Merge branch 'even-more-HDF5-postprocessing' into development
This commit is contained in:
Philip Eisenlohr
commit
b06c5bd686
2
PRIVATE
2
PRIVATE
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@ -1 +1 @@
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Subproject commit 5c5adbd8ccc0210fd6507431db8ec82ecec75352
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Subproject commit 93564092d20e0c9553245418874ddc3b4484f3dd
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@ -1,9 +1,10 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os
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import numpy as np
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import argparse
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import numpy as np
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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@ -23,9 +24,9 @@ parser.add_argument('filenames', nargs='+',
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parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
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help='name of subdirectory to hold output')
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parser.add_argument('--mat', nargs='+',
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help='labels for materialpoint/homogenization',dest='mat')
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help='labels for materialpoint',dest='mat')
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parser.add_argument('--con', nargs='+',
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help='labels for constituent/crystallite/constitutive',dest='con')
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help='labels for constituent',dest='con')
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options = parser.parse_args()
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@ -46,32 +47,27 @@ for filename in options.filenames:
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coords = np.concatenate((z[:,:,:,None],y[:,:,:,None],x[:,:,:,None]),axis = 3)
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for i,inc in enumerate(results.increments):
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for i,inc in enumerate(results.iter_visible('increments')):
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print('Output step {}/{}'.format(i+1,len(results.increments)))
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header = '1 header\n'
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data = np.array([inc['inc'] for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])
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data = np.array([int(inc[3:]) for j in range(np.product(results.grid))]).reshape([np.product(results.grid),1])
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header+= 'inc'
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coords = coords.reshape([np.product(results.grid),3])
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data = np.concatenate((data,coords),1)
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header+=' 1_pos 2_pos 3_pos'
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results.active['increments'] = [inc]
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for label in options.con:
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for o in results.c_output_types:
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results.active['c_output_types'] = [o]
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for c in results.constituents:
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results.active['constituents'] = [c]
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for p in results.iter_visible('con_physics'):
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for c in results.iter_visible('constituents'):
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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label = x[0].split('/')[-1]
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array = results.read_dataset(x,0)
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d = int(np.product(np.shape(array)[1:]))
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array = np.reshape(array,[np.product(results.grid),d])
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data = np.concatenate((data,array),1)
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data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
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if d>1:
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header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
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@ -79,18 +75,14 @@ for filename in options.filenames:
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header+=' '+label
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for label in options.mat:
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for o in results.m_output_types:
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results.active['m_output_types'] = [o]
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for m in results.materialpoints:
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results.active['materialpoints'] = [m]
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for p in results.iter_visible('mat_physics'):
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for m in results.iter_visible('materialpoints'):
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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label = x[0].split('/')[-1]
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array = results.read_dataset(x,0)
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d = int(np.product(np.shape(array)[1:]))
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array = np.reshape(array,[np.product(results.grid),d])
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data = np.concatenate((data,array),1)
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data = np.concatenate((data,np.reshape(array,[np.product(results.grid),d])),1)
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if d>1:
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header+= ''.join([' {}_{}'.format(j+1,label) for j in range(d)])
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@ -102,5 +94,5 @@ for filename in options.filenames:
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os.mkdir(dirname)
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except FileExistsError:
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pass
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file_out = '{}_inc{:04d}.txt'.format(filename.split('.')[0],inc['inc'])
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file_out = '{}_{}.txt'.format(filename.split('.')[0],inc)
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np.savetxt(os.path.join(dirname,file_out),data,header=header,comments='')
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@ -1,12 +1,14 @@
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#!/usr/bin/env python3
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# -*- coding: UTF-8 no BOM -*-
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import os,vtk
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import numpy as np
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import os
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import argparse
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import damask
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import numpy as np
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import vtk
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from vtk.util import numpy_support
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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@ -24,9 +26,9 @@ parser.add_argument('filenames', nargs='+',
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parser.add_argument('-d','--dir', dest='dir',default='postProc',metavar='string',
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help='name of subdirectory to hold output')
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parser.add_argument('--mat', nargs='+',
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help='labels for materialpoint/homogenization',dest='mat')
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help='labels for materialpoint',dest='mat')
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parser.add_argument('--con', nargs='+',
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help='labels for constituent/crystallite/constitutive',dest='con')
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help='labels for constituent',dest='con')
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options = parser.parse_args()
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@ -55,18 +57,17 @@ for filename in options.filenames:
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rGrid.SetZCoordinates(coordArray[2])
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for i,inc in enumerate(results.increments):
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for i,inc in enumerate(results.iter_visible('increments')):
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print('Output step {}/{}'.format(i+1,len(results.increments)))
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vtk_data = []
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results.active['increments'] = [inc]
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results.set_visible('materialpoints',False)
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results.set_visible('constituents', True)
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for label in options.con:
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for o in results.c_output_types:
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results.active['c_output_types'] = [o]
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if o != 'generic':
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for c in results.constituents:
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results.active['constituents'] = [c]
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for p in results.iter_visible('con_physics'):
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if p != 'generic':
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for c in results.iter_visible('constituents'):
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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@ -76,14 +77,37 @@ for filename in options.filenames:
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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rGrid.GetCellData().AddArray(vtk_data[-1])
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else:
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results.active['constituents'] = results.constituents
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = results.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/')[1]+'/generic/'+label)
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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rGrid.GetCellData().AddArray(vtk_data[-1])
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results.set_visible('constituents', False)
