def get_environmentalKernels_singleprocess(atoms, nocenters=None, chem_channels=True, centerweight=1.0,
gaussian_width=0.5, cutoff=3.5, cutoff_transition_width=0.5,
nmax=8, lmax=6, chemicalKernelmat=None, chemicalKernel=None,
chemicalProjection=None,
nthreads=4, nprocess=0, nchunks=0,isDeltaKernel=True,
dispbar=False,is_fast_average=False):
if nocenters is None:
nocenters = []
# Chooses the function to use to compute the kernel between two frames
get_envKernel = choose_envKernel_func(nthreads,isDeltaKernel)
# Builds the kernel matrix from the species present in the frames and a specified chemical
# kernel function
if chemicalKernelmat is not None:
pass
elif chemicalProjection is not None:
pass
elif chemicalKernelmat is None and chemicalKernel is not None:
chemicalKernelmat = Atoms2ChemicalKernelmat(atoms, chemicalKernel=chemicalKernel)
else:
raise ValueError('wrong chemicalKernelmat and/or chemicalKernel input')
# get the soap for every local environement
frames = get_Soaps(atoms, nocenters=nocenters, chem_channels=chem_channels, centerweight=centerweight,
gaussian_width=gaussian_width, cutoff=cutoff, cutoff_transition_width=cutoff_transition_width,
nmax=nmax, lmax=lmax, nprocess=nprocess,chemicalProjection=chemicalProjection,
dispbar=dispbar,is_fast_average=is_fast_average)
# get the environmental kernels as a dictionary
environmentalKernels = framesprod(frames, frameprodFunc=get_envKernel, chemicalKernelmat=chemicalKernelmat,
dispbar=dispbar)
return environmentalKernels
def framesprod_wrapper(kargs):
keys = kargs.keys()
get_envKernel = kargs.pop('frameprodFunc')
queue = kargs.pop('queue')
# to disable the progressbar
dispbar = kargs.pop('dispbar')
if 'fpointers1' in keys:
fpointers1 = kargs.pop('fpointers1')
fpointers2 = kargs.pop('fpointers2')
atoms1 = [qp.Atoms(fpointer=fpointer1) for fpointer1 in fpointers1]
chemicalKernelmat = kargs.pop('chemicalKernelmat')
frames1 = get_Soaps(atoms1, dispbar=dispbar, **kargs)
if fpointers2 is not None:
atoms2 = [qp.Atoms(fpointer=fpointer2) for fpointer2 in fpointers2]
frames2 = get_Soaps(atoms2, dispbar=dispbar, **kargs)
else:
frames2 = None
kargs = {
'frames1': frames1,
'frames2': frames2,
'chemicalKernelmat': chemicalKernelmat
}
elif 'atoms1' in keys:
atoms1 = kargs.pop('atoms1')
atoms2 = kargs.pop('atoms2')
chemicalKernelmat = kargs.pop('chemicalKernelmat')
frames1 = get_Soaps(atoms1, dispbar=dispbar, **kargs)
if atoms2 is not None:
frames2 = get_Soaps(atoms2, dispbar=dispbar, **kargs)
else:
frames2 = None
kargs = {
'frames1': frames1,
'frames2': frames2,
'chemicalKernelmat': chemicalKernelmat
}
return framesprod(queue=queue, frameprodFunc=get_envKernel, **kargs)
def get(self):
parser = flask_restful.reqparse.RequestParser()
argument_names = [
'atoms', 'nocenters', 'chem_channels', 'centerweight',
'gaussian_width', 'spkitMax', 'chemicalProjection',
'is_fast_average', 'cutoff', 'cutoff_transition_width', 'nmax',
'lmax'
]
for argument_name in argument_names:
parser.add_argument(ARGUMENTS[argument_name])
args = parser.parse_args(strict=True)
if args['spkitMax']:
args['spkitMax'] = json.loads(args['spkitMax'])
args['atoms'] = json.loads(args['atoms'])
args['atoms'] = [atoms_utils.loads(atoms) for atoms in args['atoms']]
args['atoms'] = [ase2qp(atoms) for atoms in args['atoms']]
soaps = get_Soaps(**args)
soaps = [{key: value.tolist()
for key, value in soap.iteritems()} for soap in soaps]
return flask.jsonify(soaps)
'chem_channels': True,
'nocenters': nocenters
}
# DELTA CHEMICAL KERNEL hard coded
chemicalKernelmat = Atoms2ChemicalKernelmat(atoms1,
atoms2=atoms2,
chemicalKernel=deltaKernel)
# Chooses the function to use to compute the kernel between two frames
get_envKernel = choose_envKernel_func(nthreads, isDeltaKernel=True)
####################################################################################
# get the soap for every local environement
print 'Compute xSoap {} with {} process from {}'.format(
xlim, nprocess, filename)
frames1 = get_Soaps(atoms1, nprocess=nprocess, **soap_params)
print 'Compute xSoap {} with {} process from {}: done {}'.format(
xlim, nprocess, filename, s2hms(time.time() - st))
if atoms2 is None:
frames2 = None
print 'no atoms 2, Computing upper triangular sub matrix'
else:
print 'Compute ySoap {} process from {}'.format(
ylim, nprocess, filename)
frames2 = get_Soaps(atoms2, nprocess=nprocess, **soap_params)
print 'Compute ySoap {} process from {}: done {}'.format(
ylim, nprocess, filename, s2hms(time.time() - st))
########################################################################################
# get the environmental kernels as a dictionary
def get_environmentalKernels_mt_mp_chunks(atoms,
nocenters=None,
chem_channels=True,
centerweight=1.0,
gaussian_width=0.5,
cutoff=3.5,
cutoff_transition_width=0.5,
nmax=8,
lmax=6,
chemicalKernelmat=None,
chemicalKernel=None,
chemicalProjection=None,
nthreads=4,
nprocess=2,
nchunks=2,
islow_memory=False,
isDeltaKernel=True,
dispbar=False,
is_fast_average=False):
if nocenters is None:
nocenters = []
# Builds the kernel matrix from the species present in the frames and a specified chemical
# kernel function
if chemicalKernelmat is not None:
pass
elif chemicalProjection is not None:
pass
elif (chemicalKernelmat is None) and (chemicalKernel is not None):
chemicalKernelmat = Atoms2ChemicalKernelmat(
atoms, chemicalKernel=chemicalKernel)
else:
raise ValueError('wrong chemicalKernelmat and/or chemicalKernel input')
Natoms = len(atoms)
NenvKernels = Natoms * (Natoms + 1) / 2.
