DAMASK_EICMD/python/damask/dadf5.py

546 lines
20 KiB
Python

from queue import Queue
import re
import h5py
import numpy as np
from . import util
# ------------------------------------------------------------------
class DADF5():
"""
Read and write to DADF5 files.
DADF5 files contain DAMASK results.
"""
# ------------------------------------------------------------------
def __init__(self,filename):
"""
Opens an existing DADF5 file.
Parameters
----------
filename : str
name of the DADF5 file to be openend.
"""
with h5py.File(filename,'r') as f:
if f.attrs['DADF5-major'] != 0 or f.attrs['DADF5-minor'] != 2:
raise TypeError('Unsupported DADF5 version {} '.format(f.attrs['DADF5-version']))
self.structured = 'grid' in f['geometry'].attrs.keys()
if self.structured:
self.grid = f['geometry'].attrs['grid']
self.size = f['geometry'].attrs['size']
r=re.compile('inc[0-9]+')
self.increments = [{'inc': int(u[3:]),
'time': round(f[u].attrs['time/s'],12),
} for u in f.keys() if r.match(u)]
self.Nmaterialpoints, self.Nconstituents = np.shape(f['mapping/cellResults/constituent'])
self.materialpoints = [m.decode() for m in np.unique(f['mapping/cellResults/materialpoint']['Name'])]
self.constituents = [c.decode() for c in np.unique(f['mapping/cellResults/constituent'] ['Name'])]
self.c_output_types = []
for c in self.constituents:
for o in f['inc{:05}/constituent/{}'.format(self.increments[0]['inc'],c)].keys():
self.c_output_types.append(o)
self.c_output_types = list(set(self.c_output_types)) # make unique
self.m_output_types = []
for m in self.materialpoints:
for o in f['inc{:05}/materialpoint/{}'.format(self.increments[0]['inc'],m)].keys():
self.m_output_types.append(o)
self.m_output_types = list(set(self.m_output_types)) # make unique
self.visible= {'increments': self.increments, # ToDo:simplify, activity only positions that translate into (no complex types)
'constituents': self.constituents,
'materialpoints': self.materialpoints,
'constituent': range(self.Nconstituents), # ToDo: stupid naming
'c_output_types': self.c_output_types,
'm_output_types': self.m_output_types}
self.filename = filename
def __visible_set(self,output,t,p):
valid = set(p)
choice = [output] if isinstance(output,str) else output
self.visible[t] = list(valid.intersection(choice))
def __visible_add(self,output,t,p):
choice = [output] if isinstance(output,str) else output
valid = set(p).intersection(choice)
existing = set(self.visible[t])
self.visible[t] = list(existing.add(valid))
def __visible_del(self,output,t):
choice = [output] if isinstance(output,str) else output
existing = set(self.visible[t])
self.visible[t] = list(existing.remove(choice))
def __visible_iter(self,t):
a = self.visible[t]
last_a = a.copy()
for i in a:
if last_a != self.visible[t]:
self.__visible_set(a,t,a)
raise Exception
self.__visible_set(i,t,a)
last_a = self.visible[t]
yield i
self.__visible_set(a,t,a)
def constituent_output_iter(self):
return self.__visible_iter('c_output_types')
def constituent_output_set(self,output):
self.__visible_set(output,'c_output_types',self.c_output_types)
def constituent_output_add(self,output):
self.__visible_add(output,'c_output_types',self.c_output_types)
def constituent_output_del(self,output):
self.__visible_del(output,'c_output_types')
def materialpoint_output_iter(self):
return self.__visible_iter('m_output_types')
def materialpoint_output_set(self,output):
self.__visible_set(output,'m_output_types',self.m_output_types)
def materialpoint_output_add(self,output):
self.__visible_add(output,'m_output_types',self.m_output_types)
def materialpoint_output_del(self,output):
self.__visible_del(output,'m_output_types')
def constituent_iter(self):
return self.__visible_iter('constituents')
def constituent_set(self,output):
self.__visible_set(output,'constituents',self.constituents)
def constituent_add(self,output):
self.__visible_add(output,'constituents',self.constituents)
def constituent_del(self,output):
self.__visible_del(output,'constituents')
def materialpoint_iter(self):
return self.__visible_iter('materialpoints')
def materialpoint_set(self,output):
self.__visible_set(output,'materialpoints',self.materialpoints)
def materialpoint_add(self,output):
self.__visible_add(output,'materialpoints',self.materialpoints)
def materialpoint_del(self,output):
self.__visible_del(output,'materialpoints')
# ToDo: store increments, select icrements (trivial), position, and time
def get_groups(self,l): #group_with_data(datasets)
"""
Get groups that contain all requested datasets.
Parameters
----------
l : list of str
Names of datasets that need to be located in the group.