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results.set_visible('materialpoints',True)
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for label in options.mat:
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for p in results.iter_visible('mat_physics'):
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if p != 'generic':
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for m in results.iter_visible('materialpoints'):
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = results.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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rGrid.GetCellData().AddArray(vtk_data[-1])
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else:
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x = results.get_dataset_location(label)
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if len(x) == 0:
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continue
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array = results.read_dataset(x,0)
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shape = [array.shape[0],np.product(array.shape[1:])]
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vtk_data.append(numpy_support.numpy_to_vtk(num_array=array.reshape(shape),deep=True,array_type= vtk.VTK_DOUBLE))
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vtk_data[-1].SetName('1_'+x[0].split('/',1)[1])
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rGrid.GetCellData().AddArray(vtk_data[-1])
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if results.structured:
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@ -95,7 +119,7 @@ for filename in options.filenames:
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os.mkdir(dirname)
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except FileExistsError:
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pass
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file_out = '{}_inc{:04d}.{}'.format(filename.split('.')[0],inc['inc'],writer.GetDefaultFileExtension())
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file_out = '{}_{}.{}'.format(filename.split('.')[0],inc,writer.GetDefaultFileExtension())
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writer.SetCompressorTypeToZLib()
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writer.SetDataModeToBinary()
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@ -146,7 +146,7 @@ for name in filenames:
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neg = np.where(D < 0.0) # find negative eigenvalues ...
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D[neg] *= -1. # ... flip value ...
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V[:,neg] *= -1. # ... and vector
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for theStrain in strains:
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for theStrain in strains:
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d = operator(theStretch,theStrain,D) # operate on eigenvalues of U or V
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eps = np.dot(V,np.dot(np.diag(d),V.T)).reshape(9) # build tensor back from eigenvalue/vector basis
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@ -1,23 +1,31 @@
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# -*- coding: UTF-8 no BOM -*-
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import h5py
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from queue import Queue
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import re
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import glob
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import h5py
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import numpy as np
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from . import util
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# ------------------------------------------------------------------
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class DADF5():
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"""Read and write to DADF5 files"""
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"""
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Read and write to DADF5 files.
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DADF5 files contain DAMASK results.
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"""
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# ------------------------------------------------------------------
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def __init__(self,
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filename,
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mode = 'r',
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):
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def __init__(self,filename):
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"""
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Opens an existing DADF5 file.
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if mode not in ['a','r']:
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print('Invalid file access mode')
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with h5py.File(filename,mode):
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pass
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Parameters
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----------
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filename : str
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name of the DADF5 file to be openend.
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"""
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with h5py.File(filename,'r') as f:
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if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 2:
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@ -30,92 +38,198 @@ class DADF5():
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self.size = f['geometry'].attrs['size']
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r=re.compile('inc[0-9]+')
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self.increments = [{'inc': int(u[3:]),
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'time': round(f[u].attrs['time/s'],12),
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} for u in f.keys() if r.match(u)]
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self.constituents = np.unique(f['mapping/cellResults/constituent']['Name']).tolist() # ToDo: I am not to happy with the name
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self.constituents = [c.decode() for c in self.constituents]
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self.materialpoints = np.unique(f['mapping/cellResults/materialpoint']['Name']).tolist() # ToDo: I am not to happy with the name
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self.materialpoints = [m.decode() for m in self.materialpoints]
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self.Nconstituents = [i for i in range(np.shape(f['mapping/cellResults/constituent'])[1])]
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self.Nmaterialpoints = np.shape(f['mapping/cellResults/constituent'])[0]
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self.c_output_types = []
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for c in self.constituents:
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for o in f['inc{:05}/constituent/{}'.format(self.increments[0]['inc'],c)].keys():
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self.c_output_types.append(o)
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self.c_output_types = list(set(self.c_output_types)) # make unique
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self.increments = [i for i in f.keys() if r.match(i)]
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self.times = [round(f[i].attrs['time/s'],12) for i in self.increments]
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self.m_output_types = []
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self.Nmaterialpoints, self.Nconstituents = np.shape(f['mapping/cellResults/constituent'])
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self.materialpoints = [m.decode() for m in np.unique(f['mapping/cellResults/materialpoint']['Name'])]
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self.constituents = [c.decode() for c in np.unique(f['mapping/cellResults/constituent'] ['Name'])]
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self.con_physics = []
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for c in self.constituents:
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self.con_physics += f['inc00000/constituent/{}'.format(c)].keys()
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self.con_physics = list(set(self.con_physics)) # make unique
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self.mat_physics = []
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for m in self.materialpoints:
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for o in f['inc{:05}/materialpoint/{}'.format(self.increments[0]['inc'],m)].keys():
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self.m_output_types.append(o)
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self.m_output_types = list(set(self.m_output_types)) # make unique
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|
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self.active= {'increments': self.increments,
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self.mat_physics += f['inc00000/materialpoint/{}'.format(m)].keys()
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self.mat_physics = list(set(self.mat_physics)) # make unique
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|
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self.visible= {'increments': self.increments, # ToDo:simplify, activity only positions that translate into (no complex types)
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'constituents': self.constituents,
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'materialpoints': self.materialpoints,
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'constituent': self.Nconstituents,
|
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'c_output_types': self.c_output_types,
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'm_output_types': self.m_output_types}
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|
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'constituent': range(self.Nconstituents), # ToDo: stupid naming
|
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'con_physics': self.con_physics,
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'mat_physics': self.mat_physics}
|
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|
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self.filename = filename
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self.mode = mode
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|
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|
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def __manage_visible(self,datasets,what,action):
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"""Manages the visibility of the groups."""
