def from_ase(atoms, specorder=None):
"""
Convert ASE Atoms object to NAPSystem object.
"""
spcorder = []
if specorder is not None:
spcorder = specorder
symbols = atoms.get_chemical_symbols()
spos = atoms.get_scaled_positions()
vels = atoms.get_velocities()
cell = atoms.get_cell()
celli = np.linalg.inv(cell)
if spos is None:
raise ValueError('ASE atoms object has no atom in it.')
#...Initialize and remake self.specorder
for s in symbols:
if s not in spcorder:
spcorder.append(s)
nsys = NAPSystem(specorder=spcorder)
# nsys = cls(specorder=spcorder)
nsys.alc = 1.0
nsys.a1[:] = atoms.cell[0]
nsys.a2[:] = atoms.cell[1]
nsys.a3[:] = atoms.cell[2]
#...First, initialize arrays
natm = len(atoms)
sids = [0 for i in range(natm)]
poss = np.array(spos)
if vels is None:
vels = np.zeros((natm, 3))
else:
vels = np.array(vels)
frcs = np.zeros((natm, 3))
#...Create arrays to be installed into nsys.atoms
sids = [nsys.specorder.index(si) + 1 for si in symbols]
nsys.atoms.sid = sids
nsys.atoms[['x', 'y', 'z']] = poss
for i in range(len(vels)):
vels[i] = np.dot(celli, vels[i])
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
return nsys
def read_pmd(fname='pmdini', specorder=None):
nsys = NAPSystem()
if specorder is not None:
nsys.specorder = specorder
incatm = 0
with open(fname, 'r') as f:
iline = 0
symbol = None
for line in f.readlines():
if line[0] in ('#', '!'): # comment line
if 'specorder:' in line: # overwrite specorder if specified in file
data = line.split()
specorder = [d for d in data[2:len(data)]]
if nsys.specorder and set(
nsys.specorder) != set(specorder):
print(' WARNING: specorders are inconsistent, ' +
'use one in the file.')
nsys.specorder = specorder
else:
if nsys.specorder is None or len(nsys.specorder) == 0:
raise ValueError(
'Specorder must be specified via the file or an argument.'
)
iline = iline + 1
data = line.split()
# 1st: lattice constant
if iline == 1:
nsys.alc = float(data[0])
# 2nd-4th: cell vectors
elif iline == 2:
nsys.a1 = np.array([float(x) for x in data])
elif iline == 3:
nsys.a2 = np.array([float(x) for x in data])
elif iline == 4:
nsys.a3 = np.array([float(x) for x in data])
# 5th-7th: velocity of cell vectors
elif 5 <= iline <= 7:
pass
# 8th: num of atoms
elif iline == 8:
natm = int(data[0])
sids = [0 for i in range(natm)]
# poss = [ np.zeros(3) for i in range(natm) ]
# vels = [ np.zeros(3) for i in range(natm) ]
# frcs = [ np.zeros(3) for i in range(natm) ]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
# 9th-: atom positions
else:
if incatm > natm:
break
fdata = [float(x) for x in data]
tag = fdata[0]
sid, ifmv, num = decode_tag(tag)
# poss[incatm][:] = fdata[1:4]
# vels[incatm][:] = fdata[4:7]
poss[incatm, :] = fdata[1:4]
vels[incatm, :] = fdata[4:7]
sids[incatm] = sid
incatm += 1
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
return nsys
def read_CHGCAR(fname='CHGCAR', specorder=None):
"""
Read CHGCAR file and get information of cell, atoms, and volumetric data.
Parameters
----------
fname : str
File name to be read.
"""
nsys = NAPSystem()
with open(fname, 'r') as f:
# 1st line: comment
f.readline()
# 2nd: lattice constant
nsys.alc = float(f.readline().split()[0])
# 3rd-5th: cell vectors
nsys.a1 = np.array([float(x) for x in f.readline().split()])
nsys.a2 = np.array([float(x) for x in f.readline().split()])
nsys.a3 = np.array([float(x) for x in f.readline().split()])
# 6th: species names or number of each species
buff = f.readline().split()
if not buff[0].isdigit():
spcs = copy.deepcopy(buff)
buff = f.readline().split()
if specorder is None:
nsys.specorder = spcs
else:
nsys.specorder = specorder
for s in spcs:
if s not in nsys.specorder:
nsys.specorder.append(s)
num_species = np.array([int(n) for n in buff])
try:
spcs
except NameError:
spcs = nsys.specorder
#...Check number of species in POSCAR file and in specorder
if len(num_species) > len(nsys.specorder):
msg = '''
ers of species in POSCAR is greater than the one in specorder, which should be the same or less.
er of species in POSCAR = {0:d}
need to specify the species order correctly with --specorder option.
