def get_atoms():
atoms = Atoms([
Atom('Pd', [5.078689759346383, 5.410678028467162, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 4.000000000000000, 4.000000000000000]),
Atom('Pd', [7.522055777772603, 6.821356056934325, 4.000000000000000]),
Atom('Pd', [6.707600438297196, 5.410678028467162, 6.303627574066606]),
Atom('N', [4.807604264052752, 5.728625577716107, 5.919407072553396]),
Atom('H', [4.000000000000000, 5.965167390141987, 6.490469524180266]),
])
constraint = FixAtoms(mask=[a.symbol == 'Pd' for a in atoms])
atoms.set_constraint(constraint)
atoms.center(vacuum=4.0)
atoms.set_pbc(False)
return atoms
def read_aims(filename):
"""Import FHI-aims geometry type files.
Reads unitcell, atom positions and constraints from
a geometry.in file.
"""
from ase_ext import Atoms
from ase_ext.constraints import FixAtoms, FixCartesian
import numpy as np
atoms = Atoms()
fd = open(filename, 'r')
lines = fd.readlines()
fd.close()
positions = []
cell = []
symbols = []
fix = []
fix_cart = []
xyz = np.array([0, 0, 0])
i = -1
n_periodic = -1
periodic = np.array([False, False, False])
for n, line in enumerate(lines):
inp = line.split()
if inp == []:
continue
if inp[0] == 'atom':
if xyz.all():
fix.append(i)
elif xyz.any():
print(1)
fix_cart.append(FixCartesian(i, xyz))
floatvect = float(inp[1]), float(inp[2]), float(inp[3])
positions.append(floatvect)
symbols.append(inp[-1])
i += 1
xyz = np.array([0, 0, 0])
elif inp[0] == 'lattice_vector':
floatvect = float(inp[1]), float(inp[2]), float(inp[3])
cell.append(floatvect)
n_periodic = n_periodic + 1
periodic[n_periodic] = True
if inp[0] == 'constrain_relaxation':
if inp[1] == '.true.':
fix.append(i)
elif inp[1] == 'x':
xyz[0] = 1
elif inp[1] == 'y':
xyz[1] = 1
elif inp[1] == 'z':
xyz[2] = 1
if xyz.all():
fix.append(i)
elif xyz.any():
fix_cart.append(FixCartesian(i, xyz))
atoms = Atoms(symbols, positions)
if periodic.all():
atoms.set_cell(cell)
atoms.set_pbc(periodic)
if len(fix):
atoms.set_constraint([FixAtoms(indices=fix)] + fix_cart)
else:
atoms.set_constraint(fix_cart)
return atoms
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,
skin=0.0,
sorted=sorted)
nl.update(atoms)
d, c = count(nl, atoms)
atoms2 = atoms.repeat((p1 + 1, p2 + 1, p3 + 1))
nl2 = NeighborList(atoms2.numbers * 0.2 + 0.5,
skin=0.0,
sorted=sorted)
nl2.update(atoms2)
d2, c2 = count(nl2, atoms2)
c2.shape = (-1, 10)
dd = d * (p1 + 1) * (p2 + 1) * (p3 + 1) - d2
print(dd)
print(c2 - c)