rewrite pointwise add function
- all vectorized: Much faster - passing in all relevant information allows to do sanity checks and add useful meta data in HDF5 - improved readability
This commit is contained in:
Martin Diehl
parent
3db3e9e762
commit
6f008c5d5f
|
|
@ -84,7 +84,7 @@ class DADF5():
|
||||||
self.mode = mode
|
self.mode = mode
|
||||||
|
|
||||||
|
|
||||||
def get_candidates(self,l):
|
def get_groups(self,l):
|
||||||
"""
|
"""
|
||||||
Get groups that contain all requested datasets.
|
Get groups that contain all requested datasets.
|
||||||
|
|
||||||
|
|
@ -210,8 +210,8 @@ class DADF5():
|
||||||
print('unable to read materialpoint: '+ str(e))
|
print('unable to read materialpoint: '+ str(e))
|
||||||
|
|
||||||
return dataset
|
return dataset
|
||||||
|
|
||||||
|
|
||||||
def add_Cauchy(self,P='P',F='F'):
|
def add_Cauchy(self,P='P',F='F'):
|
||||||
"""
|
"""
|
||||||
Adds Cauchy stress calculated from 1st Piola-Kirchhoff stress and deformation gradient.
|
Adds Cauchy stress calculated from 1st Piola-Kirchhoff stress and deformation gradient.
|
||||||
|
|
@ -222,252 +222,224 @@ class DADF5():
|
||||||
|
|
||||||
"""
|
"""
|
||||||
def Cauchy(F,P):
|
def Cauchy(F,P):
|
||||||
return np.einsum('i,ijk,ilk->ijl',1.0/np.linalg.det(F),F,P)
|
return {
|
||||||
|
'data' : np.einsum('i,ijk,ilk->ijl',1.0/np.linalg.det(F['data']),F['data'],P['data']),
|
||||||
|
'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'
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
args = [{'label':F,'shape':[3,3],'unit':'-'},
|
requested = [{'label':F,'arg':'F'},
|
||||||
{'label':P,'shape':[3,3],'unit':'Pa'} ]
|
{'label':P,'arg':'P'} ]
|
||||||
result = {'label':'sigma',
|
|
||||||
'unit':'Pa',
|
|
||||||
'Description': 'Cauchy stress calculated from 1st Piola-Kirchhoff stress and deformation gradient'}
|
|
||||||
|
|
||||||
self.add_generic_pointwise_vectorized(Cauchy,args,None,result)
|
self.__add_generic_pointwise(Cauchy,requested)
|
||||||
|
|
||||||
|
|
||||||
def add_Mises_stress(self,stress='sigma'):
|
def add_Mises(self,x):
|
||||||
"""Adds equivalent von Mises stress."""
|
"""Adds the equivalent Mises stres of a tensor."""
|
||||||
def Mises_stress(stress):
|
def deviator(x):
|
||||||
dev = stress - np.trace(stress)/3.0*np.eye(3)
|
|
||||||
symdev = 0.5*(dev+dev.T)
|
|
||||||
return np.sqrt(np.sum(symdev*symdev.T)*3.0/2.0)
|
|
||||||
|
|
||||||
args = [{'label':stress,'shape':[3,3],'unit':'Pa'}]
|
if x['meta']['Unit'] == 'Pa':
|
||||||
result = {'label':'Mises({})'.format(stress),
|
factor = 3.0/2.0
|
||||||
'unit':'Pa',
|
elif x['meta']['Unit'] == '-':
|
||||||
'Description': 'Equivalent Mises stress'}
|
factor = 2.0/3.0
|
||||||
|
else:
|
||||||
self.add_generic_pointwise(Mises_stress,args,result)
|
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
|
||||||
|
|
||||||
|
return {
|
||||||
|
'data' : np.sqrt(np.einsum('ijk->i',dev_sym**2)*factor),
|
||||||
|
'label' : 'dev({})'.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):
|
def add_norm(self,x,ord=None):
|
||||||
"""
|
"""
|
||||||
Adds norm of vector or tensor or magnitude of a scalar.
|
Adds norm of vector or tensor or magnitude of a scalar.
|
||||||
|
See numpy.linalg.norm manual for details.