'''.format(len(num_species))
raise ValueError(msg)
natm = np.sum(num_species)
sids = [0 for i in range(natm)]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
#print("Number of atoms = {0:5d}".format(natm))
# 7th or 8th line: comment
c7 = f.readline()
if c7[0] in ('s', 'S'):
c7 = f.readline()
if c7[0] in ('c', 'C'): # positions are in Cartesian coordinate
hi = nsys.get_hmat_inv()
coord = 'cartesian'
else: # such as "Direct"
coord = 'scaled'
#...Atom positions
for i in range(natm):
buff = f.readline().split()
sid = 1
m = 0
sindex = 0
for n in num_species:
m += n
if i < m:
if spcs and nsys.specorder:
sid = nsys.specorder.index(spcs[sindex]) + 1
break
sid += 1
sindex += 1
sids[i] = sid
pos = [float(buff[0]), float(buff[1]), float(buff[2])]
if coord == 'cartesian':
x1, x2, x3 = cartesian_to_scaled(hi, pos[0], pos[1], pos[2])
elif coord == 'scaled':
x1, x2, x3 = pos[0], pos[1], pos[2]
poss[i][:] = [x1, x2, x3]
#...Up to here, code should be the same as read_POSCAR, in case of CHGCAR lines follow
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
#...Read volumetric data
f.readline() # should be one blank line
ndiv = [int(x) for x in f.readline().split()]
ndata = ndiv[0] * ndiv[1] * ndiv[2]
voldata = np.zeros(ndata)
inc = 0
while True:
line = [float(d) for d in f.readline().split()]
for d in line:
voldata[inc] = d
inc += 1
if inc >= ndata:
break
#...Stop reading CHGCAR file here, ignoring the rest of file
nsys.ndiv = copy.copy(ndiv)
nsys.voldata = np.reshape(voldata, ndiv, order='F')
return nsys
def read_xsf(fname="xsf", specorder=None):
from nappy.elements import get_symbol_from_number
nsys = NAPSystem()
if specorder is None:
nsys.specorder = []
else:
nsys.specorder = specorder
f = open(fname, 'r')
mode = 'None'
ixyz = 0
iatm = 0
natm = -1
for line in f.readlines():
if 'CRYSTAL' in line:
mode = 'CRYSTAL'
continue
elif 'PRIMVEC' in line:
mode = 'PRIMVEC'
continue
elif 'PRIMCOORD' in line:
mode = 'PRIMCOORD'
# Before going further, create inversed h-matrix
hi = nsys.get_hmat_inv()
# print 'Inversed h-matrix:'
# print hi
continue
if mode == 'CRYSTAL':
pass
elif mode == 'PRIMVEC':
if ixyz == 0:
arr = [float(x) for x in line.split()]
nsys.a1[0] = arr[0]
nsys.a1[1] = arr[1]
nsys.a1[2] = arr[2]
elif ixyz == 1:
arr = [float(x) for x in line.split()]
nsys.a2[0] = arr[0]
nsys.a2[1] = arr[1]
nsys.a2[2] = arr[2]
elif ixyz == 2:
arr = [float(x) for x in line.split()]
nsys.a3[0] = arr[0]
nsys.a3[1] = arr[1]
nsys.a3[2] = arr[2]
ixyz += 1
elif mode == 'PRIMCOORD':
data = line.split()
if len(data) == 1:
natm = int(data[0])
sids = [0 for i in range(natm)]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
continue
elif len(data) == 2:
natm = int(data[0])
nspcs = int(data[1])
sids = [0 for i in range(natm)]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
continue
elif len(data) == 4 or len(data) == 7:
if iatm >= natm:
continue
symbol = get_symbol_from_number(int(data[0]))
if symbol not in nsys.specorder:
nsys.specorder.append(symbol)
sid = nsys.specorder.index(symbol) + 1
sids[iatm] = sid
# ai.set_sid(sid)
xc = float(data[1])
yc = float(data[2])
zc = float(data[3])
xi, yi, zi = cartesian_to_scaled(hi, xc, yc, zc)
poss[iatm, :] = [xi, yi, zi]
# print 'iatm,symbol,sid,xc,yc,zc = ',iatm,symbol,sid,xc,yc,zc
else:
continue
