Merge branch 'misc-improvements' into 'development'
Misc improvements See merge request damask/DAMASK!154
This commit is contained in:
Vitesh
commit
c74ffae88c
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@ -6,7 +6,7 @@ name = 'damask'
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with open(_os.path.join(_os.path.dirname(__file__),'VERSION')) as _f:
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version = _re.sub(r'^v','',_f.readline().strip())
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# classes
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# make classes directly accessible as damask.Class
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from ._environment import Environment # noqa
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from ._table import Table # noqa
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from ._vtk import VTK # noqa
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@ -291,7 +291,7 @@ class Geom:
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comments = []
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for i,line in enumerate(content[:header_length]):
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items = line.lower().strip().split()
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items = line.split('#')[0].lower().strip().split()
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key = items[0] if items else ''
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if key == 'grid':
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grid = np.array([ int(dict(zip(items[1::2],items[2::2]))[i]) for i in ['a','b','c']])
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@ -307,7 +307,7 @@ class Geom:
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microstructure = np.empty(grid.prod()) # initialize as flat array
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i = 0
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for line in content[header_length:]:
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items = line.split()
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items = line.split('#')[0].split()
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if len(items) == 3:
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if items[1].lower() == 'of':
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items = np.ones(int(items[0]))*float(items[2])
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@ -1,5 +1,5 @@
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from scipy import spatial
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import numpy as np
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from scipy import spatial as _spatial
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import numpy as _np
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def _ks(size,grid,first_order=False):
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"""
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@ -11,16 +11,16 @@ def _ks(size,grid,first_order=False):
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physical size of the periodic field.
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"""
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k_sk = np.where(np.arange(grid[0])>grid[0]//2,np.arange(grid[0])-grid[0],np.arange(grid[0]))/size[0]
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k_sk = _np.where(_np.arange(grid[0])>grid[0]//2,_np.arange(grid[0])-grid[0],_np.arange(grid[0]))/size[0]
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if grid[0]%2 == 0 and first_order: k_sk[grid[0]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
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k_sj = np.where(np.arange(grid[1])>grid[1]//2,np.arange(grid[1])-grid[1],np.arange(grid[1]))/size[1]
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k_sj = _np.where(_np.arange(grid[1])>grid[1]//2,_np.arange(grid[1])-grid[1],_np.arange(grid[1]))/size[1]
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if grid[1]%2 == 0 and first_order: k_sj[grid[1]//2] = 0 # Nyquist freq=0 for even grid (Johnson, MIT, 2011)
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k_si = np.arange(grid[2]//2+1)/size[2]
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k_si = _np.arange(grid[2]//2+1)/size[2]
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kk, kj, ki = np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
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return np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
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kk, kj, ki = _np.meshgrid(k_sk,k_sj,k_si,indexing = 'ij')
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return _np.concatenate((ki[:,:,:,None],kj[:,:,:,None],kk[:,:,:,None]),axis = 3)
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def curl(size,field):
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@ -33,18 +33,18 @@ def curl(size,field):
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physical size of the periodic field.
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"""
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n = np.prod(field.shape[3:])
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n = _np.prod(field.shape[3:])
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k_s = _ks(size,field.shape[:3],True)
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e = np.zeros((3, 3, 3))
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e = _np.zeros((3, 3, 3))
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e[0, 1, 2] = e[1, 2, 0] = e[2, 0, 1] = +1.0 # Levi-Civita symbol
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e[0, 2, 1] = e[2, 1, 0] = e[1, 0, 2] = -1.0
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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curl_ = (np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 3
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np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*np.pi) # tensor, 3x3 -> 3x3
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field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
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curl_ = (_np.einsum('slm,ijkl,ijkm ->ijks', e,k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 3
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_np.einsum('slm,ijkl,ijknm->ijksn',e,k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3x3
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return np.fft.irfftn(curl_,axes=(0,1,2),s=field.shape[:3])
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return _np.fft.irfftn(curl_,axes=(0,1,2),s=field.shape[:3])
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def divergence(size,field):
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@ -57,14 +57,14 @@ def divergence(size,field):
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physical size of the periodic field.
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"""
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n = np.prod(field.shape[3:])
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n = _np.prod(field.shape[3:])
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k_s = _ks(size,field.shape[:3],True)
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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div_ = (np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*np.pi if n == 3 else # vector, 3 -> 1
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np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*np.pi) # tensor, 3x3 -> 3
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field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
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div_ = (_np.einsum('ijkl,ijkl ->ijk', k_s,field_fourier)*2.0j*_np.pi if n == 3 else # vector, 3 -> 1
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_np.einsum('ijkm,ijklm->ijkl',k_s,field_fourier)*2.0j*_np.pi) # tensor, 3x3 -> 3
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return np.fft.irfftn(div_,axes=(0,1,2),s=field.shape[:3])
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return _np.fft.irfftn(div_,axes=(0,1,2),s=field.shape[:3])
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def gradient(size,field):
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@ -77,17 +77,17 @@ def gradient(size,field):
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physical size of the periodic field.
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"""
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n = np.prod(field.shape[3:])
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n = _np.prod(field.shape[3:])
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k_s = _ks(size,field.shape[:3],True)
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field_fourier = np.fft.rfftn(field,axes=(0,1,2))
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grad_ = (np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*np.pi if n == 1 else # scalar, 1 -> 3
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np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*np.pi) # vector, 3 -> 3x3
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field_fourier = _np.fft.rfftn(field,axes=(0,1,2))
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grad_ = (_np.einsum('ijkl,ijkm->ijkm', field_fourier,k_s)*2.0j*_np.pi if n == 1 else # scalar, 1 -> 3
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_np.einsum('ijkl,ijkm->ijklm',field_fourier,k_s)*2.0j*_np.pi) # vector, 3 -> 3x3
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return np.fft.irfftn(grad_,axes=(0,1,2),s=field.shape[:3])
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return _np.fft.irfftn(grad_,axes=(0,1,2),s=field.shape[:3])
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def cell_coord0(grid,size,origin=np.zeros(3)):
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def cell_coord0(grid,size,origin=_np.zeros(3)):
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"""
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Cell center positions (undeformed).
