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_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 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 make_polycrystal(grns,uc,n1,n2,n3,two_dim=False):
"""
THIS ROUTINE IS NOT THAT UNIVERSAL.
Each grain has to have neighboring grains within a supercell,
otherwise there will be some unexpecting grain boundries.
In order to do so, the system should be large enough and
the number of grains should be large enough.
"""
#...Calc the minimum bond distance in unit cell and use it as penetration depth
dmin = 1.0e+30
for i in range(uc.num_atoms()-1):
for j in range(i+1,uc.num_atoms()):
dij = uc.get_distance(i,j)
dmin = min(dij,dmin)
print(' Minimum bond distance in the unitcell: ',dmin)
dmin = dmin *DMIN_RATE
penetration_depth = dmin*2
print(' Minimum bond distance allowed in the new system: ',dmin)
sv,nsv= shift_vector(two_dim)
# print(' nsv =',nsv)
# for i in range(nsv):
# print(' i,sv[i]=',i,sv[i])
nsys= NAPSystem(specorder=uc.specorder)
nsys.set_lattice(uc.alc,uc.a1*n1,uc.a2*n2,uc.a3*n3)
hmat = nsys.get_hmat()
hmati = nsys.get_hmat_inv()
nmax = n1*n2*n3 *uc.num_atoms()
sidsl = np.zeros(nmax,dtype=int)
symsl = []
possl = np.zeros((nmax,3))
velsl = np.zeros((nmax,3))
frcsl = np.zeros((nmax,3))
ix0 = -n1/2-1
ix1 = n1/2+2
iy0 = -n2/2-1
iy1 = n2/2+2
iz0 = -n3/2-1
iz1 = n3/2+2
if two_dim:
if n3 != 1:
raise ValueError('n3 should be 1 in case two_dim is ON.')
iz0 = 0
iz1 = 1
print(' x range = ',ix0,ix1)
print(' y range = ',iy0,iy1)
print(' z range = ',iz0,iz1)
inc = 0
for ig in range(len(grns)):
grain= grns[ig]
rmat= grain.rmat # Rotation matrix of the grain
pi= grain.point # Grain center in reduced coordinate
api= np.dot(hmat,pi) # Grain center in Cartessian coordinate
print(' grain-ID = ',ig+1)
for ix in range(ix0,ix1):
# print('ix=',ix)
for iy in range(iy0,iy1):
for iz in range(iz0,iz1):
for m in range(uc.num_atoms()):
sidt = uc.get_atom_attr(m,'sid')
rt= np.zeros((3,))
pm = uc.get_atom_attr(m,'pos')
rt[0]= (pm[0]+ix)/n1
rt[1]= (pm[1]+iy)/n2
rt[2]= (pm[2]+iz)/n3
#...rt to absolute position
art= np.dot(hmat,rt)
#...Rotate
ari= np.dot(rmat,art)
#...Shift origin to the grain center
ari[0]= ari[0]+api[0]
ari[1]= ari[1]+api[1]
ari[2]= ari[2]+api[2]
#...check distance from all the grain points
di= distance(ari,api,two_dim)
isOutside= False
for jg in range(len(grns)):
gj= grns[jg]
for isv in range(nsv):
pj= gj.point
if jg == ig:
if not two_dim and isv == 13:
continue
elif two_dim and isv == 4:
continue
svi= sv[isv]
pj= pj +svi
apj = np.dot(hmat,pj)
dj= distance(ari,apj,two_dim)
if dj +penetration_depth < di: # Allow some penetration here
isOutside= True
break
if isOutside:
break
if isOutside:
break
#...here ri is inside this grain, register it
#...Cartessian coord to reduced coord
ri = np.dot(hmati,ari)
ri[0]= pbc(ri[0])
ri[1]= pbc(ri[1])
ri[2]= pbc(ri[2])
sidsl[inc] = sidt
possl[inc] = ri
velsl[inc,:] = 0.0
frcsl[inc,:] = 0.0
symsl.append(nsys.specorder[sidt-1])
inc += 1
if inc > nmax:
raise ValueError('inc > nmax')
#...Create filled arrays from non-filled ones
poss = np.array(possl[:inc])
vels = np.array(velsl[:inc])
frcs = np.array(frcsl[:inc])
nsys.add_atoms(symsl,poss,vels,frcs)
#...remove too-close atoms at the grain boundaries
print(' Making pair list in order to remove close atoms...')
print(' Number of atoms: ',nsys.num_atoms())
nsys.make_pair_list(RCUT)
nsys.write('POSCAR_orig')
short_pairs = []
# dmin2= dmin**2
# xij= np.zeros((3,))
print(' Making the list of SHORT pairs...')
for ia in range(nsys.num_atoms()):
lst= nsys.get_atom_attr(ia,'lspr')
for j in range(len(lst)):
ja= lst[j]
if ja > ia:
continue
dij = nsys.get_distance(ia,ja)
if dij < dmin:
short_pairs.append((ia,ja,dij))
print(' Number of short pairs: ',len(short_pairs))
#...Remove only relevant atoms, not all the atoms in the short_pairs.
ls_remove = []
ls_not_remove = []
for pair in short_pairs:
ia = pair[0]
ja = pair[1]
if ia not in ls_not_remove and ja not in ls_not_remove:
ls_remove.append(ia)
ls_not_remove.append(ja)
elif ia not in ls_not_remove:
ls_remove.append(ia)
elif ja not in ls_not_remove:
ls_remove.append(ja)
else: # Both atoms are already in not_remove list, which should be avoided.
ls_not_remove.remove(ia)
ls_remove.append(ia)
ls_not_remove.append(ja)
#...Remove double registered IDs
ls_remove = uniq(ls_remove)
print(' Number of to be removed atoms: ',len(ls_remove))
nsys.remove_atoms(*ls_remove)
return nsys