iatm += 1
nsys.alc = 1.0
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
f.close()
return nsys
def read_lammps_data(fname="data.lammps", atom_style='atomic', specorder=None):
nsys = NAPSystem()
if specorder is None:
nsys.specorder = []
else:
nsys.specorder = specorder
f = open(fname, 'r')
mode = 'None'
iatm = 0
symbol = None
nsys.alc = 1.0
xy = 0.0
xz = 0.0
yz = 0.0
for line in f.readlines():
data = line.split()
if mode == 'None':
if 'atoms' in line:
natm = int(data[0])
sids = [0 for i in range(natm)]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
elif 'atom types' in line:
nspcs = int(data[0])
elif 'xlo' in line:
xlo = float(data[0])
xhi = float(data[1])
elif 'ylo' in line:
ylo = float(data[0])
yhi = float(data[1])
elif 'zlo' in line:
zlo = float(data[0])
zhi = float(data[1])
elif 'xy' in line:
xy = float(data[0])
xz = float(data[1])
yz = float(data[2])
elif 'Atoms' in line:
mode = 'Atoms'
#...Cell info (xhi,xlo,...) should already be read
# nsys.a1 = np.array([xhi-xlo,xy,xz],dtype=float)
# nsys.a2 = np.array([0.0,yhi-ylo,yz],dtype=float)
# nsys.a3 = np.array([0.0,0.0,zhi-zlo],dtype=float)
nsys.a1 = np.array([xhi - xlo, 0.0, 0.0], dtype=float)
nsys.a2 = np.array([xy, yhi - ylo, 0.0], dtype=float)
nsys.a3 = np.array([xz, yz, zhi - zlo], dtype=float)
hmat = nsys.get_hmat()
hmati = np.linalg.inv(hmat)
continue
elif mode == 'Atoms':
if len(data) >= 5 and iatm < natm:
idat = 0
# ai = Atom()
idat += 1
# ai.set_sid(int(data[idat]))
sid = int(data[idat])
sids[iatm] = sid
if nsys.specorder:
symbol = nsys.specorder[sid - 1]
# if symbol and ai.symbol != symbol:
# ai.set_symbol(symbol)
# if atom_style == 'charge':
# idat += 1
# chg = float(data[idat])
# # ai.set_aux('charge',chg)
# if aux_names and 'charge' not in aux_names:
idat += 1
x0 = float(data[idat])
idat += 1
y0 = float(data[idat])
idat += 1
z0 = float(data[idat])
x = hmati[0, 0] * x0 + hmati[0, 1] * y0 + hmati[0, 2] * z0
y = hmati[1, 0] * x0 + hmati[1, 1] * y0 + hmati[1, 2] * z0
z = hmati[2, 0] * x0 + hmati[2, 1] * y0 + hmati[2, 2] * z0
x = pbc(x)
y = pbc(y)
z = pbc(z)
poss[iatm, :] = [x, y, z]
iatm += 1
f.close()
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
return nsys
def read_dump(fname="dump", specorder=None):
nsys = NAPSystem()
f = open(fname, 'r')
mode = 'None'
ixyz = 0
iatm = 0
natm = -1
symbol = None
if specorder is None:
nsys.specorder = []
else:
nsys.specorder = specorder
nsys.alc = 1.0
xy = 0.0
xz = 0.0
yz = 0.0
aux_exists = {
'x': -1,
'y': -1,
'z': -1,
'xu': -1,
'yu': -1,
'zu': -1,
'fx': -1,
'fy': -1,
'fz': -1,
'ekin': -1,
'epot': -1,
'sxx': -1,
'syy': -1,
'szz': -1,
'syz': -1,
'sxz': -1,
'sxy': -1,
'chg': -1,
'chi': -1
}
ivx = -1
ivy = -1
ivz = -1
ifx = -1
ify = -1
ifz = -1
for line in f.readlines():
data = line.split()
if 'ITEM' in line:
if 'NUMBER OF ATOMS' in line:
mode = 'NUMBER OF ATOMS'
continue
elif 'BOX BOUNDS' in line:
mode = 'BOX BOUNDS'
continue
elif 'ATOMS' in line:
mode = 'ATOMS'
aux_names = [name for i, name in enumerate(data) if i > 1]
aux_names.remove('id')
aux_names.remove('type')
if ('x' not in aux_names and 'xu' not in aux_names) or \
('y' not in aux_names and 'zu' not in aux_names) or \
('z' not in aux_names and 'zu' not in aux_names):
raise ValueError(
'Not enough coordinate info.\nCheck the dump file format.'