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@ -103,7 +103,7 @@ def cell_coord0(grid,size,origin=np.zeros(3)):
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"""
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start = origin + size/grid*.5
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end = origin + size - size/grid*.5
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return np.mgrid[start[0]:end[0]:grid[0]*1j,start[1]:end[1]:grid[1]*1j,start[2]:end[2]:grid[2]*1j].T
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return _np.mgrid[start[0]:end[0]:grid[0]*1j,start[1]:end[1]:grid[1]*1j,start[2]:end[2]:grid[2]*1j].T
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def cell_displacement_fluct(size,F):
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@ -118,19 +118,19 @@ def cell_displacement_fluct(size,F):
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deformation gradient field.
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"""
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integrator = 0.5j*size/np.pi
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integrator = 0.5j*size/_np.pi
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k_s = _ks(size,F.shape[:3],False)
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k_s_squared = np.einsum('...l,...l',k_s,k_s)
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k_s_squared = _np.einsum('...l,...l',k_s,k_s)
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k_s_squared[0,0,0] = 1.0
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displacement = -np.einsum('ijkml,ijkl,l->ijkm',
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np.fft.rfftn(F,axes=(0,1,2)),
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displacement = -_np.einsum('ijkml,ijkl,l->ijkm',
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_np.fft.rfftn(F,axes=(0,1,2)),
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k_s,
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integrator,
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) / k_s_squared[...,np.newaxis]
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) / k_s_squared[...,_np.newaxis]
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return np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
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return _np.fft.irfftn(displacement,axes=(0,1,2),s=F.shape[:3])
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def cell_displacement_avg(size,F):
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@ -145,8 +145,8 @@ def cell_displacement_avg(size,F):
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deformation gradient field.
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"""
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F_avg = np.average(F,axis=(0,1,2))
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return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),cell_coord0(F.shape[:3][::-1],size))
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F_avg = _np.average(F,axis=(0,1,2))
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return _np.einsum('ml,ijkl->ijkm',F_avg-_np.eye(3),cell_coord0(F.shape[:3][::-1],size))
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def cell_displacement(size,F):
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@ -164,7 +164,7 @@ def cell_displacement(size,F):
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return cell_displacement_avg(size,F) + cell_displacement_fluct(size,F)
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def cell_coord(size,F,origin=np.zeros(3)):
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def cell_coord(size,F,origin=_np.zeros(3)):
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"""
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Cell center positions.
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@ -193,17 +193,17 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
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expect coord0 data to be ordered (x fast, z slow).
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"""
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coords = [np.unique(coord0[:,i]) for i in range(3)]
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mincorner = np.array(list(map(min,coords)))
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maxcorner = np.array(list(map(max,coords)))
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grid = np.array(list(map(len,coords)),'i')
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size = grid/np.maximum(grid-1,1) * (maxcorner-mincorner)
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coords = [_np.unique(coord0[:,i]) for i in range(3)]
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mincorner = _np.array(list(map(min,coords)))
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maxcorner = _np.array(list(map(max,coords)))
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grid = _np.array(list(map(len,coords)),'i')
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size = grid/_np.maximum(grid-1,1) * (maxcorner-mincorner)
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delta = size/grid
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origin = mincorner - delta*.5
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# 1D/2D: size/origin combination undefined, set origin to 0.0
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size [np.where(grid==1)] = origin[np.where(grid==1)]*2.
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origin[np.where(grid==1)] = 0.0
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size [_np.where(grid==1)] = origin[_np.where(grid==1)]*2.
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origin[_np.where(grid==1)] = 0.0
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if grid.prod() != len(coord0):
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raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
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@ -211,13 +211,13 @@ def cell_coord0_gridSizeOrigin(coord0,ordered=True):
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start = origin + delta*.5
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end = origin - delta*.5 + size
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if not np.allclose(coords[0],np.linspace(start[0],end[0],grid[0])) and \
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np.allclose(coords[1],np.linspace(start[1],end[1],grid[1])) and \
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np.allclose(coords[2],np.linspace(start[2],end[2],grid[2])):
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if not _np.allclose(coords[0],_np.linspace(start[0],end[0],grid[0])) and \
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_np.allclose(coords[1],_np.linspace(start[1],end[1],grid[1])) and \
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_np.allclose(coords[2],_np.linspace(start[2],end[2],grid[2])):
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raise ValueError('Regular grid spacing violated.')
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if ordered and not np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)):
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raise ValueError('Input data is not a regular grid.')
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if ordered and not _np.allclose(coord0.reshape(tuple(grid[::-1])+(3,)),cell_coord0(grid,size,origin)):
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raise ValueError('I_nput data is not a regular grid.')
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return (grid,size,origin)
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@ -235,7 +235,7 @@ def coord0_check(coord0):
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cell_coord0_gridSizeOrigin(coord0,ordered=True)
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def node_coord0(grid,size,origin=np.zeros(3)):
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def node_coord0(grid,size,origin=_np.zeros(3)):
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"""
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Nodal positions (undeformed).
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@ -249,7 +249,7 @@ def node_coord0(grid,size,origin=np.zeros(3)):
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physical origin of the periodic field. Defaults to [0.0,0.0,0.0].
