Merge branch 'misc-improvements' into 'development'
Misc improvements See merge request damask/DAMASK!300
This commit is contained in:
Sharan Roongta
commit
ca71b73799
23
Makefile
23
Makefile
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@ -2,27 +2,20 @@ SHELL = /bin/sh
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########################################################################################
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# Makefile for the installation of DAMASK
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########################################################################################
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DAMASK_ROOT = $(shell python3 -c "import os,sys; print(os.path.normpath(os.path.realpath(os.path.expanduser('$(pwd)'))))")
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.PHONY: all
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all: grid mesh processing
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.PHONY: grid
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grid: build/grid
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@(cd build/grid;make -j${DAMASK_NUM_THREADS} all install;)
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grid:
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@cmake -B build/grid -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
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@cmake --build build/grid --parallel ${DAMASK_NUM_THRADS}
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@cmake --install build/grid
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.PHONY: mesh
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mesh: build/mesh
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@(cd build/mesh; make -j${DAMASK_NUM_THREADS} all install;)
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.PHONY: build/grid
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build/grid:
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@mkdir -p build/grid
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@(cd build/grid; cmake -Wno-dev -DDAMASK_SOLVER=GRID -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
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.PHONY: build/mesh
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build/mesh:
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@mkdir -p build/mesh
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@(cd build/mesh; cmake -Wno-dev -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${DAMASK_ROOT} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP} ../../;)
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mesh:
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@cmake -B build/mesh -DDAMASK_SOLVER=MESH -DCMAKE_INSTALL_PREFIX=${PWD} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DBUILDCMD_POST=${BUILDCMD_POST} -DBUILDCMD_PRE=${BUILDCMD_PRE} -DOPTIMIZATION=${OPTIMIZATION} -DOPENMP=${OPENMP}
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@cmake --build build/mesh --parallel ${DAMASK_NUM_THRADS}
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@cmake --install build/mesh
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.PHONY: clean
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clean:
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2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit fd99d76d1eaa42fd36971ff2f79a59d98534fc27
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Subproject commit 08f8aea465a1b5e476b584bcae7927d113919b1d
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@ -57,7 +57,7 @@ class Colormap(mpl.colors.ListedColormap):
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ax1.imshow(np.linspace(0,1,self.N).reshape(1,-1),
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aspect='auto', cmap=self, interpolation='nearest')
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plt.show(block = False)
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return self.name
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return 'Colormap: '+self.name
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@staticmethod
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@ -7,7 +7,8 @@ import warnings
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import numpy as np
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import pandas as pd
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import h5py
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from scipy import ndimage,spatial
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from scipy import ndimage, spatial
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from vtk.util.numpy_support import vtk_to_numpy as vtk_to_np
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from . import environment
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from . import VTK
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@ -43,12 +44,15 @@ class Grid:
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def __repr__(self):
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"""Basic information on grid definition."""
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mat_min = np.nanmin(self.material)
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mat_max = np.nanmax(self.material)
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mat_N = self.N_materials
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return util.srepr([
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f'cells a b c: {util.srepr(self.cells, " x ")}',
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f'size x y z: {util.srepr(self.size, " x ")}',
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f'origin x y z: {util.srepr(self.origin," ")}',
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f'# materials: {self.N_materials}',
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f'max material: {np.nanmax(self.material)}',
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f'# materials: {mat_N}' + ('' if mat_min == 0 and mat_max+1 == mat_N else
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f' (min: {mat_min}, max: {mat_max})')
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])
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@ -104,9 +108,9 @@ class Grid:
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@material.setter
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def material(self,material):
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if len(material.shape) != 3:
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raise ValueError(f'Invalid material shape {material.shape}.')
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raise ValueError(f'invalid material shape {material.shape}')
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elif material.dtype not in np.sctypes['float'] + np.sctypes['int']:
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raise TypeError(f'Invalid material data type {material.dtype}.')