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# allow True/False and string arguments
|
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if datasets is True:
|
||||
datasets = ['*']
|
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elif datasets is False:
|
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datasets = []
|
||||
choice = [datasets] if isinstance(datasets,str) else datasets
|
||||
|
||||
valid = [e for e_ in [glob.fnmatch.filter(getattr(self,what) ,s) for s in choice] for e in e_]
|
||||
existing = set(self.visible[what])
|
||||
|
||||
if action == 'set':
|
||||
self.visible[what] = valid
|
||||
elif action == 'add':
|
||||
self.visible[what] = list(existing.union(valid))
|
||||
elif action == 'del':
|
||||
self.visible[what] = list(existing.difference_update(valid))
|
||||
|
||||
|
||||
def __time_to_inc(self,start,end):
|
||||
selected = []
|
||||
for i,time in enumerate(self.times):
|
||||
if start <= time < end:
|
||||
selected.append(self.increments[i])
|
||||
return selected
|
||||
|
||||
|
||||
def set_by_time(self,start,end):
|
||||
self.__manage_visible(self.__time_to_inc(start,end),'increments','set')
|
||||
|
||||
|
||||
def add_by_time(self,start,end):
|
||||
self.__manage_visible(self.__time_to_inc(start,end),'increments','add')
|
||||
|
||||
|
||||
def del_by_time(self,start,end):
|
||||
self.__manage_visible(self.__time_to_inc(start,end),'increments','del')
|
||||
|
||||
|
||||
def iter_visible(self,what):
|
||||
"""Iterates over visible items by setting each one visible."""
|
||||
datasets = self.visible[what]
|
||||
last_datasets = datasets.copy()
|
||||
for dataset in datasets:
|
||||
if last_datasets != self.visible[what]:
|
||||
self.__manage_visible(datasets,what,'set')
|
||||
raise Exception
|
||||
self.__manage_visible(dataset,what,'set')
|
||||
last_datasets = self.visible[what]
|
||||
yield dataset
|
||||
self.__manage_visible(datasets,what,'set')
|
||||
|
||||
|
||||
def set_visible(self,what,datasets):
|
||||
self.__manage_visible(datasets,what,'set')
|
||||
|
||||
|
||||
def add_visible(self,what,datasets):
|
||||
self.__manage_visible(datasets,what,'add')
|
||||
|
||||
|
||||
def del_visible(self,what,datasets):
|
||||
self.__manage_visible(datasets,what,'del')
|
||||
|
||||
|
||||
def groups_with_datasets(self,datasets):
|
||||
"""
|
||||
Get groups that contain all requested datasets.
|
||||
|
||||
Only groups within inc?????/constituent/*_*/* inc?????/materialpoint/*_*/*
|
||||
are considered as they contain the data.
|
||||
Single strings will be treated as list with one entry.
|
||||
|
||||
Wild card matching is allowed, but the number of arguments need to fit.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
datasets : iterable or str or boolean
|
||||
|
||||
Examples
|
||||
--------
|
||||
datasets = False matches no group
|
||||
datasets = True matches all groups
|
||||
datasets = ['F','P'] matches a group with ['F','P','sigma']
|
||||
datasets = ['*','P'] matches a group with ['F','P']
|
||||
datasets = ['*'] does not match a group with ['F','P','sigma']
|
||||
datasets = ['*','*'] does not match a group with ['F','P','sigma']
|
||||
datasets = ['*','*','*'] matches a group with ['F','P','sigma']
|
||||
|
||||
"""
|
||||
if datasets is False: return []
|
||||
sets = [datasets] if isinstance(datasets,str) else datasets
|
||||
|
||||
groups = []
|
||||
|
||||
with h5py.File(self.filename,'r') as f:
|
||||
for i in self.iter_visible('increments'): #ToDo: Merge path only once at the end '/'.join(listE)
|
||||
for c in self.iter_visible('constituents'):
|
||||
for p in self.iter_visible('con_physics'):
|
||||
group = '/'.join([i,'constituent',c,p])
|
||||
if sets is True:
|
||||
groups.append(group)
|
||||
else:
|
||||
match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
|
||||
if len(set(match)) == len(sets) : groups.append(group)
|
||||
for m in self.iter_visible('materialpoints'):
|
||||
for p in self.iter_visible('mat_physics'):
|
||||
group = '/'.join([i,'materialpoint',m,p])
|
||||
if sets is True:
|
||||
groups.append(group)
|
||||
else:
|
||||
match = [e for e_ in [glob.fnmatch.filter(f[group].keys(),s) for s in sets] for e in e_]
|
||||
if len(set(match)) == len(sets) : groups.append(group)
|
||||
return groups
|
||||
|
||||
|
||||
def list_data(self):
|
||||
"""Shows information on all datasets in the file"""
|
||||
"""Shows information on all active datasets in the file."""