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"""
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return np.mgrid[origin[0]:size[0]+origin[0]:(grid[0]+1)*1j,
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return _np.mgrid[origin[0]:size[0]+origin[0]:(grid[0]+1)*1j,
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origin[1]:size[1]+origin[1]:(grid[1]+1)*1j,
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origin[2]:size[2]+origin[2]:(grid[2]+1)*1j].T
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@ -281,8 +281,8 @@ def node_displacement_avg(size,F):
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deformation gradient field.
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"""
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F_avg = np.average(F,axis=(0,1,2))
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return np.einsum('ml,ijkl->ijkm',F_avg-np.eye(3),node_coord0(F.shape[:3][::-1],size))
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F_avg = _np.average(F,axis=(0,1,2))
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return _np.einsum('ml,ijkl->ijkm',F_avg-_np.eye(3),node_coord0(F.shape[:3][::-1],size))
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def node_displacement(size,F):
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@ -300,7 +300,7 @@ def node_displacement(size,F):
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return node_displacement_avg(size,F) + node_displacement_fluct(size,F)
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def node_coord(size,F,origin=np.zeros(3)):
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def node_coord(size,F,origin=_np.zeros(3)):
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"""
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Nodal positions.
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@ -319,18 +319,18 @@ def node_coord(size,F,origin=np.zeros(3)):
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def cell_2_node(cell_data):
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"""Interpolate periodic cell data to nodal data."""
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n = ( cell_data + np.roll(cell_data,1,(0,1,2))
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+ np.roll(cell_data,1,(0,)) + np.roll(cell_data,1,(1,)) + np.roll(cell_data,1,(2,))
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+ np.roll(cell_data,1,(0,1)) + np.roll(cell_data,1,(1,2)) + np.roll(cell_data,1,(2,0)))*0.125
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n = ( cell_data + _np.roll(cell_data,1,(0,1,2))
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+ _np.roll(cell_data,1,(0,)) + _np.roll(cell_data,1,(1,)) + _np.roll(cell_data,1,(2,))
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+ _np.roll(cell_data,1,(0,1)) + _np.roll(cell_data,1,(1,2)) + _np.roll(cell_data,1,(2,0)))*0.125
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return np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
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return _np.pad(n,((0,1),(0,1),(0,1))+((0,0),)*len(cell_data.shape[3:]),mode='wrap')
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def node_2_cell(node_data):
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"""Interpolate periodic nodal data to cell data."""
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c = ( node_data + np.roll(node_data,1,(0,1,2))
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+ np.roll(node_data,1,(0,)) + np.roll(node_data,1,(1,)) + np.roll(node_data,1,(2,))
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+ np.roll(node_data,1,(0,1)) + np.roll(node_data,1,(1,2)) + np.roll(node_data,1,(2,0)))*0.125
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c = ( node_data + _np.roll(node_data,1,(0,1,2))
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+ _np.roll(node_data,1,(0,)) + _np.roll(node_data,1,(1,)) + _np.roll(node_data,1,(2,))
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+ _np.roll(node_data,1,(0,1)) + _np.roll(node_data,1,(1,2)) + _np.roll(node_data,1,(2,0)))*0.125
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return c[:-1,:-1,:-1]
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@ -347,23 +347,23 @@ def node_coord0_gridSizeOrigin(coord0,ordered=False):
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expect coord0 data to be ordered (x fast, z slow).
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"""
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coords = [np.unique(coord0[:,i]) for i in range(3)]
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mincorner = np.array(list(map(min,coords)))
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maxcorner = np.array(list(map(max,coords)))
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grid = np.array(list(map(len,coords)),'i') - 1
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coords = [_np.unique(coord0[:,i]) for i in range(3)]
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mincorner = _np.array(list(map(min,coords)))
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maxcorner = _np.array(list(map(max,coords)))
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grid = _np.array(list(map(len,coords)),'i') - 1
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size = maxcorner-mincorner
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origin = mincorner
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if (grid+1).prod() != len(coord0):
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raise ValueError('Data count {} does not match grid {}.'.format(len(coord0),grid))
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if not np.allclose(coords[0],np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
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np.allclose(coords[1],np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
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np.allclose(coords[2],np.linspace(mincorner[2],maxcorner[2],grid[2]+1)):
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if not _np.allclose(coords[0],_np.linspace(mincorner[0],maxcorner[0],grid[0]+1)) and \
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_np.allclose(coords[1],_np.linspace(mincorner[1],maxcorner[1],grid[1]+1)) and \
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_np.allclose(coords[2],_np.linspace(mincorner[2],maxcorner[2],grid[2]+1)):
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raise ValueError('Regular grid spacing violated.')
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if ordered and not np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)):
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raise ValueError('Input data is not a regular grid.')
|
||||
if ordered and not _np.allclose(coord0.reshape(tuple((grid+1)[::-1])+(3,)),node_coord0(grid,size,origin)):
|
||||
raise ValueError('I_nput data is not a regular grid.')
|
||||
|
||||
return (grid,size,origin)
|
||||
|
||||
|
|
@ -386,10 +386,10 @@ def regrid(size,F,new_grid):
|
|||
+ cell_displacement_avg(size,F) \
|
||||
+ cell_displacement_fluct(size,F)
|
||||
|
||||
outer = np.dot(np.average(F,axis=(0,1,2)),size)
|
||||
outer = _np.dot(_np.average(F,axis=(0,1,2)),size)
|
||||
for d in range(3):
|
||||
c[np.where(c[:,:,:,d]<0)] += outer[d]
|
||||
c[np.where(c[:,:,:,d]>outer[d])] -= outer[d]
|
||||
c[_np.where(c[:,:,:,d]<0)] += outer[d]
|
||||
c[_np.where(c[:,:,:,d]>outer[d])] -= outer[d]
|
||||
|
||||
tree = spatial.cKDTree(c.reshape(-1,3),boxsize=outer)
|
||||
tree = _spatial.cKDTree(c.reshape(-1,3),boxsize=outer)
|
||||
return tree.query(cell_coord0(new_grid,outer))[1].flatten()
|
||||
|
|
|
|||
|
|
@ -1,4 +1,4 @@
|
|||
import numpy as np
|
||||
import numpy as _np
|
||||
|
||||
def Cauchy(P,F):
|
||||
"""
|
||||
|
|
@ -14,10 +14,10 @@ def Cauchy(P,F):
|
|||
First Piola-Kirchhoff stress.