"""
groups = []
if type(l) is not list:
raise TypeError('Candidates should be given as a list')
with h5py.File(self.filename,'r') as f:
for g in self.get_active_groups():
if set(l).issubset(f[g].keys()): groups.append(g)
return groups
def get_active_groups(self): # rename: get_groups needed? merge with datasets and have [] and ['*']
"""Get groups that are currently considered for evaluation."""
groups = []
for i in self.visible['increments']:
group_inc = 'inc{:05}'.format(i['inc']) #ToDo: Merge path only once at the end '/'.join(listE)
for c in self.visible['constituents']:
for t in self.visible['c_output_types']:
groups.append('/'.join([group_inc,'constituent',c,t]))
for m in self.visible['materialpoints']:
for t in self.visible['m_output_types']:
groups.append('/'.join([group_inc,'materialpoint',m,t]))
return groups
def list_data(self): # print_datasets and have [] and ['*'], loop over all increment, soll auf anderen basieren (get groups with sternchen)
"""Shows information on all active datasets in the file."""
with h5py.File(self.filename,'r') as f:
group_inc = 'inc{:05}'.format(self.visible['increments'][0]['inc']) #ToDo: Merge path only once at the end '/'.join(listE)
for c in self.visible['constituents']:
print('\n'+c)
group_constituent = group_inc+'/constituent/'+c
for t in self.visible['c_output_types']:
print(' {}'.format(t))
group_output_types = group_constituent+'/'+t
try:
for x in f[group_output_types].keys():
print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
except KeyError:
pass
for m in self.visible['materialpoints']:
group_materialpoint = group_inc+'/materialpoint/'+m
for t in self.visible['m_output_types']:
print(' {}'.format(t))
group_output_types = group_materialpoint+'/'+t
try:
for x in f[group_output_types].keys():
print(' {} ({})'.format(x,f[group_output_types+'/'+x].attrs['Description'].decode()))
except KeyError:
pass
def get_dataset_location(self,label): # names
"""Returns the location of all active datasets with given label.""" #ToDo: Merge path only once at the end '/'.join(listE)
path = []
with h5py.File(self.filename,'r') as f:
for i in self.visible['increments']:
group_inc = 'inc{:05}'.format(i['inc'])
for c in self.visible['constituents']:
for t in self.visible['c_output_types']:
try:
p = '/'.join([group_inc,'constituent',c,t,label])
f[p]
path.append(p)
except KeyError as e:
print('unable to locate constituents dataset: '+ str(e))
for m in self.visible['materialpoints']:
for t in self.visible['m_output_types']:
try:
p = '/'.join([group_inc,'materialpoint',m,t,label])
f[p]
path.append(p)
except KeyError as e:
print('unable to locate materialpoints dataset: '+ str(e))
return path
def read_dataset(self,path,c):
"""
Dataset for all points/cells.
If more than one path is given, the dataset is composed of the individual contributions
"""
with h5py.File(self.filename,'r') as f:
shape = (self.Nmaterialpoints,) + np.shape(f[path[0]])[1:]
if len(shape) == 1: shape = shape +(1,)
dataset = np.full(shape,np.nan)
for pa in path:
label = pa.split('/')[2]
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,:]
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,:]
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'],P['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 deviator(x):
if x['meta']['Unit'] == 'Pa': #ToDo: Should we use this? Then add_Cauchy and add_strain_tensors also should perform sanity checks
factor = 3.0/2.0
elif x['meta']['Unit'] == '-':
factor = 2.0/3.0
else:
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' : 'Mises({})'.format(x['label']),
'meta' : {
'Unit' : x['meta']['Unit'],
'Description' : 'Mises equivalent stress of {} ({})'.format(x['label'],x['meta']['Description']),
'Creator' : 'dadf5.py:add_Mises_stress vXXXXX'
}
}
requested = [{'label':x,'arg':'x'}]
self.__add_generic_pointwise(deviator,requested)
def add_norm(self,x,ord=None):
"""
Adds norm of vector or tensor or magnitude of a scalar.
See numpy.linalg.norm manual for details.
"""
def norm(x,ord):
o = ord
if len(x['data'].shape) == 1:
axis = 0
t = 'scalar'
if o is None: o = 2
elif 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'],ord),
'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_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_strain_tensor(self,t,ord,defgrad='F'): #ToDo: Use t and ord
"""Adds the a strain tensor."""
def strain_tensor(defgrad,t,ord):
# def operator(stretch,strain,eigenvalues):
#"""Albrecht Bertram: Elasticity and Plasticity of Large Deformations An Introduction (3rd Edition, 2012), p. 102"""
#return {
# 'V#ln': np.log(eigenvalues) ,
# 'U#ln': np.log(eigenvalues) ,
# 'V#Biot': ( np.ones(3,'d') - 1.0/eigenvalues ) ,
# 'U#Biot': ( eigenvalues - np.ones(3,'d') ) ,
# 'V#Green': ( np.ones(3,'d') - 1.0/eigenvalues/eigenvalues) *0.5,
# 'U#Green': ( eigenvalues*eigenvalues - np.ones(3,'d')) *0.5,
# }[stretch+'#'+strain]
(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 = np.log(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.get_groups([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()