polishing
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@ -842,78 +842,6 @@ class Geom:
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comments = self.comments+[util.execution_stamp('Geom','vicinity_offset')],
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)
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def ShowGB(self,periodic=False):
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"""
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Create an extra VTK file to show grain boundaries as feature edges.
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Parameters
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----------
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periodic : Boolean, optional
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Show boundaries at periodic nodes too. Defaults to False.
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"""
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v = VTK.from_polyData(grid_filters.node_coord0(self.grid,self.size,self.origin).reshape(-1,3,order='F'))
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cells = vtk.vtkCellArray()
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index={}
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nodes={}
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nodes_PBC={}
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if periodic:
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nodes_PBC['0']=np.array([])
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nodes_PBC['1']=np.array([])
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nodes_PBC['2']=np.array([])
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else:
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nodes_PBC['0']=np.concatenate((
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np.arange(0 , np.prod(self.grid+1) , (self.grid[0]+1) ),
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np.arange(self.grid[0] , np.prod(self.grid+1) , (self.grid[0]+1) ) ))
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nodes_PBC['2']=np.concatenate((
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np.arange(0 , np.prod(self.grid[:2]+1) , 1 ),
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np.arange(np.prod(self.grid+1) - np.prod(self.grid[:2]+1), \
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np.prod(self.grid+1) , 1 ) ))
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nodes_PBC['1']=np.concatenate((
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np.concatenate([np.arange((i)*np.prod(self.grid[:2]+1), \
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(i)*np.prod(self.grid[:2]+1)+ (self.grid[0]+1)) for i in range(self.grid[2]+1)]) ,
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np.concatenate([np.arange( (i+1)*np.prod(self.grid[:2]+1)-(self.grid[0]+1),\
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(i+1)*np.prod(self.grid[:2]+1)) for i in range(self.grid[2]+1)]) ))
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for d_s in [0,1,2]:
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base_nodes = np.where(self.material==np.roll(self.material,1,d_s),False,True)
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for d in [0,1,2]:
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if d_s == d:
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base_nodes = np.concatenate((base_nodes,np.take(base_nodes,[0],d)),d)
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else:
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base_nodes = np.concatenate((base_nodes,np.logical_and(np.take(base_nodes,[0],d),False)),d)
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nodes['{}'.format(d_s)]= np.argwhere(base_nodes.flatten(order='F'))[:,0]
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index['{}'.format(d_s)]=np.isin(nodes['{}'.format(d_s)],nodes_PBC['{}'.format(d_s)],assume_unique=True,invert=True)
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for p in nodes['0'][index['0']]:
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q = vtk.vtkQuad()
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q.GetPointIds().SetId(0, p)
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q.GetPointIds().SetId(1, p+(self.grid[0]+1))
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q.GetPointIds().SetId(2, p+np.prod(self.grid[:2]+1)+(self.grid[0]+1))
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q.GetPointIds().SetId(3, p+np.prod(self.grid[:2]+1))
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cells.InsertNextCell(q)
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for p in nodes['1'][index['1']]:
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q = vtk.vtkQuad()
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q.GetPointIds().SetId(0, p)
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q.GetPointIds().SetId(1, p+np.prod(self.grid[:2]+1))
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q.GetPointIds().SetId(2, p+np.prod(self.grid[:2]+1)+1)
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q.GetPointIds().SetId(3, p+1)
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cells.InsertNextCell(q)
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for p in nodes['2'][index['2']]:
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q = vtk.vtkQuad()
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q.GetPointIds().SetId(0, p)
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q.GetPointIds().SetId(1, p+1)
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q.GetPointIds().SetId(2, p+(self.grid[0]+1)+1)
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q.GetPointIds().SetId(3, p+(self.grid[0]+1))
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cells.InsertNextCell(q)
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v.vtk_data.SetPolys(cells)
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v.save('GrainBoundaries')
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def get_grain_boundaries(self,periodic=True,direction='x'):
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"""
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Create mesh in VTK to show grain boundaries as feature edges.
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@ -921,7 +849,7 @@ class Geom:
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Parameters
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----------
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periodic : Boolean, optional
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Show boundaries at periodic nodes too. Defaults to True.
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Show boundaries across periodicity. Defaults to True.
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direction : string
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Show grain boundaries only across a certain direction. ['x','y','z']
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@ -938,9 +866,9 @@ class Geom:
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for d in [0,1,2]:
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extra_layer = np.take(mask,[0],d) if d_s == d else np.zeros_like(np.take(mask,[0],d),bool)
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mask = np.concatenate((mask,extra_layer),d)
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if d_s == 0 and periodic: mask[0,:,:] = mask[-1,:,:] = False
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if d_s == 1 and periodic: mask[:,0,:] = mask[:,-1,:] = False
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if d_s == 2 and periodic: mask[:,:,0] = mask[:,:,-1] = False
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if d_s == 0 and not periodic: mask[0,:,:] = mask[-1,:,:] = False
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if d_s == 1 and not periodic: mask[:,0,:] = mask[:,-1,:] = False
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if d_s == 2 and not periodic: mask[:,:,0] = mask[:,:,-1] = False
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base_nodes = np.argwhere(mask.flatten(order='F')).reshape(-1,1)
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connectivity = np.block([base_nodes + o[d_s][d] for d in range(4)])
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return VTK.from_unstructuredGrid(coord,connectivity,'QUAD')
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