|
||||
|
||||
"""
|
||||
if np.shape(F) == np.shape(P) == (3,3):
|
||||
sigma = 1.0/np.linalg.det(F) * np.dot(P,F.T)
|
||||
if _np.shape(F) == _np.shape(P) == (3,3):
|
||||
sigma = 1.0/_np.linalg.det(F) * _np.dot(P,F.T)
|
||||
else:
|
||||
sigma = np.einsum('i,ijk,ilk->ijl',1.0/np.linalg.det(F),P,F)
|
||||
sigma = _np.einsum('i,ijk,ilk->ijl',1.0/_np.linalg.det(F),P,F)
|
||||
return symmetric(sigma)
|
||||
|
||||
|
||||
|
|
@ -31,8 +31,8 @@ def deviatoric_part(T):
|
|||
Tensor of which the deviatoric part is computed.
|
||||
|
||||
"""
|
||||
return T - np.eye(3)*spherical_part(T) if np.shape(T) == (3,3) else \
|
||||
T - np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),[T.shape[0],3,3]),spherical_part(T))
|
||||
return T - _np.eye(3)*spherical_part(T) if _np.shape(T) == (3,3) else \
|
||||
T - _np.einsum('ijk,i->ijk',_np.broadcast_to(_np.eye(3),[T.shape[0],3,3]),spherical_part(T))
|
||||
|
||||
|
||||
def eigenvalues(T_sym):
|
||||
|
|
@ -48,7 +48,7 @@ def eigenvalues(T_sym):
|
|||
Symmetric tensor of which the eigenvalues are computed.
|
||||
|
||||
"""
|
||||
return np.linalg.eigvalsh(symmetric(T_sym))
|
||||
return _np.linalg.eigvalsh(symmetric(T_sym))
|
||||
|
||||
|
||||
def eigenvectors(T_sym,RHS=False):
|
||||
|
|
@ -65,13 +65,13 @@ def eigenvectors(T_sym,RHS=False):
|
|||
Enforce right-handed coordinate system. Default is False.
|
||||
|
||||
"""
|
||||
(u,v) = np.linalg.eigh(symmetric(T_sym))
|
||||
(u,v) = _np.linalg.eigh(symmetric(T_sym))
|
||||
|
||||
if RHS:
|
||||
if np.shape(T_sym) == (3,3):
|
||||
if np.linalg.det(v) < 0.0: v[:,2] *= -1.0
|
||||
if _np.shape(T_sym) == (3,3):
|
||||
if _np.linalg.det(v) < 0.0: v[:,2] *= -1.0
|
||||
else:
|
||||
v[np.linalg.det(v) < 0.0,:,2] *= -1.0
|
||||
v[_np.linalg.det(v) < 0.0,:,2] *= -1.0
|
||||
return v
|
||||
|
||||
|
||||
|
|
@ -99,7 +99,7 @@ def maximum_shear(T_sym):
|
|||
|
||||
"""
|
||||
w = eigenvalues(T_sym)
|
||||
return (w[0] - w[2])*0.5 if np.shape(T_sym) == (3,3) else \
|
||||
return (w[0] - w[2])*0.5 if _np.shape(T_sym) == (3,3) else \
|
||||
(w[:,0] - w[:,2])*0.5
|
||||
|
||||
|
||||
|
|
@ -141,10 +141,10 @@ def PK2(P,F):
|
|||
Deformation gradient.
|
||||
|
||||
"""
|
||||
if np.shape(F) == np.shape(P) == (3,3):
|
||||
S = np.dot(np.linalg.inv(F),P)
|
||||
if _np.shape(F) == _np.shape(P) == (3,3):
|
||||
S = _np.dot(_np.linalg.inv(F),P)
|
||||
else:
|
||||
S = np.einsum('ijk,ikl->ijl',np.linalg.inv(F),P)
|
||||
S = _np.einsum('ijk,ikl->ijl',_np.linalg.inv(F),P)
|
||||
return symmetric(S)
|
||||
|
||||
|
||||
|
|
@ -187,14 +187,14 @@ def spherical_part(T,tensor=False):
|
|||
|
||||
"""
|
||||
if T.shape == (3,3):
|
||||
sph = np.trace(T)/3.0
|
||||
return sph if not tensor else np.eye(3)*sph
|
||||
sph = _np.trace(T)/3.0
|
||||
return sph if not tensor else _np.eye(3)*sph
|
||||
else:
|
||||
sph = np.trace(T,axis1=1,axis2=2)/3.0
|
||||
sph = _np.trace(T,axis1=1,axis2=2)/3.0
|
||||
if not tensor:
|
||||
return sph
|
||||
else:
|
||||
return np.einsum('ijk,i->ijk',np.broadcast_to(np.eye(3),(T.shape[0],3,3)),sph)
|
||||
return _np.einsum('ijk,i->ijk',_np.broadcast_to(_np.eye(3),(T.shape[0],3,3)),sph)
|
||||
|
||||
|
||||
def strain_tensor(F,t,m):
|
||||
|
|
@ -216,22 +216,22 @@ def strain_tensor(F,t,m):
|
|||
"""
|
||||
F_ = F.reshape(1,3,3) if F.shape == (3,3) else F
|
||||
if t == 'V':
|
||||
B = np.matmul(F_,transpose(F_))
|
||||
w,n = np.linalg.eigh(B)
|
||||
B = _np.matmul(F_,transpose(F_))
|
||||
w,n = _np.linalg.eigh(B)
|
||||
elif t == 'U':
|
||||
C = np.matmul(transpose(F_),F_)
|
||||
w,n = np.linalg.eigh(C)
|
||||
C = _np.matmul(transpose(F_),F_)
|
||||
w,n = _np.linalg.eigh(C)
|
||||
|
||||
if m > 0.0:
|
||||
eps = 1.0/(2.0*abs(m)) * (+ np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n))
|
||||
- np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
|
||||