|
||||
with h5py.File(self.filename,'r') as f:
|
||||
group_inc = 'inc{:05}'.format(self.active['increments'][0]['inc'])
|
||||
for c in self.active['constituents']:
|
||||
print('\n'+c)
|
||||
group_constituent = group_inc+'/constituent/'+c
|
||||
for t in self.active['c_output_types']:
|
||||
print(' {}'.format(t))
|
||||
group_output_types = group_constituent+'/'+t
|
||||
i = 'inc{:05}'.format(0)
|
||||
for c in self.iter_visible('constituents'):
|
||||
print('{}'.format(c))
|
||||
for p in self.iter_visible('con_physics'):
|
||||
print(' {}'.format(p))
|
||||
try:
|
||||
for x in f[group_output_types].keys():
|
||||
print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
|
||||
except:
|
||||
k = '/'.join([i,'constituent',c,p])
|
||||
for d in f[k].keys():
|
||||
print(' {} ({})'.format(d,f[k+'/'+d].attrs['Description'].decode()))
|
||||
except KeyError:
|
||||
pass
|
||||
for m in self.active['materialpoints']:
|
||||
group_materialpoint = group_inc+'/materialpoint/'+m
|
||||
for t in self.active['m_output_types']:
|
||||
print(' {}'.format(t))
|
||||
group_output_types = group_materialpoint+'/'+t
|
||||
for m in self.iter_visible('materialpoints'):
|
||||
print('{}'.format(m))
|
||||
for p in self.iter_visible('mat_physics'):
|
||||
print(' {}'.format(p))
|
||||
try:
|
||||
for x in f[group_output_types].keys():
|
||||
print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
|
||||
except:
|
||||
k = '/'.join([i,'materialpoint',m,p])
|
||||
for d in f[k].keys():
|
||||
print(' {} ({})'.format(d,f[k+'/'+d].attrs['Description'].decode()))
|
||||
except KeyError:
|
||||
pass
|
||||
|
||||
|
||||
def get_dataset_location(self,label):
|
||||
"""Returns the location of all active datasets with given label"""
|
||||
"""Returns the location of all active datasets with given label."""
|
||||
path = []
|
||||
with h5py.File(self.filename,'r') as f:
|
||||
for i in self.active['increments']:
|
||||
group_inc = 'inc{:05}'.format(i['inc'])
|
||||
|
||||
for c in self.active['constituents']:
|
||||
group_constituent = group_inc+'/constituent/'+c
|
||||
for t in self.active['c_output_types']:
|
||||
for i in self.iter_visible('increments'):
|
||||
for c in self.iter_visible('constituents'):
|
||||
for p in self.iter_visible('con_physics'):
|
||||
try:
|
||||
f[group_constituent+'/'+t+'/'+label]
|
||||
path.append(group_constituent+'/'+t+'/'+label)
|
||||
except Exception as e:
|
||||
k = '/'.join([i,'constituent',c,p,label])
|
||||
f[k]
|
||||
path.append(k)
|
||||
except KeyError as e:
|
||||
print('unable to locate constituents dataset: '+ str(e))
|
||||
|
||||
for m in self.active['materialpoints']:
|
||||
group_materialpoint = group_inc+'/materialpoint/'+m
|
||||
for t in self.active['m_output_types']:
|
||||
for m in self.iter_visible('materialpoints'):
|
||||
for p in self.iter_visible('mat_physics'):
|
||||
try:
|
||||
f[group_materialpoint+'/'+t+'/'+label]
|
||||
path.append(group_materialpoint+'/'+t+'/'+label)
|
||||
except Exception as e:
|
||||
k = '/'.join([i,'materialpoint',m,p,label])
|
||||
f[k]
|
||||
path.append(k)
|
||||
except KeyError as e:
|
||||
print('unable to locate materialpoints dataset: '+ str(e))
|
||||
|
||||
return path
|
||||
|
|
@ -123,7 +237,7 @@ class DADF5():
|
|||
|
||||
def read_dataset(self,path,c):
|
||||
"""
|
||||
Dataset for all points/cells
|
||||
Dataset for all points/cells.