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raise TypeError(f'invalid material data type {material.dtype}')
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else:
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self._material = np.copy(material)
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@ -123,7 +127,7 @@ class Grid:
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@size.setter
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def size(self,size):
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if len(size) != 3 or any(np.array(size) <= 0):
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raise ValueError(f'Invalid size {size}.')
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raise ValueError(f'invalid size {size}')
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else:
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self._size = np.array(size)
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@ -135,7 +139,7 @@ class Grid:
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@origin.setter
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def origin(self,origin):
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if len(origin) != 3:
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raise ValueError(f'Invalid origin {origin}.')
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raise ValueError(f'invalid origin {origin}')
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else:
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self._origin = np.array(origin)
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@ -178,6 +182,10 @@ class Grid:
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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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for i,c in enumerate([v.vtk_data.GetXCoordinates(),v.vtk_data.GetYCoordinates(),v.vtk_data.GetZCoordinates()]):
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if not np.allclose(vtk_to_np(c),np.linspace(bbox[0][i],bbox[1][i],cells[i]+1)):
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raise ValueError('regular grid spacing violated')
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return Grid(material = v.get('material').reshape(cells,order='F'),
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size = bbox[1] - bbox[0],
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origin = bbox[0],
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@ -211,7 +219,7 @@ class Grid:
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except ValueError:
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header_length,keyword = (-1, 'invalid')
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if not keyword.startswith('head') or header_length < 3:
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raise TypeError('Header length information missing or invalid')
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raise TypeError('header length information missing or invalid')
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comments = []
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content = f.readlines()
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@ -243,7 +251,7 @@ class Grid:
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i += len(items)
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if i != cells.prod():
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raise TypeError(f'Invalid file: expected {cells.prod()} entries, found {i}')
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raise TypeError(f'invalid file: expected {cells.prod()} entries, found {i}')
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if not np.any(np.mod(material,1) != 0.0): # no float present
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material = material.astype('int') - (1 if material.min() > 0 else 0)
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@ -628,7 +636,7 @@ class Grid:
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"""
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valid = ['x','y','z']
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if not set(directions).issubset(valid):
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raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
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raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
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limits = [None,None] if reflect else [-2,0]
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mat = self.material.copy()
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@ -660,7 +668,7 @@ class Grid:
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"""
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valid = ['x','y','z']
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if not set(directions).issubset(valid):
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raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
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raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
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mat = np.flip(self.material, (valid.index(d) for d in directions if d in valid))
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@ -913,7 +921,7 @@ class Grid:
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"""
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valid = ['x','y','z']
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if not set(directions).issubset(valid):
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raise ValueError(f'Invalid direction {set(directions).difference(valid)} specified.')
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raise ValueError(f'invalid direction {set(directions).difference(valid)} specified')
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o = [[0, self.cells[0]+1, np.prod(self.cells[:2]+1)+self.cells[0]+1, np.prod(self.cells[:2]+1)],
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[0, np.prod(self.cells[:2]+1), np.prod(self.cells[:2]+1)+1, 1],
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@ -784,7 +784,7 @@ class Result:
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@staticmethod
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def _add_IPF_color(q,l):
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def _add_IPF_color(l,q):
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m = util.scale_to_coprime(np.array(l))
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try:
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lattice = {'fcc':'cF','bcc':'cI','hex':'hP'}[q['meta']['Lattice']]
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@ -805,16 +805,17 @@ class Result:
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'Creator': 'add_IPF_color'
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}
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}
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def add_IPF_color(self,q,l):
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def add_IPF_color(self,l,q='O'):
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"""
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Add RGB color tuple of inverse pole figure (IPF) color.
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Parameters
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----------
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q : str
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Label of the dataset containing the crystallographic orientation as quaternions.
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l : numpy.array of shape (3)
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Lab frame direction for inverse pole figure.
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q : str
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Label of the dataset containing the crystallographic orientation as quaternions.
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Defaults to 'O'.