|
||||||
Todo
|
|
||||||
----
|
|
||||||
The output unit should be the input unit.
|
|
||||||
The ord parameter should be taken into account.
|
|
||||||
The whole thing should be vectorized. This requires to parse optional arguments to func.
|
|
||||||
|
|
||||||
"""
|
"""
|
||||||
args = [{'label':x,'shape':None,'unit':None}]
|
def norm(x,ord):
|
||||||
result = {'label':'norm_{}({})'.format(str(ord),x),
|
|
||||||
'unit':'n/a',
|
if len(x['data'].shape) == 1:
|
||||||
'Description': 'Norm of vector or tensor or magnitude of a scalar. See numpy.linalg.norm manual for details'}
|
axis = 0
|
||||||
|
t = 'scalar'
|
||||||
|
elif len(x['data'].shape) == 2:
|
||||||
|
axis = 1
|
||||||
|
t = 'vector'
|
||||||
|
elif len(x['data'].shape) == 3:
|
||||||
|
axis = (1,2)
|
||||||
|
t = 'tensor'
|
||||||
|
else:
|
||||||
|
raise ValueError
|
||||||
|
|
||||||
|
return {
|
||||||
|
'data' : np.linalg.norm(x['data'],ord=ord,axis=axis,keepdims=True),
|
||||||
|
'label' : 'norm({})'.format(x['label']),
|
||||||
|
'meta' : {
|
||||||
|
'Unit' : x['meta']['Unit'],
|
||||||
|
'Description' : 'Norm of {} {} ({})'.format(t,x['label'],x['meta']['Description']),
|
||||||
|
'Creator' : 'dadf5.py:add_norm vXXXXX'
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
requested = [{'label':x,'arg':'x'}]
|
||||||
|
|
||||||
self.add_generic_pointwise(np.linalg.norm,args,result)
|
self.__add_generic_pointwise(norm,requested,{'ord':ord})
|
||||||
|
|
||||||
|
|
||||||
def add_determinant(self,a):
|
|
||||||
"""Adds the determinant of a tensor."""
|
|
||||||
# ToDo: The output unit should be the input unit
|
|
||||||
args = [{'label':a,'shape':[3,3],'unit':None}]
|
|
||||||
result = {'label':'det({})'.format(a),
|
|
||||||
'unit':'n/a',
|
|
||||||
'Description': 'Determinant of a tensor'}
|
|
||||||
|
|
||||||
self.add_generic_pointwise_vectorized(np.linalg.det,args,result)
|
|
||||||
|
|
||||||
|
|
||||||
def add_spherical(self,a):
|
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."""
|
"""Adds the spherical component of a tensor."""
|
||||||
def spherical(m):
|
def spherical(x):
|
||||||
return (m[0,0]+m[1,1]+m[2,2])/3.0
|
|
||||||
|
if not np.all(np.array(x['data'].shape[1:]) == np.array([3,3])):
|
||||||
|
raise ValueError
|
||||||
|
|
||||||
# ToDo: The output unit should be the input unit
|
return {
|
||||||
args = [{'label':a,'shape':[3,3],'unit':None}]
|
'data' : np.trace(x['data'],axis1=1,axis2=2)/3.0,
|
||||||
result = {'label':'sph({})'.format(a),
|
'label' : 'sph({})'.format(x['label']),
|
||||||
'unit':'n/a',
|
'meta' : {
|
||||||
'Description': 'Spherical component of a tensor'}
|
'Unit' : x['meta']['Unit'],
|
||||||
|
'Description' : 'Spherical component of tensor {} ({})'.format(x['label'],x['meta']['Description']),
|
||||||
|
'Creator' : 'dadf5.py:add_spherical vXXXXX'
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
self.add_generic_pointwise(spherical,args,result)
|
requested = [{'label':x,'arg':'x'}]
|
||||||
|
|
||||||
|
self.__add_generic_pointwise(spherical,requested)
|
||||||
def add_deviator(self,a):
|
|
||||||
|
|
||||||
|
def add_deviator(self,x):
|
||||||
"""Adds the deviator of a tensor."""
|
"""Adds the deviator of a tensor."""
