def get_soap_locals(obj, Hpos, rCutHard=8.0, NradBas=5, Lmax=5, atoms_list=None):
assert Lmax <= 9, "l cannot exceed 9. Lmax={}".format(Lmax)
assert Lmax >= 0, "l cannot be negative.Lmax={}".format(Lmax)
assert rCutHard < 10.0001 , "hard redius cuttof cannot be larger than 10 Angs. rCut={}".format(rCutHard)
assert rCutHard > 4.999 , "hard redius cuttof cannot be lower than 5 Ang. rCut={}".format(rCutHard)
assert NradBas >= 2 , "number of basis functions cannot be lower than 2. NradBas={}".format(NradBas)
assert NradBas <= 10 , "number of basis functions cannot exceed 10. NradBas={}".format(NradBas)
# get clusgeo internal format for c-code
Apos, typeNs, py_Ntypes, atomtype_lst, totalAN = format_ase2clusgeo(obj)
# flatten Hpos array
Hpos = np.array(Hpos)
py_Hsize = Hpos.shape[0]
Hpos = Hpos.flatten()
alp, bet = genBasis.getBasisFunc(rCutHard, NradBas)
#Declaring main soap array, for atoms in atoms_list
if atoms_list == None:
atoms_list = atomtype_lst
soap_nfeature = NradBas**2*(Lmax+1)
soap = np.zeros((py_Hsize, soap_nfeature*len(atoms_list)))
# convert int to c_int
alphas = (c_double*len(alp))(*alp)
betas = (c_double*len(bet))(*bet)
l = c_int(Lmax)
Hsize = c_int(py_Hsize)
Ntypes = c_int(py_Ntypes)
totalAN = c_int(totalAN)
rCutHard = c_double(rCutHard)
Nsize = c_int(NradBas)
#convert int array to c_int array
typeNs = (c_int * len(typeNs))(*typeNs)
print(l, Hsize, Ntypes, totalAN, typeNs, Nsize)
# convert to c_double arrays
#Apos
axyz = (c_double * len(Apos))(*Apos.tolist())
#Hpos
hxyz = (c_double * len(Hpos))(*Hpos.tolist())
### START SOAP###
path_to_so = os.path.dirname(os.path.abspath(__file__))
libsoap = CDLL(path_to_so + '/src/libsoapPy.so')
libsoap.soap.argtypes = [POINTER (c_double),POINTER (c_double), POINTER (c_double),POINTER (c_double),POINTER (c_double), POINTER (c_int),c_double,c_int,c_int,c_int,c_int,c_int]
libsoap.soap.restype = POINTER (c_double)
# double* c, double* Apos,double* Hpos,int* typeNs,
# int totalAN,int Ntypes,int Nsize, int l, int Hsize);
c = (c_double*(soap_nfeature*py_Ntypes*py_Hsize))()
c = libsoap.soap( c, axyz, hxyz, alphas, betas, typeNs, rCutHard, totalAN, Ntypes, Nsize, l, Hsize)
# return c;
soap_part = np.ctypeslib.as_array( c, shape=(py_Hsize,soap_nfeature*py_Ntypes))
for i in range(py_Hsize):
for j_ind, j in enumerate(atoms_list):
if j in atomtype_lst:
j_ind_part = atomtype_lst.tolist().index(j)
soap[i, soap_nfeature*j_ind:soap_nfeature*(j_ind+1)] = soap_part[i, soap_nfeature*j_ind_part:soap_nfeature*(j_ind_part+1)]
return soap
def create(atoms_list,N, L, cutoff = 0, all_atomtypes=[]):
"""Takes a trajectory xyz file and writes soap features
"""
myAlphas, myBetas = genBasis.getBasisFunc(cutoff, N)
# get information about feature length
n_datapoints = len(atoms_list)
atoms = atoms_list[0]
x = get_lastatom_soap(atoms, cutoff, myAlphas, myBetas,N,L, all_atomtypes=all_atomtypes)
n_features = x.shape[1]
print("soap first", x.shape)
print(n_datapoints, n_features)
soapmatrix = np.zeros((n_datapoints, n_features))
i = -1
for atoms in atoms_list:
i +=1
#atoms
print("Processing " + str(atoms.info)," Run time: " + str(time.time()-t0_total), end="\r")
soapmatrix[i,:] = get_lastatom_soap(atoms, cutoff, myAlphas, myBetas, N, L, all_atomtypes=all_atomtypes)
print("")
# infos
print("shape", soapmatrix.shape)
return soapmatrix
if len(args.arguments) > 1:
print('Too many arguments')
exit(1)
trajfile = args.arguments[0]
rootname = trajfile.replace(".xyz", "")
traj = ase.io.read(trajfile, index=":")
print("number of snapshots:", len(traj))
feature_mat = np.zeros((len(traj), 21))
NMAX = 10
LMAX = 9
RCUT = 8.0
myAlphas, myBetas = genBasis.getBasisFunc(RCUT, NMAX)
n_datapoints = len(traj)
for i, atoms in zip(np.arange(len(traj)), traj):
print(i)
cluster = atoms[:-1]
last_atom = atoms[-1]
distmat = get_distance_matrix(atoms)
# get number of nearest neighbours, classify as top, bridge, hollow, 4-fold hollow
first_shell, nn_dist_lst, nn_type, n_atoms_per_type_lst = get_first_shell(
atoms, NN_CUTOFF, distmat)
nnn = len(nn_dist_lst)
print("number of nearest neighbours", nnn)
soap_array = get_sitecenteredsoap(cluster,