)
try:
ix = aux_names.index('x') + 2
except Exception:
ix = aux_names.index('xu') + 2
try:
iy = aux_names.index('y') + 2
except Exception:
iy = aux_names.index('yu') + 2
try:
iz = aux_names.index('z') + 2
# iauxstart = 5
except Exception:
iz = aux_names.index('zu') + 2
# iauxstart = 5
try:
ivx = aux_names.index('vx') + 2
ivy = aux_names.index('vy') + 2
ivz = aux_names.index('vz') + 2
# iauxstart = 8
except Exception:
pass
try:
ifx = aux_names.index('fx') + 2
ify = aux_names.index('fy') + 2
ifz = aux_names.index('fz') + 2
except Exception:
pass
# for s in ('x','xu','y','yu','z','zu','vx','vy','vz'):
# if s in aux_names:
# aux_names.remove(s)
if len(aux_names) > 0:
auxs = np.zeros((natm, len(aux_names)))
continue
elif 'TIMESTEP' in line:
mode = 'TIMESTEP'
continue
if mode == 'TIMESTEP':
timestep = int(data[0])
elif mode == 'NUMBER OF ATOMS':
natm = int(data[0])
sids = [0 for i in range(natm)]
# poss = [ np.zeros(3) for i in range(natm) ]
# vels = [ np.zeros(3) for i in range(natm) ]
# frcs = [ np.zeros(3) for i in range(natm) ]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
elif mode == 'BOX BOUNDS':
if ixyz == 0:
xlo_bound = float(data[0])
xhi_bound = float(data[1])
if len(data) > 2:
xy = float(data[2])
elif ixyz == 1:
ylo_bound = float(data[0])
yhi_bound = float(data[1])
if len(data) > 2:
xz = float(data[2])
elif ixyz == 2:
zlo_bound = float(data[0])
zhi_bound = float(data[1])
if len(data) > 2:
yz = float(data[2])
ixyz += 1
if ixyz > 2:
xlo = xlo_bound - min(0.0, xy, xz, xy + xz)
xhi = xhi_bound - max(0.0, xy, xz, xy + xz)
ylo = ylo_bound - min(0.0, yz)
yhi = yhi_bound - max(0.0, yz)
zlo = zlo_bound
zhi = zhi_bound
#...Original definition of lattice vectors could be different
# from this, because the definition in dump format
# requires y,z-components of vector a1 to be zero.
nsys.a1 = np.array([xhi - xlo, 0., 0.], dtype=float)
nsys.a2 = np.array([xy, yhi - ylo, 0.], dtype=float)
nsys.a3 = np.array([xz, yz, zhi - zlo], dtype=float)
hmat = nsys.get_hmat()
hmati = nsys.get_hmat_inv()
elif mode == 'ATOMS':
if iatm < natm:
symbol = None
if data[1].isdigit():
sid = int(data[1])
sids[iatm] = sid
symbol = nsys.specorder[sid - 1]
else:
symbol = data[1]
if symbol not in nsys.specorder:
nsys.specorder.append(symbol)
sid = nsys.specorder.index(symbol) + 1
sids[iatm] = sid
r0 = [float(data[ix]), float(data[iy]), float(data[iz])]
if ivx > 0 and ivy > 0 and ivz > 0:
v0 = [float(data[ivx]), float(data[ivy]), float(data[ivz])]
else:
v0 = [0., 0., 0.]
if ifx > 0 and ify > 0 and ifz > 0:
f0 = [float(data[ifx]), float(data[ify]), float(data[ifz])]
else:
f0 = [0., 0., 0.]