|
||||||
def deviator(m):
|
def deviator(x):
|
||||||
return m - np.eye(3)*(m[0,0]+m[1,1]+m[2,2])/3.0
|
d = x['data']
|
||||||
|
return {
|
||||||
# ToDo: The output unit should be the input unit
|
'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),
|
||||||
args = [{'label':a,'shape':[3,3],'unit':'Pa'}]
|
'label' : 'dev({})'.format(x['label']),
|
||||||
result = {'label':'dev({})'.format(a),
|
'meta' : {
|
||||||
'unit':'n/a',
|
'Unit' : x['meta']['Unit'],
|
||||||
'Description': 'Deviatoric component of a tensor'}
|
'Description' : 'Deviator of tensor {} ({})'.format(x['label'],x['meta']['Description']),
|
||||||
|
'Creator' : 'dadf5.py:add_deviator vXXXXX'
|
||||||
self.add_generic_pointwise(deviator,args,result)
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
requested = [{'label':x,'arg':'x'}]
|
||||||
|
|
||||||
|
self.__add_generic_pointwise(deviator,requested)
|
||||||
def add_strain_tensors(self,defgrad='F'):
|
|
||||||
"""Adds a strain definition."""
|
|
||||||
def strain(defgrad):
|
|
||||||
(U,S,Vh) = np.linalg.svd(defgrad) # singular value decomposition
|
|
||||||
R_inv = np.dot(U,Vh).T # inverse rotation of polar decomposition
|
|
||||||
U = np.dot(R_inv,defgrad) # F = RU
|
|
||||||
U = np.where(abs(U) < 1e-12, 0, U) # kill nasty noisy data
|
|
||||||
(D,V) = np.linalg.eig(U) # eigen decomposition (of symmetric matrix)
|
|
||||||
neg = np.where(D < 0.0) # find negative eigenvalues ...
|
|
||||||
D[neg] *= -1. # ... flip value ...
|
|
||||||
V[:,neg] *= -1. # ... and vector
|
|
||||||
for i,eigval in enumerate(D):
|
|
||||||
if np.dot(V[:,i],V[:,(i+1)%3]) != 0.0: # check each vector for orthogonality
|
|
||||||
V[:,(i+1)%3] = np.cross(V[:,(i+2)%3],V[:,i]) # correct next vector
|
|
||||||
V[:,(i+1)%3] /= np.sqrt(np.dot(V[:,(i+1)%3],V[:,(i+1)%3].conj())) # and renormalize (hyperphobic?)
|
|
||||||
d = np.log(D) # operate on eigenvalues of U o r V
|
|
||||||
return np.dot(V,np.dot(np.diag(d),V.T)).real # build tensor back from eigenvalue/vector basis
|
|
||||||
|
|
||||||
# ToDo: The output unit should be the input unit
|
|
||||||
args = [{'label':defgrad,'shape':[3,3],'unit':None}]
|
|
||||||
result = {'label':'strain({})'.format(defgrad),
|
|
||||||
'unit':'-',
|
|
||||||
'Description': 'strain (ln(V)) of a deformation gradient'}
|
|
||||||
|
|
||||||
self.add_generic_pointwise(strain,args,result)
|
|
||||||
|
|
||||||
|
|
||||||
def get_fitting(self,data):
|
def add_strain_tensor(self,t,ord,defgrad='F'):
|
||||||
groups = []
|
"""Adds the a strain tensor."""
|
||||||
if type(data) is not list:
|
def strain_tensor(defgrad,t,ord):
|
||||||
print('mist')
|
(U,S,Vh) = np.linalg.svd(defgrad['data']) # singular value decomposition
|
||||||
with h5py.File(self.filename,'r') as f:
|
R_inv = np.einsum('ijk->ikj',np.matmul(U,Vh)) # inverse rotation of polar decomposition
|
||||||
for g in self.get_candidates([l['label'] for l in data]):
|
U = np.matmul(R_inv,defgrad['data']) # F = RU
|
||||||
print(g)
|
(D,V) = np.linalg.eigh((U+np.einsum('ikj',U))*.5) # eigen decomposition (of symmetric(ed) matrix)
|
||||||
fits = True
|
|
||||||
for d in data: # ToDo: check for unit
|
|
||||||
if d['shape'] is not None:
|
|
||||||
fits = fits and np.all(np.array(f[g+'/'+d['label']].shape[1:]) == np.array(d['shape']))
|
|
||||||
if fits: groups.append(g)
|
|
||||||
return groups
|
|
||||||
|
|
||||||
|
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)) # this is wrong ...