eps = 1.0/(2.0*abs(m)) * (+ _np.matmul(n,_np.einsum('ij,ikj->ijk',w**m,n))
|
||||
- _np.broadcast_to(_np.eye(3),[F_.shape[0],3,3]))
|
||||
elif m < 0.0:
|
||||
eps = 1.0/(2.0*abs(m)) * (- np.matmul(n,np.einsum('ij,ikj->ijk',w**m,n))
|
||||
+ np.broadcast_to(np.eye(3),[F_.shape[0],3,3]))
|
||||
eps = 1.0/(2.0*abs(m)) * (- _np.matmul(n,_np.einsum('ij,ikj->ijk',w**m,n))
|
||||
+ _np.broadcast_to(_np.eye(3),[F_.shape[0],3,3]))
|
||||
else:
|
||||
eps = np.matmul(n,np.einsum('ij,ikj->ijk',0.5*np.log(w),n))
|
||||
eps = _np.matmul(n,_np.einsum('ij,ikj->ijk',0.5*_np.log(w),n))
|
||||
|
||||
return eps.reshape(3,3) if np.shape(F) == (3,3) else \
|
||||
return eps.reshape(3,3) if _np.shape(F) == (3,3) else \
|
||||
eps
|
||||
|
||||
|
||||
|
|
@ -258,8 +258,8 @@ def transpose(T):
|
|||
Tensor of which the transpose is computed.
|
||||
|
||||
"""
|
||||
return T.T if np.shape(T) == (3,3) else \
|
||||
np.transpose(T,(0,2,1))
|
||||
return T.T if _np.shape(T) == (3,3) else \
|
||||
_np.transpose(T,(0,2,1))
|
||||
|
||||
|
||||
def _polar_decomposition(T,requested):
|
||||
|
|
@ -275,17 +275,17 @@ def _polar_decomposition(T,requested):
|
|||
‘V’ for left stretch tensor and ‘U’ for right stretch tensor.
|
||||
|
||||
"""
|
||||
u, s, vh = np.linalg.svd(T)
|
||||
R = np.dot(u,vh) if np.shape(T) == (3,3) else \
|
||||
np.einsum('ijk,ikl->ijl',u,vh)
|
||||
u, s, vh = _np.linalg.svd(T)
|
||||
R = _np.dot(u,vh) if _np.shape(T) == (3,3) else \
|
||||
_np.einsum('ijk,ikl->ijl',u,vh)
|
||||
|
||||
output = []
|
||||
if 'R' in requested:
|
||||
output.append(R)
|
||||
if 'V' in requested:
|
||||
output.append(np.dot(T,R.T) if np.shape(T) == (3,3) else np.einsum('ijk,ilk->ijl',T,R))
|
||||
output.append(_np.dot(T,R.T) if _np.shape(T) == (3,3) else _np.einsum('ijk,ilk->ijl',T,R))
|
||||
if 'U' in requested:
|
||||
output.append(np.dot(R.T,T) if np.shape(T) == (3,3) else np.einsum('ikj,ikl->ijl',R,T))
|
||||
output.append(_np.dot(R.T,T) if _np.shape(T) == (3,3) else _np.einsum('ikj,ikl->ijl',R,T))
|
||||
|
||||
return tuple(output)
|
||||
|
||||
|
|
@ -303,5 +303,5 @@ def _Mises(T_sym,s):
|
|||
|
||||
"""
|
||||
d = deviatoric_part(T_sym)
|
||||
return np.sqrt(s*(np.sum(d**2.0))) if np.shape(T_sym) == (3,3) else \
|
||||
np.sqrt(s*np.einsum('ijk->i',d**2.0))
|
||||
return _np.sqrt(s*(_np.sum(d**2.0))) if _np.shape(T_sym) == (3,3) else \
|
||||
_np.sqrt(s*_np.einsum('ijk->i',d**2.0))
|
||||
|
|
|
|||
|
|
@ -9,37 +9,22 @@ from optparse import Option
|
|||
|
||||
import numpy as np
|
||||
|
||||
class bcolors:
|
||||
"""
|
||||
ASCII Colors.
|
||||
|
||||
https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
|
||||
https://stackoverflow.com/questions/287871
|
||||
"""
|
||||
|
||||
HEADER = '\033[95m'
|
||||
OKBLUE = '\033[94m'
|
||||
OKGREEN = '\033[92m'
|
||||
WARNING = '\033[93m'
|
||||
FAIL = '\033[91m'
|
||||
ENDC = '\033[0m'
|
||||
BOLD = '\033[1m'
|
||||
DIM = '\033[2m'
|
||||
UNDERLINE = '\033[4m'
|
||||
CROSSOUT = '\033[9m'
|
||||
|
||||
def disable(self):
|
||||
self.HEADER = ''
|
||||
self.OKBLUE = ''
|
||||
self.OKGREEN = ''
|
||||
self.WARNING = ''
|
||||
self.FAIL = ''
|
||||
self.ENDC = ''
|
||||
self.BOLD = ''
|
||||
self.UNDERLINE = ''
|
||||
self.CROSSOUT = ''
|
||||
|
||||
# limit visibility
|
||||
__all__=[
|
||||
'srepr',
|
||||
'croak',
|
||||
'report',
|
||||
'emph','deemph','delete','strikeout',
|
||||
'execute',
|
||||
'show_progress',
|
||||
'scale_to_coprime',
|
||||
'return_message',
|
||||
'extendableOption',
|
||||
]
|
||||
|
||||
####################################################################################################
|
||||
# Functions
|
||||
####################################################################################################
|
||||
def srepr(arg,glue = '\n'):
|
||||
r"""
|
||||
Join arguments as individual lines.