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"""
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self._add_generic_pointwise(self._add_IPF_color,{'q':q},{'l':l})
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@ -76,7 +76,8 @@ class VTK:
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nodes : numpy.ndarray of shape (:,3)
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Spatial position of the nodes.
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connectivity : numpy.ndarray of np.dtype = int
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Cell connectivity (0-based), first dimension determines #Cells, second dimension determines #Nodes/Cell.
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Cell connectivity (0-based), first dimension determines #Cells,
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second dimension determines #Nodes/Cell.
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cell_type : str
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Name of the vtk.vtkCell subclass. Tested for TRIANGLE, QUAD, TETRA, and HEXAHEDRON.
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@ -91,7 +92,9 @@ class VTK:
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vtk_data = vtk.vtkUnstructuredGrid()
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vtk_data.SetPoints(vtk_nodes)
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vtk_data.SetCells(eval(f'vtk.VTK_{cell_type.split("_",1)[-1].upper()}'),cells)
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cell_types = {'TRIANGLE':vtk.VTK_TRIANGLE, 'QUAD':vtk.VTK_QUAD,
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'TETRA' :vtk.VTK_TETRA, 'HEXAHEDRON':vtk.VTK_HEXAHEDRON}
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vtk_data.SetCells(cell_types[cell_type.split("_",1)[-1].upper()],cells)
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return VTK(vtk_data)
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@ -1,5 +1,6 @@
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import pytest
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import numpy as np
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from vtk.util.numpy_support import numpy_to_vtk as np_to_vtk
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from damask import VTK
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from damask import Grid
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@ -57,13 +58,21 @@ class TestGrid:
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new = Grid.load(tmp_path/'default.vtr')
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assert grid_equal(new,default)
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def test_invalid_vtr(self,tmp_path):
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def test_invalid_no_material(self,tmp_path):
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v = VTK.from_rectilinear_grid(np.random.randint(5,10,3)*2,np.random.random(3) + 1.0)
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v.save(tmp_path/'no_materialpoint.vtr',parallel=False)
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with pytest.raises(ValueError):
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Grid.load(tmp_path/'no_materialpoint.vtr')
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def test_invalid_material(self):
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def test_invalid_spacing(self,tmp_path,default):
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default.save(tmp_path/'spacing_ok.vtr')
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vtk = VTK.load(tmp_path/'spacing_ok.vtr')
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vtk.vtk_data.SetXCoordinates(np_to_vtk(np.sort(np.random.random(default.cells[0]))))
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vtk.save(tmp_path/'invalid_spacing.vtr',parallel=False)
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with pytest.raises(ValueError):
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Grid.load(tmp_path/'invalid_spacing.vtr')
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def test_invalid_material_type(self):
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with pytest.raises(TypeError):
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Grid(np.zeros((3,3,3),dtype='complex'),np.ones(3))
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|
|
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@ -169,7 +169,7 @@ class TestResult:
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@pytest.mark.parametrize('d',[[1,0,0],[0,1,0],[0,0,1]])
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def test_add_IPF_color(self,default,d):
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default.add_IPF_color('O',np.array(d))
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default.add_IPF_color(d,'O')
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loc = {'O': default.get_dataset_location('O'),
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'color': default.get_dataset_location('IPFcolor_[{} {} {}]'.format(*d))}
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qu = default.read_dataset(loc['O']).view(np.double).squeeze()
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|
|
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|||
|
|
@ -149,168 +149,6 @@ subroutine discretization_grid_init(restart)
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end subroutine discretization_grid_init
|
||||
|
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|
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!--------------------------------------------------------------------------------------------------
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||||
!> @brief Parses geometry file
|
||||
!> @details important variables have an implicit "save" attribute. Therefore, this function is
|
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! supposed to be called only once!
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
subroutine readGeom(grid,geomSize,origin,material)
|
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|
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integer, dimension(3), intent(out) :: &
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grid ! grid (across all processes!)