|
||||
|
||||
If more than one path is given, the dataset is composed of the individual contributions
|
||||
"""
|
||||
|
|
@ -133,25 +247,330 @@ class DADF5():
|
|||
dataset = np.full(shape,np.nan)
|
||||
for pa in path:
|
||||
label = pa.split('/')[2]
|
||||
try:
|
||||
p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
|
||||
|
||||
p = np.where(f['mapping/cellResults/constituent'][:,c]['Name'] == str.encode(label))[0]
|
||||
if len(p)>0:
|
||||
u = (f['mapping/cellResults/constituent'][p,c]['Position'])
|
||||
a = np.array(f[pa])
|
||||
if len(a.shape) == 1:
|
||||
a=a.reshape([a.shape[0],1])
|
||||
dataset[p,:] = a[u,:]
|
||||
except Exception as e:
|
||||
print('unable to read constituent: '+ str(e))
|
||||
try:
|
||||
p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
|
||||
|
||||
p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
|
||||
if len(p)>0:
|
||||
u = (f['mapping/cellResults/materialpoint'][p.tolist()]['Position'])
|
||||
a = np.array(f[pa])
|
||||
if len(a.shape) == 1:
|
||||
a=a.reshape([a.shape[0],1])
|
||||
dataset[p,:] = a[u,:]
|
||||
except Exception as e:
|
||||
print('unable to read materialpoint: '+ str(e))
|
||||
|
||||
return dataset
|
||||
|
||||
|
||||
|
||||
def add_Cauchy(self,P='P',F='F'):
|
||||
"""
|
||||
Adds Cauchy stress calculated from 1st Piola-Kirchhoff stress and deformation gradient.
|
||||
|
||||
Resulting tensor is symmetrized as the Cauchy stress should be symmetric.
|
||||
"""
|
||||
def Cauchy(F,P):
|
||||
sigma = np.einsum('i,ijk,ilk->ijl',1.0/np.linalg.det(F['data']),P['data'],F['data'])
|
||||
sigma = (sigma + np.einsum('ikj',sigma))*0.5 # enforce symmetry
|
||||
return {
|
||||
'data' : sigma,
|
||||
'label' : 'sigma',
|
||||
'meta' : {
|
||||
'Unit' : P['meta']['Unit'],
|
||||
'Description' : 'Cauchy stress calculated from {} ({}) '.format(P['label'],P['meta']['Description'])+\
|
||||
'and deformation gradient {} ({})'.format(F['label'],F['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_Cauchy vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':F,'arg':'F'},
|
||||
{'label':P,'arg':'P'} ]
|
||||
|
||||
self.__add_generic_pointwise(Cauchy,requested)
|
||||
|
||||
|
||||
def add_Mises(self,x):
|
||||
"""Adds the equivalent Mises stress or strain of a tensor."""
|
||||
def Mises(x):
|
||||
|
||||
if x['meta']['Unit'] == b'Pa': #ToDo: Should we use this? Then add_Cauchy and add_strain_tensors also should perform sanity checks
|
||||
factor = 3.0/2.0
|
||||
t = 'stress'
|
||||
elif x['meta']['Unit'] == b'1':
|
||||
factor = 2.0/3.0
|
||||
t = 'strain'
|
||||
else:
|
||||
print(x['meta']['Unit'])
|
||||
raise ValueError
|
||||
|
||||
d = x['data']
|
||||
dev = d - np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),[d.shape[0],3,3]),np.trace(d,axis1=1,axis2=2)/3.0)
|
||||
#dev_sym = (dev + np.einsum('ikj',dev))*0.5 # ToDo: this is not needed (only if the input is not symmetric, but then the whole concept breaks down)
|
||||
|
||||
return {
|
||||
'data' : np.sqrt(np.einsum('ijk->i',dev**2)*factor),
|
||||
'label' : '{}_vM'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : 'Mises equivalent {} of {} ({})'.format(t,x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_Mises_stress vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(Mises,requested)
|
||||
|
||||
|
||||
def add_norm(self,x,ord=None):
|
||||
"""
|
||||
Adds norm of vector or tensor.
|
||||
|
||||
See numpy.linalg.norm manual for details.
|
||||
"""
|
||||
def norm(x,ord):
|
||||
|
||||
o = ord
|
||||
if len(x['data'].shape) == 2:
|
||||
axis = 1
|
||||
t = 'vector'
|
||||
if o is None: o = 2
|
||||
elif len(x['data'].shape) == 3:
|
||||
axis = (1,2)
|
||||
t = 'tensor'
|
||||
if o is None: o = 'fro'
|
||||
else:
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data' : np.linalg.norm(x['data'],ord=o,axis=axis,keepdims=True),
|
||||
'label' : '|{}|_{}'.format(x['label'],o),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : '{}-Norm of {} {} ({})'.format(ord,t,x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_norm vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(norm,requested,{'ord':ord})
|
||||
|
||||
|
||||
def add_absolute(self,x):
|
||||
"""Adds absolute value."""