|
||||
|
|
@ -144,6 +129,52 @@ def execute(cmd,
|
|||
return out,error
|
||||
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
"""
|
||||
Decorate a loop with a status bar.
|
||||
|
||||
Use similar like enumerate.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
iterable : iterable/function with yield statement
|
||||
Iterable (or function with yield statement) to be decorated.
|
||||
N_iter : int
|
||||
Total # of iterations. Needed if number of iterations can not be obtained as len(iterable).
|
||||
prefix : str, optional.
|
||||
Prefix string.
|
||||
bar_length : int, optional
|
||||
Character length of bar. Defaults to 50.
|
||||
|
||||
"""
|
||||
status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length)
|
||||
|
||||
for i,item in enumerate(iterable):
|
||||
yield item
|
||||
status.update(i)
|
||||
|
||||
|
||||
def scale_to_coprime(v):
|
||||
"""Scale vector to co-prime (relatively prime) integers."""
|
||||
MAX_DENOMINATOR = 1000
|
||||
|
||||
def get_square_denominator(x):
|
||||
"""Denominator of the square of a number."""
|
||||
return fractions.Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
|
||||
|
||||
def lcm(a, b):
|
||||
"""Least common multiple."""
|
||||
return a * b // np.gcd(a, b)
|
||||
|
||||
denominators = [int(get_square_denominator(i)) for i in v]
|
||||
s = reduce(lcm, denominators) ** 0.5
|
||||
m = (np.array(v)*s).astype(np.int)
|
||||
return m//reduce(np.gcd,m)
|
||||
|
||||
|
||||
####################################################################################################
|
||||
# Classes
|
||||
####################################################################################################
|
||||
class extendableOption(Option):
|
||||
"""
|
||||
Used for definition of new option parser action 'extend', which enables to take multiple option arguments.
|
||||
|
|
@ -215,47 +246,36 @@ class _ProgressBar:
|
|||
sys.stderr.write('\n')
|
||||
sys.stderr.flush()
|
||||
|
||||
def show_progress(iterable,N_iter=None,prefix='',bar_length=50):
|
||||
|
||||
class bcolors:
|
||||
"""
|
||||
Decorate a loop with a status bar.
|
||||
|
||||
Use similar like enumerate.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
iterable : iterable/function with yield statement
|
||||
Iterable (or function with yield statement) to be decorated.
|
||||
N_iter : int
|
||||
Total # of iterations. Needed if number of iterations can not be obtained as len(iterable).
|
||||
prefix : str, optional.
|
||||
Prefix string.
|
||||
bar_length : int, optional
|
||||
Character length of bar. Defaults to 50.
|
||||
ASCII Colors.
|
||||
|
||||
https://svn.blender.org/svnroot/bf-blender/trunk/blender/build_files/scons/tools/bcolors.py
|
||||
https://stackoverflow.com/questions/287871
|
||||
"""
|
||||
status = _ProgressBar(N_iter if N_iter else len(iterable),prefix,bar_length)
|
||||
|
||||
for i,item in enumerate(iterable):
|
||||
yield item
|
||||
status.update(i)
|
||||
HEADER = '\033[95m'
|
||||
OKBLUE = '\033[94m'
|
||||
OKGREEN = '\033[92m'
|
||||
WARNING = '\033[93m'
|
||||
FAIL = '\033[91m'
|
||||
ENDC = '\033[0m'
|
||||
BOLD = '\033[1m'
|
||||
DIM = '\033[2m'
|
||||
UNDERLINE = '\033[4m'
|
||||
CROSSOUT = '\033[9m'
|
||||
|
||||
|
||||
def scale_to_coprime(v):
|
||||
"""Scale vector to co-prime (relatively prime) integers."""
|
||||
MAX_DENOMINATOR = 1000
|
||||
|
||||
def get_square_denominator(x):
|
||||
"""Denominator of the square of a number."""
|
||||
return fractions.Fraction(x ** 2).limit_denominator(MAX_DENOMINATOR).denominator
|
||||
|
||||
def lcm(a, b):
|
||||
"""Least common multiple."""
|
||||
return a * b // np.gcd(a, b)
|
||||
|
||||
denominators = [int(get_square_denominator(i)) for i in v]
|
||||
s = reduce(lcm, denominators) ** 0.5
|
||||
m = (np.array(v)*s).astype(np.int)
|
||||
return m//reduce(np.gcd,m)
|
||||
def disable(self):
|
||||
self.HEADER = ''
|
||||
self.OKBLUE = ''
|
||||
self.OKGREEN = ''
|
||||
self.WARNING = ''
|
||||
self.FAIL = ''
|
||||
self.ENDC = ''
|
||||
self.BOLD = ''
|
||||
self.UNDERLINE = ''
|
||||
self.CROSSOUT = ''
|
||||
|
||||
|
||||
class return_message:
|
||||
|
|
@ -276,4 +296,3 @@ class return_message:
|
|||
def __repr__(self):
|
||||
"""Return message suitable for interactive shells."""