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real(pReal), dimension(3), intent(out) :: &
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geomSize, & ! size (across all processes!)
|
||||
origin ! origin (across all processes!)
|
||||
integer, dimension(:), intent(out), allocatable :: &
|
||||
material
|
||||
|
||||
character(len=:), allocatable :: rawData
|
||||
character(len=65536) :: line
|
||||
integer, allocatable, dimension(:) :: chunkPos
|
||||
integer :: &
|
||||
headerLength = -1, & !< length of header (in lines)
|
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fileLength, & !< length of the geom file (in characters)
|
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fileUnit, &
|
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startPos, endPos, &
|
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myStat, &
|
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l, & !< line counter
|
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c, & !< counter for # materials in line
|
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o, & !< order of "to" packing
|
||||
e, & !< "element", i.e. spectral collocation point
|
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i, j
|
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|
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grid = -1
|
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geomSize = -1.0_pReal
|
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|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! read raw data as stream
|
||||
inquire(file = trim(interface_geomFile), size=fileLength)
|
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open(newunit=fileUnit, file=trim(interface_geomFile), access='stream',&
|
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status='old', position='rewind', action='read',iostat=myStat)
|
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if(myStat /= 0) call IO_error(100,ext_msg=trim(interface_geomFile))
|
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allocate(character(len=fileLength)::rawData)
|
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read(fileUnit) rawData
|
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close(fileUnit)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! get header length
|
||||
endPos = index(rawData,IO_EOL)
|
||||
if(endPos <= index(rawData,'head')) then ! ToDo: Should be 'header'
|
||||
startPos = len(rawData)
|
||||
call IO_error(error_ID=841, ext_msg='readGeom')
|
||||
else
|
||||
chunkPos = IO_stringPos(rawData(1:endPos))
|
||||
if (chunkPos(1) < 2) call IO_error(error_ID=841, ext_msg='readGeom')
|
||||
headerLength = IO_intValue(rawData(1:endPos),chunkPos,1)
|
||||
startPos = endPos + 1
|
||||
endif
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! read and interpret header
|
||||
origin = 0.0_pReal
|
||||
l = 0
|
||||
do while (l < headerLength .and. startPos < len(rawData))
|
||||
endPos = startPos + index(rawData(startPos:),IO_EOL) - 1
|
||||
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
|
||||
line = rawData(startPos:endPos)
|
||||
startPos = endPos + 1
|
||||
l = l + 1
|
||||
|
||||
chunkPos = IO_stringPos(trim(line))
|
||||
if (chunkPos(1) < 2) cycle ! need at least one keyword value pair
|
||||
|
||||
select case (IO_lc(IO_StringValue(trim(line),chunkPos,1)) )
|
||||
case ('grid')
|
||||
if (chunkPos(1) > 6) then
|
||||
do j = 2,6,2
|
||||
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
|
||||
case('a')
|
||||
grid(1) = IO_intValue(line,chunkPos,j+1)
|
||||
case('b')
|
||||
grid(2) = IO_intValue(line,chunkPos,j+1)
|
||||
case('c')
|