|
||||
def absolute(x):
|
||||
|
||||
return {
|
||||
'data' : np.abs(x['data']),
|
||||
'label' : '|{}|'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : 'Absolute value of {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_abs vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(absolute,requested)
|
||||
|
||||
|
||||
def add_determinant(self,x):
|
||||
"""Adds the determinant component of a tensor."""
|
||||
def determinant(x):
|
||||
|
||||
return {
|
||||
'data' : np.linalg.det(x['data']),
|
||||
'label' : 'det({})'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : 'Determinant of tensor {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_determinant vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(determinant,requested)
|
||||
|
||||
|
||||
def add_spherical(self,x):
|
||||
"""Adds the spherical component of a tensor."""
|
||||
def spherical(x):
|
||||
|
||||
if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data' : np.trace(x['data'],axis1=1,axis2=2)/3.0,
|
||||
'label' : 'sph({})'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : 'Spherical component of tensor {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_spherical vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(spherical,requested)
|
||||
|
||||
|
||||
def add_deviator(self,x):
|
||||
"""Adds the deviator of a tensor."""
|
||||
def deviator(x):
|
||||
d = x['data']
|
||||
|
||||
if not np.all(np.array(d.shape[1:]) == np.array([3,3])):
|
||||
raise ValueError
|
||||
|
||||
return {
|
||||
'data' : d - np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),[d.shape[0],3,3]),np.trace(d,axis1=1,axis2=2)/3.0),
|
||||
'label' : 'dev({})'.format(x['label']),
|
||||
'meta' : {
|
||||
'Unit' : x['meta']['Unit'],
|
||||
'Description' : 'Deviator of tensor {} ({})'.format(x['label'],x['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_deviator vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':x,'arg':'x'}]
|
||||
|
||||
self.__add_generic_pointwise(deviator,requested)
|
||||
|
||||
|
||||
def add_calculation(self,formula,label,unit='n/a',description=None,vectorized=True):
|
||||
"""
|
||||
General formula.
|
||||
|
||||
Works currently only for vectorized expressions
|
||||
|
||||
"""
|
||||
if vectorized is not True:
|
||||
raise NotImplementedError
|
||||
|
||||
def calculation(**kwargs):
|
||||
|
||||
formula = kwargs['formula']
|
||||
for d in re.findall(r'#(.*?)#',formula):
|
||||
formula = re.sub('#{}#'.format(d),"kwargs['{}']['data']".format(d),formula)
|
||||
|
||||
return {
|
||||
'data' : eval(formula),
|
||||
'label' : kwargs['label'],
|
||||
'meta' : {
|
||||
'Unit' : kwargs['unit'],
|
||||
'Description' : '{}'.format(kwargs['description']),
|
||||
'Creator' : 'dadf5.py:add_calculation vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':d,'arg':d} for d in re.findall(r'#(.*?)#',formula)] # datasets used in the formula
|
||||
pass_through = {'formula':formula,'label':label,'unit':unit,'description':description}
|
||||
|
||||
self.__add_generic_pointwise(calculation,requested,pass_through)
|
||||
|
||||
|
||||
def add_strain_tensor(self,t,ord,defgrad='F'): #ToDo: Use t and ord
|
||||
"""
|
||||
Adds the a strain tensor.
|
||||
|
||||
Albrecht Bertram: Elasticity and Plasticity of Large Deformations An Introduction (3rd Edition, 2012), p. 102.
|
||||
"""
|
||||
def strain_tensor(defgrad,t,ord):
|
||||
|
||||
operator = {
|
||||
'V#ln': lambda V: np.log(V),
|
||||
'U#ln': lambda U: np.log(U),
|
||||
'V#Biot': lambda V: np.broadcast_to(np.ones(3),[V.shape[0],3]) - 1.0/V,
|
||||
'U#Biot': lambda U: U - np.broadcast_to(np.ones(3),[U.shape[0],3]),
|
||||
'V#Green':lambda V: np.broadcast_to(np.ones(3),[V.shape[0],3]) - 1.0/V**2,
|
||||
'U#Biot': lambda U: U**2 - np.broadcast_to(np.ones(3),[U.shape[0],3]),
|
||||
}
|
||||
|
||||
(U,S,Vh) = np.linalg.svd(defgrad['data']) # singular value decomposition
|
||||
R_inv = np.einsum('ikj',np.matmul(U,Vh)) # inverse rotation of polar decomposition
|
||||
U = np.matmul(R_inv,defgrad['data']) # F = RU
|
||||
(D,V) = np.linalg.eigh((U+np.einsum('ikj',U))*.5) # eigen decomposition (of symmetric(ed) matrix)
|
||||
|
||||
neg = np.where(D < 0.0) # find negative eigenvalues ...
|
||||
D[neg[0],neg[1]] = D[neg[0],neg[1]]* -1 # ... flip value ...