|
||||
return srepr(self.message)
|
||||
|
||||
|
|
|
|||
|
|
@ -24,7 +24,7 @@ class TestGridFilters:
|
|||
n = grid_filters.node_coord0(grid,size) + size/grid*.5
|
||||
assert np.allclose(c,n)
|
||||
|
||||
@pytest.mark.parametrize('mode',[('cell'),('node')])
|
||||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
def test_grid_DNA(self,mode):
|
||||
"""Ensure that xx_coord0_gridSizeOrigin is the inverse of xx_coord0."""
|
||||
grid = np.random.randint(8,32,(3))
|
||||
|
|
@ -49,7 +49,7 @@ class TestGridFilters:
|
|||
assert np.allclose(grid_filters.node_coord(size,F) [1:-1,1:-1,1:-1],grid_filters.cell_2_node(
|
||||
grid_filters.cell_coord(size,F))[1:-1,1:-1,1:-1])
|
||||
|
||||
@pytest.mark.parametrize('mode',[('cell'),('node')])
|
||||
@pytest.mark.parametrize('mode',['cell','node'])
|
||||
def test_coord0_origin(self,mode):
|
||||
origin= np.random.random(3)
|
||||
size = np.random.random(3) # noqa
|
||||
|
|
@ -61,22 +61,24 @@ class TestGridFilters:
|
|||
elif mode == 'node':
|
||||
assert np.allclose(shifted,unshifted+np.broadcast_to(origin,tuple(grid[::-1]+1)+(3,)))
|
||||
|
||||
@pytest.mark.parametrize('mode',[('cell'),('node')])
|
||||
def test_displacement_avg_vanishes(self,mode):
|
||||
@pytest.mark.parametrize('function',[grid_filters.cell_displacement_avg,
|
||||
grid_filters.node_displacement_avg])
|
||||
def test_displacement_avg_vanishes(self,function):
|
||||
"""Ensure that random fluctuations in F do not result in average displacement."""
|
||||
size = np.random.random(3) # noqa
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.random.random(tuple(grid)+(3,3))
|
||||
F += np.eye(3) - np.average(F,axis=(0,1,2))
|
||||
assert np.allclose(eval('grid_filters.{}_displacement_avg(size,F)'.format(mode)),0.0)
|
||||
assert np.allclose(function(size,F),0.0)
|
||||
|
||||
@pytest.mark.parametrize('mode',[('cell'),('node')])
|
||||
def test_displacement_fluct_vanishes(self,mode):
|
||||
@pytest.mark.parametrize('function',[grid_filters.cell_displacement_fluct,
|
||||
grid_filters.node_displacement_fluct])
|
||||
def test_displacement_fluct_vanishes(self,function):
|
||||
"""Ensure that constant F does not result in fluctuating displacement."""
|
||||
size = np.random.random(3) # noqa
|
||||
size = np.random.random(3)
|
||||
grid = np.random.randint(8,32,(3))
|
||||
F = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3)) # noqa
|
||||
assert np.allclose(eval('grid_filters.{}_displacement_fluct(size,F)'.format(mode)),0.0)
|
||||
F = np.broadcast_to(np.random.random((3,3)), tuple(grid)+(3,3))
|
||||
assert np.allclose(function(size,F),0.0)
|
||||
|
||||
def test_regrid(self):
|
||||
size = np.random.random(3)
|
||||
|
|
|
|||
|
|
@ -0,0 +1,59 @@
|
|||
!--------------------------------------------------------------------------------------------------
|
||||
!> @author Martin Diehl, Max-Planck-Institut für Eisenforschung GmbH
|
||||
!> @brief Fortran interfaces for LAPACK routines
|
||||
!> @details https://www.netlib.org/lapack/
|
||||
!--------------------------------------------------------------------------------------------------
|
||||
module LAPACK_interface
|
||||
interface
|
||||
|
||||
subroutine dgeev(jobvl,jobvr,n,a,lda,wr,wi,vl,ldvl,vr,ldvr,work,lwork,info)
|
||||
use prec
|
||||
character, intent(in) :: jobvl,jobvr
|
||||
integer, intent(in) :: n,lda,ldvl,ldvr,lwork
|
||||
real(pReal), intent(inout), dimension(lda,n) :: a
|
||||
real(pReal), intent(out), dimension(n) :: wr,wi
|
||||
real(pReal), intent(out), dimension(ldvl,n) :: vl
|
||||
real(pReal), intent(out), dimension(ldvr,n) :: vr
|
||||
real(pReal), intent(out), dimension(max(1,lwork)) :: work
|
||||
integer, intent(out) :: info
|
||||
end subroutine dgeev
|
||||
|
||||
subroutine dgesv(n,nrhs,a,lda,ipiv,b,ldb,info)
|
||||
use prec
|
||||
integer, intent(in) :: n,nrhs,lda,ldb
|
||||
real(pReal), intent(inout), dimension(lda,n) :: a
|
||||
integer, intent(out), dimension(n) :: ipiv
|
||||
real(pReal), intent(out), dimension(ldb,nrhs) :: b
|
||||
integer, intent(out) :: info
|
||||
end subroutine dgesv
|
||||
|
||||
subroutine dgetrf(m,n,a,lda,ipiv,info)
|
||||
use prec
|
||||
integer, intent(in) :: m,n,lda
|
||||
real(pReal), intent(inout), dimension(lda,n) :: a
|
||||
integer, intent(out), dimension(min(m,n)) :: ipiv
|
||||
integer, intent(out) :: info
|
||||
end subroutine dgetrf
|
||||
|
||||
subroutine dgetri(n,a,lda,ipiv,work,lwork,info)
|
||||
use prec
|
||||
integer, intent(in) :: n,lda,lwork
|
||||
real(pReal), intent(inout), dimension(lda,n) :: a
|
||||
integer, intent(out), dimension(n) :: ipiv
|
||||
real(pReal), intent(out), dimension(max(1,lwork)) :: work
|
||||
integer, intent(out) :: info
|
||||
end subroutine dgetri
|
||||
|
||||
subroutine dsyev(jobz,uplo,n,a,lda,w,work,lwork,info)
|
||||
use prec
|
||||
character, intent(in) :: jobz,uplo
|
||||
integer, intent(in) :: n,lda,lwork
|
||||
real(pReal), intent(inout), dimension(lda,n) :: a
|
||||
real(pReal), intent(out), dimension(n) :: w
|
||||
real(pReal), intent(out), dimension(max(1,lwork)) :: work
|
||||
integer, intent(out) :: info
|
||||
end subroutine dsyev
|
||||
|
||||
end interface
|
||||
|
||||
end module LAPACK_interface
|
||||
|
|
@ -9,6 +9,7 @@
|
|||
#include "list.f90"
|
||||
#include "future.f90"
|
||||
#include "config.f90"
|
||||
#include "LAPACK_interface.f90"
|
||||
#include "math.f90"
|
||||
#include "quaternions.f90"
|
||||
#include "Lambert.f90"
|
||||
|
|
|
|||
|
|
@ -835,8 +835,6 @@ logical function integrateStress(ipc,ip,el,timeFraction)
|
|||
jacoCounterLp, &
|
||||
jacoCounterLi ! counters to check for Jacobian update
|
||||
logical :: error
|
||||
external :: &
|
||||
dgesv
|
||||
|
||||
integrateStress = .false.