|
||||||
|
for j in range(V.shape[0]): # but this is slow ...
|
||||||
|
a[j,:,:] = np.dot(V[j,:,:],np.dot(np.diag(d[j,:]),V[j,:,:].T))
|
||||||
|
print(np.max(a))
|
||||||
|
|
||||||
|
return {
|
||||||
|
'data' : a,
|
||||||
|
'label' : 'lnV({})'.format(defgrad['label']),
|
||||||
|
'meta' : {
|
||||||
|
'Unit' : defgrad['meta']['Unit'],
|
||||||
|
'Description' : 'Strain tensor {} ({})'.format(defgrad['label'],defgrad['meta']['Description']),
|
||||||
|
'Creator' : 'dadf5.py:add_deviator vXXXXX'
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
requested = [{'label':defgrad,'arg':'defgrad'}]
|
||||||
|
|
||||||
def add_generic_pointwise(self,func,args,result):
|
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.
|
General function to add pointwise data.
|
||||||
|
|
||||||
function 'func' first needs to have data arguments before other arguments
|
|
||||||
Works for functions that are pointwise defined.
|
|
||||||
"""
|
"""
|
||||||
groups = self.get_fitting(args)
|
|
||||||
|
|
||||||
def job(args):
|
|
||||||
out = args['out']
|
|
||||||
datasets_in = args['dat']
|
|
||||||
func = args['fun']
|
|
||||||
for i in range(out.shape[0]):
|
|
||||||
arg = tuple([d[i,] for d in datasets_in])
|
|
||||||
out[i,] = func(*arg)
|
|
||||||
args['results'].put({'out':out,'group':args['group']})
|
|
||||||
|
|
||||||
Nthreads = 4 # ToDo: should be a parameter
|
|
||||||
results = Queue(Nthreads+1)
|
|
||||||
|
|
||||||
todo = []
|
|
||||||
|
|
||||||
for g in groups:
|
|
||||||
with h5py.File(self.filename,'r') as f:
|
|
||||||
datasets_in = [f[g+'/'+u['label']][()] for u in args]
|
|
||||||
|
|
||||||
# figure out dimension of results
|
|
||||||
testArg = tuple([d[0,] for d in datasets_in]) # to call function with first point
|
|
||||||
out = np.empty([datasets_in[0].shape[0]] + list(func(*testArg).shape)) # shape is Npoints x shape of the results for one point
|
|
||||||
todo.append({'dat':datasets_in,'fun':func,'out':out,'group':g,'results':results})
|
|
||||||
|
|
||||||
# Instantiate a thread pool with worker threads
|
|
||||||
pool = util.ThreadPool(Nthreads)
|
|
||||||
missingResults = len(todo)
|
|
||||||
|
|
||||||
|
|
||||||
# Add the jobs in bulk to the thread pool. Alternatively you could use
|
|
||||||
# `pool.add_task` to add single jobs. The code will block here, which
|
|
||||||
# makes it possible to cancel the thread pool with an exception when
|
|
||||||
# the currently running batch of workers is finished
|
|
||||||
|
|
||||||
pool.map(job, todo[:Nthreads+1])
|
|
||||||
i = 0
|
|
||||||
while missingResults > 0:
|
|
||||||
r=results.get() # noqa
|
|
||||||
print(r['group'])
|
|
||||||
with h5py.File(self.filename,'r+') as f:
|
|
||||||
dataset_out = f[r['group']].create_dataset(result['label'],data=r['out'])
|
|
||||||
dataset_out.attrs['Unit'] = result['unit']
|
|
||||||
dataset_out.attrs['Description'] = result['Description']
|
|
||||||
dataset_out.attrs['Creator'] = 'dadf5.py v{}'.format('n/a')
|
|
||||||
missingResults-=1
|
|
||||||
try:
|
|
||||||
pool.add_task(job,todo[Nthreads+1+i])
|
|
||||||
except IndexError:
|
|
||||||
pass
|
|
||||||
i+=1
|
|
||||||
|
|
||||||
pool.wait_completion()
|
|
||||||
|
|
||||||
|
|
||||||
def add_generic_pointwise_vectorized(self,func,args,args2=None,result=None):
|
|
||||||
"""
|
|
||||||
General function to add pointwise data.