# fpointers = [frame._fpointer.copy() for frame in atoms]
# chunks1d, slices = chunk_list(fpointers, nchunks=nchunks)
# cut atomsList in chunks
if islow_memory:
frames = get_Soaps(atoms,
nocenters=nocenters,
chem_channels=chem_channels,
centerweight=centerweight,
gaussian_width=gaussian_width,
cutoff=cutoff,
is_fast_average=is_fast_average,
chemicalProjection=chemicalProjection,
cutoff_transition_width=cutoff_transition_width,
nmax=nmax,
lmax=lmax,
nprocess=nprocess)
chunks1d, slices = chunk_list(frames, nchunks=nchunks)
else:
chunks1d, slices = chunk_list(atoms, nchunks=nchunks)
soap_params = {
'centerweight': centerweight,
'gaussian_width': gaussian_width,
'cutoff': cutoff,
'cutoff_transition_width': cutoff_transition_width,
'nmax': nmax,
'lmax': lmax,
'chemicalKernelmat': chemicalKernelmat,
'chemicalProjection': chemicalProjection,
'chem_channels': chem_channels,
'nocenters': nocenters,
'is_fast_average': is_fast_average,
}
# create inputs for each block of the global kernel matrix
chunks = chunks1d_2_chuncks2d(chunks1d, **soap_params)
# new_atoms1 = {}
# new_atoms2 = {}
# for it,chunk in enumerate(chunks):
# atoms1 = chunk.pop('atoms1')
# atoms2 = chunk.pop('atoms2')
# # new_atoms1[it] = [qp.Atoms().copy_from(frame) for frame in atoms1]
# new_atoms1[it] = [frame.copy() for frame in atoms1]
# fpointers1 = [frame._fpointer.copy() for frame in new_atoms1[it]]
# if atoms2 is not None:
# # new_atoms2[it] = [qp.Atoms().copy_from(frame) for frame in atoms2]
# new_atoms2[it] = [frame.copy() for frame in atoms2]
# fpointers2 = [frame._fpointer.copy() for frame in new_atoms2[it]]
# else:
# fpointers2 = None
#
# chunk.update(**{'fpointers1':fpointers1,'fpointers2':fpointers2})
# get a list of environemental kernels
pool = mp_framesprod(chunks,
nprocess,
nthreads,
NenvKernels,
isDeltaKernel=isDeltaKernel,
dispbar=dispbar)
results = pool.run()
# reorder the list of environemental kernels into a dictionary which keys are the (i,j) of the global kernel matrix
environmentalKernels = join_envKernel(results, slices)
return environmentalKernels
# atoms: [quippy.Atoms]
# nocenters: None or [Atomic numbers to ignore]
# chem_channels: bool (whether or not to include chemical combinations)
# centerweight: float (weight of gaussian on central atom)
# gaussian_width: float (sigma of gaussian)
# cutoff: float (integration cutoff distance)
# cutoff_transition_width: float (width of sigmoid used to smooth integration cutoff)
# nmax: int (number of radial basis functions)
# lmax: int (number of spherical harmonics)
# spkitMax: dict {atomic numbers: max. number of occurrences in a structure in the set atoms}
# nprocess: int (number of subprocesses spawned)
# chemicalProjection: ???
# dispbar: bool ???
# is_fast_average: None or bool (use fast averaging to calculate average soap; no average calculated if None)
soaps = get_Soaps(atoms=quippy_atoms,
nocenters=None,
chem_channels=False,
centerweight=1.0,
gaussian_width=0.5,
cutoff=2.0,
cutoff_transition_width=0.5,
nmax=16,
lmax=14,
spkitMax=None,
nprocess=8,
chemicalProjection=None,
dispbar=False,
is_fast_average=False)
# soaps should be a list of `OrderedDict`s keyed by the species symbols + an integer (e.g. keys = ["H0", "H1", "O0"])
