import numpy.random as random
import numpy as np
from ase_ext import Atoms
from ase_ext.calculators.neighborlist import NeighborList
atoms = Atoms(numbers=list(range(10)),
cell=[(0.2, 1.2, 1.4), (1.4, 0.1, 1.6), (1.3, 2.0, -0.1)])
atoms.set_scaled_positions(3 * random.random((10, 3)) - 1)
def count(nl, atoms):
c = np.zeros(len(atoms), int)
R = atoms.get_positions()
cell = atoms.get_cell()
d = 0.0
for a in range(len(atoms)):
i, offsets = nl.get_neighbors(a)
for j in i:
c[j] += 1
c[a] += len(i)
d += (((R[i] + np.dot(offsets, cell) - R[a])**2).sum(1)**0.5).sum()
return d, c
for sorted in [False, True]:
for p1 in range(2):
for p2 in range(2):
for p3 in range(2):
print(p1, p2, p3)
atoms.set_pbc((p1, p2, p3))
nl = NeighborList(atoms.numbers * 0.2 + 0.5,
def read_vasp(filename='CONTCAR'):
"""Import POSCAR/CONTCAR type file.
Reads unitcell, atom positions and constraints from the POSCAR/CONTCAR
file and tries to read atom types from POSCAR/CONTCAR header, if this fails
the atom types are read from OUTCAR or POTCAR file.
"""
from ase_ext import Atoms, Atom
from ase_ext.constraints import FixAtoms, FixScaled
from ase_ext.data import chemical_symbols
import numpy as np
if isinstance(filename, str):
f = open(filename)
else: # Assume it's a file-like object
f = filename
# First line should contain the atom symbols , eg. "Ag Ge" in
# the same order
# as later in the file (and POTCAR for the full vasp run)
atomtypes = f.readline().split()
lattice_constant = float(f.readline())
# Now the lattice vectors
a = []
for ii in range(3):
s = f.readline().split()
floatvect = float(s[0]), float(s[1]), float(s[2])
a.append(floatvect)
basis_vectors = np.array(a) * lattice_constant
# Number of atoms. Again this must be in the same order as
# in the first line
# or in the POTCAR or OUTCAR file
atom_symbols = []
numofatoms = f.readline().split()
#vasp5.1 has an additional line which gives the atom types
#the following try statement skips this line
try:
int(numofatoms[0])
except ValueError:
numofatoms = f.readline().split()
numsyms = len(numofatoms)
if len(atomtypes) < numsyms:
# First line in POSCAR/CONTCAR didn't contain enough symbols.
atomtypes = atomtypes_outpot(f.name, numsyms)
else:
try:
for atype in atomtypes[:numsyms]:
if not atype in chemical_symbols:
raise KeyError
except KeyError:
atomtypes = atomtypes_outpot(f.name, numsyms)
for i, num in enumerate(numofatoms):
numofatoms[i] = int(num)
[atom_symbols.append(atomtypes[i]) for na in range(numofatoms[i])]
# Check if Selective dynamics is switched on
sdyn = f.readline()
selective_dynamics = sdyn[0].lower() == "s"
# Check if atom coordinates are cartesian or direct
if selective_dynamics:
ac_type = f.readline()
else:
ac_type = sdyn
cartesian = ac_type[0].lower() == "c" or ac_type[0].lower() == "k"
tot_natoms = sum(numofatoms)
atoms_pos = np.empty((tot_natoms, 3))
if selective_dynamics:
selective_flags = np.empty((tot_natoms, 3), dtype=bool)
for atom in range(tot_natoms):
ac = f.readline().split()
atoms_pos[atom] = (float(ac[0]), float(ac[1]), float(ac[2]))
if selective_dynamics:
curflag = []
for flag in ac[3:6]:
curflag.append(flag == 'F')
selective_flags[atom] = curflag
# Done with all reading
if type(filename) == str:
f.close()
if cartesian:
atoms_pos *= lattice_constant
atoms = Atoms(symbols=atom_symbols, cell=basis_vectors, pbc=True)
if cartesian:
atoms.set_positions(atoms_pos)
else:
atoms.set_scaled_positions(atoms_pos)
if selective_dynamics:
constraints = []
indices = []
for ind, sflags in enumerate(selective_flags):
if sflags.any() and not sflags.all():
constraints.append(FixScaled(atoms.get_cell(), ind, sflags))
elif sflags.all():
indices.append(ind)
if indices:
constraints.append(FixAtoms(indices))
if constraints:
atoms.set_constraint(constraints)
return atoms
