_random(size,N_seeds,cells=None,rng_seed=None):
def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=None):
"""
Seeding in space according to a Poisson disc distribution.
Place seeds according to a Poisson disc distribution.
Parameters
----------
@ -96,7 +96,7 @@ def from_Poisson_disc(size,N_seeds,N_candidates,distance,periodic=True,rng_seed=
def from_grid(grid,selection=None,invert=False,average=False,periodic=True):
"""
Create seed from existing grid description.
Create seeds from grid description.
Parameters
----------

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@ -1,25 +0,0 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

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@ -1,25 +0,0 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

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@ -1,25 +0,0 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
<CellData>
<DataArray type="Int64" Name="materialpoint" format="binary" RangeMin="1" RangeMax="41">
AQAAAACAAAAABQAAYwAAAA==eF7t0scBgkAAAEHBgBEwgDmBsf8GfTANCN/bzzSwUa8pCrYyZp8DDjliwjEnnHLGORdMmTHnkiuuuWHBklvuuOeBR5545oVX3nhnxZoPPvnimx9+GQc7GT5sqvjvhz+ZtAcJ
</DataArray>
</CellData>
<Coordinates>
<DataArray type="Float64" Name="x" format="binary" RangeMin="0" RangeMax="0.000008">
AQAAAACAAABIAAAAOgAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2D3IeNxx9YfV6DiN+22x9tFGsbchco/sAMA/fQl6g==
</DataArray>
<DataArray type="Float64" Name="y" format="binary" RangeMin="0" RangeMax="0.000005">
AQAAAACAAAAwAAAAKwAAAA==eF5jYICAvrdbF3w/tsEOQh+wC30iUFisdRLKv2D3MeNxx9YfV+wAD5wZgw==
</DataArray>
<DataArray type="Float64" Name="z" format="binary" RangeMin="0" RangeMax="0.000004">
AQAAAACAAAAoAAAAIwAAAA==eF5jYICA3rdbF3w/tsEOQh+wC3kiUFisdRLKv2AHAFVBE/w=
</DataArray>
</Coordinates>
</Piece>
</RectilinearGrid>
</VTKFile>

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@ -1,25 +0,0 @@
<?xml version="1.0"?>
<VTKFile type="RectilinearGrid" version="0.1" byte_order="LittleEndian" header_type="UInt32" compressor="vtkZLibDataCompressor">
<RectilinearGrid WholeExtent="0 8 0 5 0 4">
<Piece Extent="0 8 0 5 0 4">
<PointData>
</PointData>
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