|
||||
|
||||
|
|
|
|||
30
src/math.f90
30
src/math.f90
|
|
@ -9,6 +9,7 @@ module math
|
|||
use prec
|
||||
use IO
|
||||
use numerics
|
||||
use LAPACK_interface
|
||||
|
||||
implicit none
|
||||
public
|
||||
|
|
@ -485,18 +486,14 @@ function math_invSym3333(A)
|
|||
|
||||
real(pReal),dimension(3,3,3,3),intent(in) :: A
|
||||
|
||||
integer, dimension(6) :: ipiv6
|
||||
real(pReal), dimension(6,6) :: temp66
|
||||
real(pReal), dimension(6*(64+2)) :: work
|
||||
integer :: ierr_i, ierr_f
|
||||
external :: &
|
||||
dgetrf, &
|
||||
dgetri
|
||||
integer, dimension(6) :: ipiv6
|
||||
real(pReal), dimension(6,6) :: temp66
|
||||
real(pReal), dimension(6*6) :: work
|
||||
integer :: ierr_i, ierr_f
|
||||
|
||||
temp66 = math_sym3333to66(A)
|
||||
call dgetrf(6,6,temp66,6,ipiv6,ierr_i)
|
||||
call dgetri(6,temp66,6,ipiv6,work,size(work,1),ierr_f)
|
||||
|
||||
if (ierr_i /= 0 .or. ierr_f /= 0) then
|
||||
call IO_error(400, ext_msg = 'math_invSym3333')
|
||||
else
|
||||
|
|
@ -515,12 +512,9 @@ subroutine math_invert(InvA, error, A)
|
|||
real(pReal), dimension(size(A,1),size(A,1)), intent(out) :: invA
|
||||
logical, intent(out) :: error
|
||||
|
||||
integer, dimension(size(A,1)) :: ipiv
|
||||
real(pReal), dimension(size(A,1)*(64+2)) :: work
|
||||
integer :: ierr
|
||||
external :: &
|
||||
dgetrf, &
|
||||
dgetri
|
||||
integer, dimension(size(A,1)) :: ipiv
|
||||
real(pReal), dimension(size(A,1)**2) :: work
|
||||
integer :: ierr
|
||||
|
||||
invA = A
|
||||
call dgetrf(size(A,1),size(A,1),invA,size(A,1),ipiv,ierr)
|
||||
|
|
@ -884,9 +878,7 @@ subroutine math_eigh(m,w,v,error)
|
|||
|
||||
logical, intent(out) :: error
|
||||
integer :: ierr
|
||||
real(pReal), dimension((64+2)*size(m,1)) :: work ! block size of 64 taken from http://www.netlib.org/lapack/double/dsyev.f
|
||||
external :: &
|
||||
dsyev
|
||||
real(pReal), dimension(size(m,1)**2) :: work
|
||||
|
||||
v = m ! copy matrix to input (doubles as output) array
|
||||
call dsyev('V','U',size(m,1),v,size(m,1),w,work,size(work,1),ierr)
|
||||
|
|
@ -1041,9 +1033,7 @@ function math_eigvalsh(m)
|
|||
|
||||
real(pReal), dimension(size(m,1),size(m,1)) :: m_
|
||||
integer :: ierr
|
||||
real(pReal), dimension((64+2)*size(m,1)) :: work ! block size of 64 taken from http://www.netlib.org/lapack/double/dsyev.f
|
||||
external :: &
|
||||
dsyev
|
||||
real(pReal), dimension(size(m,1)**2) :: work
|
||||
|
||||
m_= m ! copy matrix to input (will be destroyed)
|
||||
call dsyev('N','U',size(m,1),m_,size(m,1),math_eigvalsh,work,size(work,1),ierr)
|
||||
|
|
|
|||
|
|
@ -596,8 +596,6 @@ function om2ax(om) result(ax)
|
|||
real(pReal), dimension(3,3) :: VR, devNull, om_
|
||||
integer :: ierr, i
|
||||
|
||||
external :: dgeev
|
||||
|
||||
om_ = om
|
||||
|
||||
! first get the rotation angle
|
||||
|
|
|
|||
Loading…
Reference in New Issue