||||
grid(3) = IO_intValue(line,chunkPos,j+1)
|
||||
end select
|
||||
enddo
|
||||
endif
|
||||
|
||||
case ('size')
|
||||
if (chunkPos(1) > 6) then
|
||||
do j = 2,6,2
|
||||
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
|
||||
case('x')
|
||||
geomSize(1) = IO_floatValue(line,chunkPos,j+1)
|
||||
case('y')
|
||||
geomSize(2) = IO_floatValue(line,chunkPos,j+1)
|
||||
case('z')
|
||||
geomSize(3) = IO_floatValue(line,chunkPos,j+1)
|
||||
end select
|
||||
enddo
|
||||
endif
|
||||
|
||||
case ('origin')
|
||||
if (chunkPos(1) > 6) then
|
||||
do j = 2,6,2
|
||||
select case (IO_lc(IO_stringValue(line,chunkPos,j)))
|
||||
case('x')
|
||||
origin(1) = IO_floatValue(line,chunkPos,j+1)
|
||||
case('y')
|
||||
origin(2) = IO_floatValue(line,chunkPos,j+1)
|
||||
case('z')
|
||||
origin(3) = IO_floatValue(line,chunkPos,j+1)
|
||||
end select
|
||||
enddo
|
||||
endif
|
||||
|
||||
end select
|
||||
|
||||
enddo
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! sanity checks
|
||||
if(any(grid < 1)) &
|
||||
call IO_error(error_ID = 842, ext_msg='grid (readGeom)')
|
||||
if(any(geomSize < 0.0_pReal)) &
|
||||
call IO_error(error_ID = 842, ext_msg='size (readGeom)')
|
||||
|
||||
allocate(material(product(grid)), source = -1) ! too large in case of MPI (shrink later, not very elegant)
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
! read and interpret content
|
||||
e = 1
|
||||
do while (startPos < len(rawData))
|
||||
endPos = startPos + index(rawData(startPos:),IO_EOL) - 1
|
||||
if (endPos < startPos) endPos = len(rawData) ! end of file without new line
|
||||
line = rawData(startPos:endPos)
|
||||
startPos = endPos + 1
|
||||
l = l + 1
|
||||
chunkPos = IO_stringPos(trim(line))
|
||||
|
||||
noCompression: if (chunkPos(1) /= 3) then
|
||||
c = chunkPos(1)
|
||||
material(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
|
||||
else noCompression
|
||||
compression: if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'of') then
|
||||
c = IO_intValue(line,chunkPos,1)
|
||||
material(e:e+c-1) = [(IO_intValue(line,chunkPos,3),i = 1,IO_intValue(line,chunkPos,1))]
|
||||
else if (IO_lc(IO_stringValue(line,chunkPos,2)) == 'to') then compression
|
||||
c = abs(IO_intValue(line,chunkPos,3) - IO_intValue(line,chunkPos,1)) + 1
|
||||
o = merge(+1, -1, IO_intValue(line,chunkPos,3) > IO_intValue(line,chunkPos,1))
|
||||
material(e:e+c-1) = [(i, i = IO_intValue(line,chunkPos,1),IO_intValue(line,chunkPos,3),o)]
|
||||
else compression
|
||||
c = chunkPos(1)
|
||||
material(e:e+c-1) = [(IO_intValue(line,chunkPos,i+1), i=0, c-1)]
|
||||
endif compression
|
||||
endif noCompression
|
||||
|
||||
e = e+c
|
||||
end do
|
||||
|
||||
if (e-1 /= product(grid)) call IO_error(error_ID = 843, el=e)
|
||||
|
||||
end subroutine readGeom
|
||||
|
||||
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
!> @brief Parse vtk rectilinear grid (.vtr)
|
||||
!> @details https://vtk.org/Wiki/VTK_XML_Formats
|
||||
|
|
@ -566,12 +404,12 @@ subroutine readVTR(grid,geomSize,origin,material)
|
|||
size_deflated = temp(4:)
|
||||
bytes_inflated = base64_to_bytes(base64_str(base64_nChar(headerLen)+1_pI64:))
|
||||
|
||||
allocate(bytes(0))
|
||||
allocate(bytes(sum(size_inflated)))
|
||||
e = 0_pI64
|
||||
do b = 1, nBlock
|
||||
s = e + 1_pI64
|
||||
e = s + size_deflated(b) - 1_pI64
|
||||
bytes = [bytes,zlib_inflate(bytes_inflated(s:e),size_inflated(b))]
|
||||
bytes(sum(size_inflated(:b-1))+1_pI64:sum(size_inflated(:b))) = zlib_inflate(bytes_inflated(s:e),size_inflated(b))
|
||||
enddo
|
||||
|
||||
end function asBytes_compressed
|
||||
|
|
|
|||
Loading…
Reference in New Issue