|
||||
V[neg[0],:,neg[1]] = V[neg[0],:,neg[1]]* -1 # ... and vector
|
||||
|
||||
d = operator['V#ln'](D)
|
||||
a = np.matmul(V,np.einsum('ij,ikj->ijk',d,V))
|
||||
|
||||
return {
|
||||
'data' : a,
|
||||
'label' : 'ln(V)({})'.format(defgrad['label']),
|
||||
'meta' : {
|
||||
'Unit' : defgrad['meta']['Unit'],
|
||||
'Description' : 'Strain tensor ln(V){} ({})'.format(defgrad['label'],defgrad['meta']['Description']),
|
||||
'Creator' : 'dadf5.py:add_deviator vXXXXX'
|
||||
}
|
||||
}
|
||||
|
||||
requested = [{'label':defgrad,'arg':'defgrad'}]
|
||||
|
||||
self.__add_generic_pointwise(strain_tensor,requested,{'t':t,'ord':ord})
|
||||
|
||||
|
||||
def __add_generic_pointwise(self,func,datasets_requested,extra_args={}):
|
||||
"""
|
||||
General function to add pointwise data.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
func : function
|
||||
Function that calculates a new dataset from one or more datasets per HDF5 group.
|
||||
datasets_requested : list of dictionaries
|
||||
Details of the datasets to be used: label (in HDF5 file) and arg (argument to which the data is parsed in func).
|
||||
extra_args : dictionary, optional
|
||||
Any extra arguments parsed to func.
|
||||
|
||||
"""
|
||||
def job(args):
|
||||
"""Call function with input data + extra arguments, returns results + group."""
|
||||
args['results'].put({**args['func'](**args['in']),'group':args['group']})
|
||||
|
||||
|
||||
N_threads = 1 # ToDo: should be a parameter
|
||||
|
||||
results = Queue(N_threads)
|
||||
pool = util.ThreadPool(N_threads)
|
||||
N_added = N_threads + 1
|
||||
|
||||
todo = []
|
||||
# ToDo: It would be more memory efficient to read only from file when required, i.e. do to it in pool.add_task
|
||||
for group in self.groups_with_datasets([d['label'] for d in datasets_requested]):
|
||||
with h5py.File(self.filename,'r') as f:
|
||||
datasets_in = {}
|
||||
for d in datasets_requested:
|
||||
loc = f[group+'/'+d['label']]
|
||||
data = loc[()]
|
||||
meta = {k:loc.attrs[k] for k in loc.attrs.keys()}
|
||||
datasets_in[d['arg']] = {'data': data, 'meta' : meta, 'label' : d['label']}
|
||||
|
||||
todo.append({'in':{**datasets_in,**extra_args},'func':func,'group':group,'results':results})
|
||||
|
||||
pool.map(job, todo[:N_added]) # initialize
|
||||
|
||||
N_not_calculated = len(todo)
|
||||
while N_not_calculated > 0:
|
||||
result = results.get()
|
||||
with h5py.File(self.filename,'a') as f: # write to file
|
||||
dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
|
||||
for k in result['meta'].keys():
|
||||
dataset_out.attrs[k] = result['meta'][k]
|
||||
N_not_calculated-=1
|
||||
|
||||
if N_added < len(todo): # add more jobs
|
||||
pool.add_task(job,todo[N_added])
|
||||
N_added +=1
|
||||
|
||||
pool.wait_completion()
|
||||
|
|
|
|||
|
|
@ -4,6 +4,9 @@ import os
|
|||
import subprocess
|
||||
import shlex
|
||||
from optparse import Option
|
||||
from queue import Queue
|
||||
from threading import Thread
|
||||
|
||||
|
||||
import numpy as np
|
||||
|
||||
|
|
@ -464,3 +467,46 @@ def curve_fit_bound(f, xdata, ydata, p0=None, sigma=None, bounds=None, **kw):
|
|||
pcov = np.inf
|
||||
|
||||
return (popt, pcov, infodict, errmsg, ier) if return_full else (popt, pcov)
|
||||
|
||||
class Worker(Thread):
|
||||
"""Thread executing tasks from a given tasks queue"""
|
||||
|
||||
def __init__(self, tasks):
|
||||
Thread.__init__(self)
|
||||
self.tasks = tasks
|
||||
self.daemon = True
|
||||
self.start()
|
||||
|
||||
def run(self):
|
||||
while True:
|
||||
func, args, kargs = self.tasks.get()
|
||||
try:
|
||||
func(*args, **kargs)
|
||||
except Exception as e:
|
||||
# An exception happened in this thread
|
||||
print(e)
|
||||
finally:
|
||||
# Mark this task as done, whether an exception happened or not
|
||||