|
|
||||||
|
|
||||||
function 'func' first needs to have data arguments before other arguments
|
|
||||||
Works for vectorized functions.
|
|
||||||
"""
|
|
||||||
groups = self.get_fitting(args)
|
|
||||||
|
|
||||||
def job(args):
|
def job(args):
|
||||||
"""
|
"""
|
||||||
A job. It has different args!
|
Call function with input data + extra arguments, returns results + group.
|
||||||
"""
|
"""
|
||||||
print('args for job',args)
|
args['results'].put({**args['func'](**args['in']),'group':args['group']})
|
||||||
out = args['out']
|
|
||||||
datasets_in = args['dat']
|
|
||||||
func = args['fun']
|
|
||||||
# try:
|
|
||||||
# out = func(*datasets_in,*args['fun_args'])
|
|
||||||
# except:
|
|
||||||
out = func(*datasets_in)
|
|
||||||
args['results'].put({'out':out,'group':args['group']})
|
|
||||||
|
|
||||||
Nthreads = 4 # ToDo: should be a parameter
|
|
||||||
results = Queue(Nthreads+1)
|
N_threads = 1 # ToDo: should be a parameter
|
||||||
|
|
||||||
|
results = Queue(N_threads)
|
||||||
|
pool = util.ThreadPool(N_threads)
|
||||||
|
N_added = N_threads + 1
|
||||||
|
|
||||||
todo = []
|
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 g in groups:
|
for group in self.get_groups([d['label'] for d in datasets_requested]):
|
||||||
with h5py.File(self.filename,'r') as f:
|
with h5py.File(self.filename,'r') as f:
|
||||||
datasets_in = [f[g+'/'+u['label']][()] for u in args]
|
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']}
|
||||||
|
|
||||||
if args2 is not None:
|
todo.append({'in':{**datasets_in,**extra_args},'func':func,'group':group,'results':results})
|
||||||
todo.append({'dat':datasets_in,'fun':func,'group':g,'results':results,'func_args':args,'out':None})
|
|
||||||
else:
|
|
||||||
todo.append({'dat':datasets_in,'fun':func,'group':g,'results':results,'out':None})
|
|
||||||
|
|
||||||
# Instantiate a thread pool with worker threads
|
pool.map(job, todo[:N_added]) # initialize
|
||||||
pool = util.ThreadPool(Nthreads)
|
|
||||||
missingResults = len(todo)
|
|
||||||
|
|
||||||
|
N_not_calculated = len(todo)
|
||||||
pool.map(job, todo[:Nthreads+1])
|
while N_not_calculated > 0:
|
||||||
i = 0
|
result = results.get()
|
||||||
while missingResults > 0:
|
with h5py.File(self.filename,self.mode) as f: # write to file
|
||||||
r=results.get() # noqa
|
dataset_out = f[result['group']].create_dataset(result['label'],data=result['data'])
|
||||||
print(r['group'])
|
for k in result['meta'].keys():
|
||||||
with h5py.File(self.filename,'r+') as f:
|
dataset_out.attrs[k] = result['meta'][k]
|
||||||
dataset_out = f[r['group']].create_dataset(result['label'],data=r['out'])
|
N_not_calculated-=1
|
||||||
dataset_out.attrs['Unit'] = result['unit']
|
|
||||||
dataset_out.attrs['Description'] = result['Description']
|
if N_added < len(todo): # add more jobs
|
||||||
dataset_out.attrs['Creator'] = 'dadf5.py v{}'.format('n/a')
|
pool.add_task(job,todo[N_added])
|
||||||
missingResults-=1
|
N_added +=1
|
||||||
try:
|
|
||||||
pool.add_task(job,todo[Nthreads+1+i])
|
|
||||||
except IndexError:
|
|
||||||
pass
|
|
||||||
i+=1
|
|
||||||
|
|
||||||
pool.wait_completion()
|
pool.wait_completion()
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue