adjusting for strict prospector checking
This commit is contained in:
Martin Diehl
parent
a6c69a744b
commit
953ba53211
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@ -1,20 +1,35 @@
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# -*- coding: UTF-8 no BOM -*-
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import h5py
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import re
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import numpy as np
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from queue import Queue
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import re
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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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"""
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Opens an existing DADF5 file.
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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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mode : str, optional
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filemode for opening, either 'r' or 'a'.
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"""
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if mode not in ['a','r']:
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print('Invalid file access mode')
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else:
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@ -95,7 +110,7 @@ class DADF5():
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return groups
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def list_data(self):
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"""Shows information on all datasets in the file"""
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"""Shows information on all datasets in the file."""
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with h5py.File(self.filename,'r') as f:
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group_inc = 'inc{:05}'.format(self.active['increments'][0]['inc'])
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for c in self.active['constituents']:
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@ -107,7 +122,7 @@ class DADF5():
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try:
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for x in f[group_output_types].keys():
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print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
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except:
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except KeyError:
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pass
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for m in self.active['materialpoints']:
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group_materialpoint = group_inc+'/materialpoint/'+m
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@ -117,12 +132,12 @@ class DADF5():
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try:
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for x in f[group_output_types].keys():
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print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
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except:
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except KeyError:
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pass
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def get_dataset_location(self,label):
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"""Returns the location of all active datasets with given label"""
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"""Returns the location of all active datasets with given label."""
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path = []
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with h5py.File(self.filename,'r') as f:
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for i in self.active['increments']:
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@ -134,7 +149,7 @@ class DADF5():
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try:
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f[group_constituent+'/'+t+'/'+label]
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path.append(group_constituent+'/'+t+'/'+label)
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except Exception as e:
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except KeyError as e:
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print('unable to locate constituents dataset: '+ str(e))
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for m in self.active['materialpoints']:
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@ -143,7 +158,7 @@ class DADF5():
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try:
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f[group_materialpoint+'/'+t+'/'+label]
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path.append(group_materialpoint+'/'+t+'/'+label)
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except Exception as e:
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except KeyError as e:
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print('unable to locate materialpoints dataset: '+ str(e))
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return path
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@ -151,7 +166,7 @@ class DADF5():
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def read_dataset(self,path,c):
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"""
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Dataset for all points/cells
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Dataset for all points/cells.
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If more than one path is given, the dataset is composed of the individual contributions
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"""
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@ -168,7 +183,7 @@ class DADF5():
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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except Exception as e:
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except KeyError as e:
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print('unable to read constituent: '+ str(e))
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try:
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p = np.where(f['mapping/cellResults/materialpoint']['Name'] == str.encode(label))[0]
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@ -177,7 +192,7 @@ class DADF5():
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if len(a.shape) == 1:
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a=a.reshape([a.shape[0],1])
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dataset[p,:] = a[u,:]
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except Exception as e:
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except KeyError as e:
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print('unable to read materialpoint: '+ str(e))
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return dataset
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@ -190,6 +205,7 @@ class DADF5():
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Todo
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----
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The einsum formula is completely untested!
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"""
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def Cauchy(F,P):
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return np.einsum('i,ijk,ilk->ijl',1.0/np.linalg.det(F),F,P)
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@ -204,7 +220,7 @@ class DADF5():
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def add_Mises_stress(self,stress='sigma'):
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"""Adds equivalent von Mises stress"""
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"""Adds equivalent von Mises stress."""
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def Mises_stress(stress):
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dev = stress - np.trace(stress)/3.0*np.eye(3)
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symdev = 0.5*(dev+dev.T)
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@ -230,7 +246,7 @@ class DADF5():
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def add_determinant(self,a):
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"""Adds the determinant of a tensor"""
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"""Adds the determinant of a tensor."""
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# ToDo: The output unit should be the input unit
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args = [{'label':a,'shape':[3,3],'unit':None}]
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result = {'label':'det({})'.format(a),
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@ -241,7 +257,7 @@ class DADF5():
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def add_spherical(self,a):
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"""Adds the spherical component of a tensor"""
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"""Adds the spherical component of a tensor."""
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def spherical(m):
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return (m[0,0]+m[1,1]+m[2,2])/3.0
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@ -255,7 +271,7 @@ class DADF5():
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def add_deviator(self,a):
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"""Adds the deviator of a tensor"""
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"""Adds the deviator of a tensor."""
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def deviator(m):
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return m - np.eye(3)*(m[0,0]+m[1,1]+m[2,2])/3.0
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@ -270,7 +286,7 @@ class DADF5():
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def add_strain_tensors(self,defgrad='F'):
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"""Adds a strain definition"""
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"""Adds a strain definition."""
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def strain(defgrad):
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(U,S,Vh) = np.linalg.svd(defgrad) # singular value decomposition
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R_inv = np.dot(U,Vh).T # inverse rotation of polar decomposition
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@ -313,7 +329,7 @@ class DADF5():
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def add_generic_pointwise(self,func,args,result):
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"""
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Ggeneral function to add pointwise data.
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General function to add pointwise data.
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function 'func' first needs to have data arguments before other arguments
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Works for functions that are pointwise defined.
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@ -366,7 +382,7 @@ class DADF5():
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missingResults-=1
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try:
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pool.add_task(job,todo[Nthreads+1+i])
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except:
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except IndexError:
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pass
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i+=1
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@ -375,7 +391,7 @@ class DADF5():
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def add_generic_pointwise_vectorized(self,func,args,result):
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"""
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Ggeneral function to add pointwise data
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General function to add pointwise data.
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function 'func' first needs to have data arguments before other arguments
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Works for vectorized functions.
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@ -399,12 +415,8 @@ class DADF5():
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datasets_in = [f[g+'/'+u['label']][()] for u in args]
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# figure out dimension of results
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for d in datasets_in:
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print('input shape',d.shape)
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testArg = tuple([d[0:1,] for d in datasets_in]) # to call function with first point
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#print('testArg',testArg)
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out = np.empty([datasets_in[0].shape[0]] + list(func(*testArg).shape[1:])) # shape is Npoints x shape of the results for one point
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print('estimated output shape',out.shape)
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todo.append({'dat':datasets_in,'fun':func,'out':out,'group':g,'results':results})
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# Instantiate a thread pool with worker threads
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@ -430,7 +442,7 @@ class DADF5():
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missingResults-=1
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try:
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pool.add_task(job,todo[Nthreads+1+i])
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except:
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except IndexError:
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pass
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i+=1
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