def structure2aSys(structure,idoffset=1):
"""
Converts Structure object of pymatgen to NAPSystem object in nap.
Args:
structure (Structure): pymatgen Structure object to be converted
to NAPSystem object..
Returns:
aSys (NAPSystem):
"""
lattice= structure.lattice
alc= 1.0
a1= np.array(lattice.matrix[0])
a2= np.array(lattice.matrix[1])
a3= np.array(lattice.matrix[2])
#... rescale a? vectors
a1= a1/alc
a2= a2/alc
a3= a3/alc
aSys= NAPSystem()
aSys.set_lattice(alc,a1,a2,a3)
for ia in range(structure.num_sites):
ai= Atom()
si= structure[ia]
crd= si.frac_coords
ai.set_pos(crd[0],crd[1],crd[2])
sid= structure.symbol_set.index(si.species_string)+idoffset
ai.set_sid(sid)
ai.set_id(ia+1)
aSys.add_atom(ai)
return aSys
def xdatcar2poscars(fname='XDATCAR', nskip=1):
f = open(fname, 'r')
isys = 0
while True:
#....."Direct configuration= #"
try:
line = f.readline()
#...Check configuration
if not "Direct configuration=" in line:
alc, a1, a2, a3, species, num_atoms = read_header(f)
# print(species)
# print(num_atoms)
natm = 0
for n in num_atoms:
natm += n
continue
elif len(line.split()) == 0:
break
except:
break
#...Skip reading this configuration if requested
if not isys % nskip == 0:
for i in range(natm):
f.readline()
isys += 1
continue
#...Following lines: atom positions
#...Make a NAPSystem from these information and write to POSCAR_#####
nsys = NAPSystem(specorder=species)
nsys.set_lattice(alc, a1, a2, a3)
inc = 0
for inum, ni in enumerate(num_atoms):
for j in range(ni):
inc += 1
ai = Atom()
ai.set_id(inc)
ai.set_symbol(species[inum])
data = f.readline().split()
# print(data)
if not is_number(data[0]):
raise ValueError('Wrong format?')
x1, x2, x3 = [float(x) for x in data[0:3]]
ai.set_pos(x1, x2, x3)
ai.set_vel(0.0, 0.0, 0.0)
nsys.add_atom(ai)
foutname = 'POSCAR_{0:05d}'.format(isys)
print(' >>> ' + foutname)
nsys.write_POSCAR(fname=foutname)
isys += 1
f.close()
return None
def xdatcar2poscars(fname='XDATCAR',nskip=1):
f= open(fname,'r')
isys = 0
while True:
#....."Direct configuration= #"
try:
line = f.readline()
#...Check configuration
if not "Direct configuration=" in line:
alc,a1,a2,a3,species,num_atoms = read_header(f)
# print(species)
# print(num_atoms)
natm = 0
for n in num_atoms:
natm += n
continue
elif len(line.split()) == 0:
break
except:
break
#...Skip reading this configuration if requested
if not isys%nskip == 0:
for i in range(natm):
f.readline()
isys += 1
continue
#...Following lines: atom positions
#...Make a NAPSystem from these information and write to POSCAR_#####
nsys = NAPSystem(specorder=species)
nsys.set_lattice(alc,a1,a2,a3)
inc = 0
for inum,ni in enumerate(num_atoms):
for j in range(ni):
inc += 1
ai = Atom()
ai.set_id(inc)
ai.set_symbol(species[inum])
data= f.readline().split()
# print(data)
if not is_number(data[0]):
raise ValueError('Wrong format?')
x1,x2,x3 = [ float(x) for x in data[0:3] ]
ai.set_pos(x1,x2,x3)
ai.set_vel(0.0,0.0,0.0)
nsys.add_atom(ai)
foutname = 'POSCAR_{0:05d}'.format(isys)
print(' >>> '+foutname)
nsys.write_POSCAR(fname=foutname)
isys += 1
f.close()
return None