self.tasks.task_done()
|
||||
|
||||
|
||||
class ThreadPool:
|
||||
"""Pool of threads consuming tasks from a queue"""
|
||||
|
||||
def __init__(self, num_threads):
|
||||
self.tasks = Queue(num_threads)
|
||||
for _ in range(num_threads):
|
||||
Worker(self.tasks)
|
||||
|
||||
def add_task(self, func, *args, **kargs):
|
||||
"""Add a task to the queue"""
|
||||
self.tasks.put((func, args, kargs))
|
||||
|
||||
def map(self, func, args_list):
|
||||
"""Add a list of tasks to the queue"""
|
||||
for args in args_list:
|
||||
self.add_task(func, args)
|
||||
|
||||
def wait_completion(self):
|
||||
"""Wait for completion of all the tasks in the queue"""
|
||||
self.tasks.join()
|
||||
|
|
|
|||
|
|
@ -97,11 +97,16 @@ subroutine config_init
|
|||
|
||||
enddo
|
||||
|
||||
if (size(config_homogenization) < 1) call IO_error(160,ext_msg='<homogenization>')
|
||||
if (size(config_microstructure) < 1) call IO_error(160,ext_msg='<microstructure>')
|
||||
if (size(config_crystallite) < 1) call IO_error(160,ext_msg='<crystallite>')
|
||||
if (size(config_phase) < 1) call IO_error(160,ext_msg='<phase>')
|
||||
if (size(config_texture) < 1) call IO_error(160,ext_msg='<texture>')
|
||||
if (.not. allocated(config_homogenization) .or. size(config_homogenization) < 1) &
|
||||
call IO_error(160,ext_msg='<homogenization>')
|
||||
if (.not. allocated(config_microstructure) .or. size(config_microstructure) < 1) &
|
||||
call IO_error(160,ext_msg='<microstructure>')
|
||||
if (.not. allocated(config_crystallite) .or. size(config_crystallite) < 1) &
|
||||
call IO_error(160,ext_msg='<crystallite>')
|
||||
if (.not. allocated(config_phase) .or. size(config_phase) < 1) &
|
||||
call IO_error(160,ext_msg='<phase>')
|
||||
if (.not. allocated(config_texture) .or. size(config_texture) < 1) &
|
||||
call IO_error(160,ext_msg='<texture>')
|
||||
|
||||
|
||||
inquire(file='numerics.config', exist=fileExists)
|
||||
|
|
|
|||
|
|
@ -800,6 +800,8 @@ subroutine homogenization_results
|
|||
|
||||
integer :: p
|
||||
character(len=256) :: group
|
||||
|
||||
real(pReal), dimension(:,:,:), allocatable :: temp
|
||||
|
||||
do p=1,size(config_name_homogenization)
|
||||
group = trim('current/materialpoint')//'/'//trim(config_name_homogenization(p))
|
||||
|
|
@ -812,7 +814,17 @@ subroutine homogenization_results
|
|||
case(HOMOGENIZATION_rgc_ID)
|
||||
call mech_RGC_results(homogenization_typeInstance(p),group)
|
||||
end select
|
||||
|
||||
|
||||
group = trim('current/materialpoint')//'/'//trim(config_name_homogenization(p))//'/generic'
|
||||
call HDF5_closeGroup(results_addGroup(group))
|
||||
|
||||
!temp = reshape(materialpoint_F,[3,3,discretization_nIP*discretization_nElem])
|
||||
!call results_writeDataset(group,temp,'F',&
|
||||
! 'deformation gradient','1')
|
||||
!temp = reshape(materialpoint_P,[3,3,discretization_nIP*discretization_nElem])
|
||||
!call results_writeDataset(group,temp,'P',&
|
||||
! '1st Piola-Kirchoff stress','Pa')
|
||||
|
||||
enddo
|
||||
#endif
|
||||
end subroutine homogenization_results
|
||||
|
|
|
|||
|
|
@ -747,13 +747,13 @@ pure function lattice_symmetrizeC66(struct,C66)
|
|||
case (LATTICE_iso_ID)
|
||||
do k=1,3
|
||||
forall(j=1:3) lattice_symmetrizeC66(k,j) = C66(1,2)
|
||||
lattice_symmetrizeC66(k,k) = C66(1,1)
|
||||
lattice_symmetrizeC66(k,k) = C66(1,1)
|
||||
lattice_symmetrizeC66(k+3,k+3) = 0.5_pReal*(C66(1,1)-C66(1,2))
|
||||
enddo
|
||||
case (LATTICE_fcc_ID,LATTICE_bcc_ID)
|
||||
do k=1,3
|
||||
forall(j=1:3) lattice_symmetrizeC66(k,j) = C66(1,2)
|
||||
lattice_symmetrizeC66(k,k) = C66(1,1)
|
||||
forall(j=1:3) lattice_symmetrizeC66(k,j) = C66(1,2)
|
||||
lattice_symmetrizeC66(k,k) = C66(1,1)
|
||||
lattice_symmetrizeC66(k+3,k+3) = C66(4,4)
|
||||
enddo
|
||||
case (LATTICE_hex_ID)
|
||||
|
|
|
|||
Loading…
Reference in New Issue