sgm = float(args['--sigma'])
if sgm < 0.0:
sgm = abs(sgm) * width
specorder = args['--specorder'].split(',')
if 'None' in specorder and not files[0].find('POSCAR') > -1:
raise ValueError(
'ERROR: specorder must be specified, unless files are POSCAR format.'
)
if sid == 0:
raise ValueError('ERROR: sid should be specified and should not be 0.')
files.sort(key=get_key, reverse=True)
nsys0 = NAPSystem(fname=files[0], specorder=specorder)
a, b, c = nsys0.get_lattice_angles()
if abs(a-np.pi/2) > 180.0/np.pi or abs(b-np.pi/2) > 180.0/np.pi \
or abs(c-np.pi/2) > 180.0/np.pi:
raise ValueError(
'ERROR: Currently only available for orthogonal lattice, a,b,c=',
a, b, c)
ndivs = get_num_division(nsys0, width)
if np.dot(ndivs, ndivs) > 10000000:
raise ValueError('ERROR: ndivs too large.', ndivs)
else:
print(' # of divisions = {0:d} {1:d} {2:d}'.format(*ndivs))
pdist = np.zeros(ndivs, dtype=float)
for f in files:
print(' Reading {0:s}...'.format(f))
nsys = NAPSystem(fname=f, specorder=specorder)
sid = int(args['--sid'])
width = float(args['-w'])
sgm = float(args['--sigma'])
if sgm < 0.0:
sgm = abs(sgm)*width
specorder = args['--specorder'].split(',')
if 'None' in specorder and not files[0].find('POSCAR') > -1:
raise ValueError('ERROR: specorder must be specified, unless files are POSCAR format.')
if sid == 0:
raise ValueError('ERROR: sid should be specified and should not be 0.')
files.sort(key=get_key,reverse=True)
nsys0 = NAPSystem(fname=files[0],specorder=specorder)
a,b,c = nsys0.get_lattice_angles()
if abs(a-np.pi/2) > 180.0/np.pi or abs(b-np.pi/2) > 180.0/np.pi \
or abs(c-np.pi/2) > 180.0/np.pi:
raise ValueError('ERROR: Currently only available for orthogonal lattice, a,b,c=',a,b,c)
ndivs = get_num_division(nsys0,width)
if np.dot(ndivs,ndivs) > 10000000:
raise ValueError('ERROR: ndivs too large.',ndivs)
else:
print(' # of divisions = {0:d} {1:d} {2:d}'.format(*ndivs))
pdist = np.zeros(ndivs,dtype=float)
for f in files:
print(' Reading {0:s}...'.format(f))
nsys = NAPSystem(fname=f,specorder=specorder)
pdist += get_prob_dist(ndivs,nsys,sid,sgm)
pdist = normalize_pdist(pdist,nsys0,sid)
def reduce_cij(atoms0, cij0, eps=1.e-4):
"""
Reduce number of independent Cij according to the crystal system of original cell.
It is not Cij=Cji.
"""
cij = cij0
symdata = spglib.get_symmetry_dataset(atoms0)
nsys = NAPSystem(ase_atoms=atoms0)
sgnum = symdata['number']
a, b, c = nsys.get_lattice_lengths()
alpha, beta, gamma = nsys.get_lattice_angles()
aeqb = abs(a - b) < eps * min(a, b)
beqc = abs(b - c) < eps * min(b, c)
ceqa = abs(c - a) < eps * min(c, a)
aleqpi2 = abs(alpha - np.pi / 2) < eps * np.pi / 2
bteqpi2 = abs(beta - np.pi / 2) < eps * np.pi / 2
gmeqpi2 = abs(gamma - np.pi / 2) < eps * np.pi / 2
print('Spacegroup number = ', sgnum, ' ==> ', end='')
if 0 < sgnum <= 2: # Triclinic
print('Triclinic')
pass
elif sgnum <= 15: # Monoclinic
print('Monoclinic')
pass
elif sgnum <= 74: # Orthorhombic
print('Orthorhombic')
pass
elif sgnum <= 142: # Tetragonal
print('Tetragonal')
pass
elif sgnum <= 194: # Hexagonal
print('Hexagonal')
print('Number of independent C_ij elements are reduced to 6.')
print('C_66 should be 1/2(C_11-C_12) but this is not enforced now.')