sr = np.dot(hmati, r0)
sv = np.dot(hmati, v0)
sr[0] = pbc(sr[0])
sr[1] = pbc(sr[1])
sr[2] = pbc(sr[2])
# poss[iatm][:] = sr[:]
# vels[iatm][:] = sv[:]
poss[iatm, :] = sr[:]
vels[iatm, :] = sv[:]
frcs[iatm, :] = f0[:]
if len(aux_names) > 0:
# auxs[iatm,:] = [ float(x) for x in data[iauxstart:] ]
auxs[iatm, :] = [float(x) for x in data[2:]]
iatm += 1
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
for ia in range(len(aux_names)):
name = aux_names[ia]
if name in ('x', 'xu', 'y', 'yu', 'z', 'zu', 'vx', 'vy', 'vz', 'fx',
'fy', 'fz'):
continue
aux = auxs[:, ia]
nsys.atoms[name] = aux.tolist()
f.close()
return nsys
def read_POSCAR(fname='POSCAR', specorder=None):
nsys = NAPSystem()
with open(fname, 'r') as f:
# 1st line: comment
f.readline()
# 2nd: lattice constant
nsys.alc = float(f.readline().split()[0])
# 3rd-5th: cell vectors
nsys.a1 = np.array([float(x) for x in f.readline().split()])
nsys.a2 = np.array([float(x) for x in f.readline().split()])
nsys.a3 = np.array([float(x) for x in f.readline().split()])
# 6th: species names or number of each species
buff = f.readline().split()
if not buff[0].isdigit():
spcs = copy.deepcopy(buff)
buff = f.readline().split()
if specorder is None:
nsys.specorder = spcs
else:
nsys.specorder = specorder
for s in spcs:
if s not in nsys.specorder:
nsys.specorder.append(s)
num_species = np.array([int(n) for n in buff])
try:
spcs
except NameError:
spcs = nsys.specorder
#...Check number of species in POSCAR file and in specorder
if len(num_species) > len(nsys.specorder):
msg = '''
ers of species in POSCAR is greater than the one in specorder, which should be the same or less.
er of species in POSCAR = {0:d}
need to specify the species order correctly with --specorder option.
'''.format(len(num_species))
raise ValueError(msg)
natm = np.sum(num_species)
sids = [0 for i in range(natm)]
# poss = [ np.zeros(3) for i in range(natm) ]
# vels = [ np.zeros(3) for i in range(natm) ]
# frcs = [ np.zeros(3) for i in range(natm) ]
poss = np.zeros((natm, 3))
vels = np.zeros((natm, 3))
frcs = np.zeros((natm, 3))
#print("Number of atoms = {0:5d}".format(natm))
# 7th or 8th line: comment
c7 = f.readline()
if c7[0] in ('s', 'S'):
c7 = f.readline()
if c7[0] in ('c', 'C'): # positions are in Cartesian coordinate
hi = nsys.get_hmat_inv()
coord = 'cartesian'
else: # such as "Direct"
coord = 'scaled'
#...Atom positions
for i in range(natm):
buff = f.readline().split()
sid = 1
m = 0
sindex = 0
for n in num_species:
m += n
if i < m:
if spcs and nsys.specorder:
sid = nsys.specorder.index(spcs[sindex]) + 1
break
sid += 1
sindex += 1
sids[i] = sid
pos = [float(buff[0]), float(buff[1]), float(buff[2])]
if coord == 'cartesian':
x1, x2, x3 = cartesian_to_scaled(hi, pos[0], pos[1], pos[2])
elif coord == 'scaled':
x1, x2, x3 = pos[0], pos[1], pos[2]
poss[i, :] = [x1, x2, x3]
nsys.atoms[['x', 'y', 'z']] = poss
nsys.atoms[['vx', 'vy', 'vz']] = vels
nsys.atoms[['fx', 'fy', 'fz']] = frcs
nsys.atoms['sid'] = sids
return nsys
def to_given_vector(infile,specorder,a1new,a2new,a3new):
psys = NAPSystem(fname=infile,specorder=specorder)
psys.assign_pbc()
psys.a1 = psys.a1 *psys.alc
psys.a2 = psys.a2 *psys.alc
psys.a3 = psys.a3 *psys.alc
psys.alc = 1.0
print('a1 = ',psys.a1)
print('a2 = ',psys.a2)
print('a3 = ',psys.a3)
pos = psys.get_real_positions()
spos = psys.get_scaled_positions()
for i in range(min(len(psys.atoms),10)):
a = psys.atoms[i]
print('{0:5d} {1:s}'.format(a.id,a.symbol)
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(spos[i,0],
spos[i,1],
spos[i,2])
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(pos[i,0],
pos[i,1],
pos[i,2]))
# print(psys.get_scaled_positions())
# print(psys.get_real_positions())
# sa1new = np.zeros(3,dtype=float)
# sa2new = np.zeros(3,dtype=float)
# sa3new = np.zeros(3,dtype=float)
#tmp = raw_input('Input new a1 vector: ')
#a1new[:] = [ float(x) for x in tmp.split(',') ]
# sa1new[:] = [ 0.5, 0.5, 0.0]
#tmp = raw_input('Input new a2 vector: ')
#a2new[:] = [ float(x) for x in tmp.split(',') ]
# sa2new[:] = [ 0.0, 1.0, 0.0 ]
#tmp = raw_input('Input new a3 vector: ')
#a3new[:] = [ float(x) for x in tmp.split(',') ]
# sa3new[:] = [ 0.5, 0.5, 1.0 ]
hmat = psys.get_hmat()
a1new = np.dot(hmat,sa1new)
a2new = np.dot(hmat,sa2new)
a3new = np.dot(hmat,sa3new)
print('new a1 in hmat_orig =',sa1new)
print('new a2 in hmat_orig =',sa2new)
print('new a3 in hmat_orig =',sa3new)
print('new a1 =',a1new)
print('new a2 =',a2new)
print('new a3 =',a3new)
psnew = NAPSystem(specorder=specorder)
psnew.set_lattice(psys.alc,a1new,a2new,a3new)