if not aleqpi2:
c22 = (cij[1, 1] + cij[2, 2]) / 2
c13 = (cij[0, 1] + cij[0, 2]) / 2
c55 = (cij[4, 4] + cij[5, 5]) / 2
cij[1, 1] = cij[2, 2] = c22
cij[0, 1] = cij[0, 2] = c13
cij[4, 4] = cij[5, 5] = c55
elif not bteqpi2:
c11 = (cij[0, 0] + cij[2, 2]) / 2
c12 = (cij[0, 1] + cij[1, 2]) / 2
c44 = (cij[3, 3] + cij[5, 5]) / 2
cij[0, 0] = cij[2, 2] = c11
cij[0, 1] = cij[1, 2] = c12
cij[3, 3] = cij[5, 5] = c44
elif not gmeqpi2:
c11 = (cij[0, 0] + cij[1, 1]) / 2
c12 = (cij[0, 2] + cij[1, 2]) / 2
c44 = (cij[3, 3] + cij[4, 4]) / 2
cij[0, 0] = cij[1, 1] = c11
cij[0, 2] = cij[1, 2] = c12
cij[3, 3] = cij[4, 4] = c44
elif sgnum <= 230: # Cubic
print('Cubic')
print('Number of independent C_ij elements are reduced to 3.')
c11 = (cij[0, 0] + cij[1, 1] + cij[2, 2]) / 3
c12 = (cij[0, 1] + cij[0, 2] + cij[1, 2]) / 3
c44 = (cij[3, 3] + cij[4, 4] + cij[5, 5]) / 3
cij[0, 0] = cij[1, 1] = cij[2, 2] = c11
cij[0, 1] = cij[0, 2] = cij[1, 2] = c12
cij[3, 3] = cij[4, 4] = cij[5, 5] = c44
else:
raise ValueError('Invalid space group number, ', sgnum)
# Just symmetrize Cij
for i in range(6):
for j in range(i, 6):
cij[j, i] = cij[i, j]
return cij
def reduce_cij(atoms0,cij0,eps=1.e-4):
"""
Reduce number of independent Cij according to the crystal system of original cell.
It is not Cij=Cji.
"""
cij = cij0
symdata = spglib.get_symmetry_dataset(atoms0)
napsys = NAPSystem(ase_atoms=atoms0)
sgnum = symdata['number']
print('Spacegroup number = ',sgnum,' ==> ',end='')
a,b,c = napsys.get_lattice_lengths()
alpha,beta,gamma = napsys.get_lattice_angles()
aeqb = abs(a-b) < eps*min(a,b)
beqc = abs(b-c) < eps*min(b,c)
ceqa = abs(c-a) < eps*min(c,a)
aleqpi2 = abs(alpha-np.pi/2) < eps*np.pi/2
bteqpi2 = abs(beta -np.pi/2) < eps*np.pi/2
gmeqpi2 = abs(gamma-np.pi/2) < eps*np.pi/2
if 0 < sgnum <= 2: # Triclinic
print('Triclinic')
pass
elif sgnum <= 15: # Monoclinic
print('Monoclinic')
pass
elif sgnum <= 74: # Orthorhombic
print('Orthorhombic')
pass
elif sgnum <= 142: # Tetragonal
print('Tetragonal')
pass
elif sgnum <= 194: # Hexagonal
print('Hexagonal')
print('Number of independent C_ij elements are reduced to 6.')
print('C_66 should be 1/2(C_11-C_12) but this is not enforced now.')
if not aleqpi2:
c22 = (cij[1,1] +cij[2,2])/2
c13 = (cij[0,1] +cij[0,2])/2
c55 = (cij[4,4] +cij[5,5])/2
cij[1,1] = cij[2,2] = c22
cij[0,1] = cij[0,2] = c13
cij[4,4] = cij[5,5] = c55
elif not bteqpi2:
c11 = (cij[0,0] +cij[2,2])/2
c12 = (cij[0,1] +cij[1,2])/2
c44 = (cij[3,3] +cij[5,5])/2
cij[0,0] = cij[2,2] = c11
cij[0,1] = cij[1,2] = c12
cij[3,3] = cij[5,5] = c44
elif not gmeqpi2:
c11 = (cij[0,0] +cij[1,1])/2
c12 = (cij[0,2] +cij[1,2])/2
c44 = (cij[3,3] +cij[4,4])/2
cij[0,0] = cij[1,1] = c11
cij[0,2] = cij[1,2] = c12
cij[3,3] = cij[4,4] = c44
elif sgnum <= 230: # Cubic
print('Cubic')
print('Number of independent C_ij elements are reduced to 3.')
c11 = (cij[0,0] +cij[1,1] +cij[2,2])/3
c12 = (cij[0,1] +cij[0,2] +cij[1,2])/3
c44 = (cij[3,3] +cij[4,4] +cij[5,5])/3
cij[0,0] = cij[1,1] = cij[2,2] = c11
cij[0,1] = cij[0,2] = cij[1,2] = c12
cij[3,3] = cij[4,4] = cij[5,5] = c44
else:
raise ValueError('Invalid space group number, ',sgnum)
# Just symmetrize Cij
for i in range(6):
for j in range(i,6):
cij[j,i] = cij[i,j]
return cij