# Expand the original system for the search of atoms to be included
# in the new system.
# First, compute how much we have to expand the original system
hi = np.linalg.inv(hmat)
icsa1new = [0,0,0]
icsa2new = [0,0,0]
icsa3new = [0,0,0]
for i in range(3):
if sa1new[i] < 0.0:
icsa1new[i] = int(sa1new[i]-1.0)
else:
icsa1new[i] = int(sa1new[i]+1.0)
if sa2new[i] < 0.0:
icsa2new[i] = int(sa2new[i]-1.0)
else:
icsa2new[i] = int(sa2new[i]+1.0)
if sa3new[i] < 0.0:
icsa3new[i] = int(sa3new[i]-1.0)
else:
icsa3new[i] = int(sa3new[i]+1.0)
print(icsa1new)
print(icsa2new)
print(icsa3new)
for i in range(3):
if icsa1new[i] == 0:
raise RuntimeError('icsa1new[i] == 0')
if icsa2new[i] == 0:
raise RuntimeError('icsa2new[i] == 0')
if icsa3new[i] == 0:
raise RuntimeError('icsa3new[i] == 0')
irange1 = (min(icsa1new[0],icsa2new[0],icsa3new[0]),
max(icsa1new[0],icsa2new[0],icsa3new[0]))
irange2 = (min(icsa1new[1],icsa2new[1],icsa3new[1]),
max(icsa1new[1],icsa2new[1],icsa3new[1]))
irange3 = (min(icsa1new[2],icsa2new[2],icsa3new[2]),
max(icsa1new[2],icsa2new[2],icsa3new[2]))
print('irange1: ',irange1)
print('irange2: ',irange2)
print('irange3: ',irange3)
expos = []
symbols = psys.get_symbols()
print('symbols :',symbols)
exsymbols = []
print('Expanding the original system...')
for n3 in range(min(0,irange3[0]),irange3[1]):
for n2 in range(min(0,irange2[0]),irange2[1]):
for n1 in range(min(0,irange1[0]),irange1[1]):
for ia in range(len(spos)):
sposi = copy.deepcopy(spos[ia])
sposi[0] += n1
sposi[1] += n2
sposi[2] += n3
posi = np.dot(hmat,sposi)
symbol = symbols[ia]
# print(ia,n1,n2,n3,symbol,sposi)
expos.append(posi)
exsymbols.append(symbol)
print('Extracting the atoms inside the new unit vectors...')
hmat= psnew.get_hmat()
hi = np.linalg.inv(hmat)
for ia,posi in enumerate(expos):
sposi = np.dot(hi,posi)
if 0.0 <= sposi[0] < 1.0 and \
0.0 <= sposi[1] < 1.0 and \
0.0 <= sposi[2] < 1.0:
atom = Atom()
symbol = exsymbols[ia]
print('{0:5d} {1:s}'.format(ia,symbol)
+' {0:12.5f} {1:12.5f} {2:12.5f}'.format(sposi[0],
sposi[1],
sposi[2]))
atom.set_symbol(symbol)
atom.set_pos(sposi[0],sposi[1],sposi[2])
psnew.add_atom(atom)
tmp = None
#tmp = raw_input('Input periodic shift vector if you want: ')
tmp = ' 0.5, 0.0, 0.5'
if tmp:
shift = [ float(x) for x in tmp.split(',')]
for a in psnew.atoms:
a.pos[0] += shift[0]
a.pos[1] += shift[1]
a.pos[2] += shift[2]
psnew.assign_pbc()
psnew.write_POSCAR(infile+'.new')
print('Check '+infile+'.new')
