import numpy as np
import ase
from ase.data import chemical_symbols
from ase.utils import reader, writer
cfg_default_fields = np.array(['positions', 'momenta', 'numbers', 'magmoms'])
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@writer
def write_cfg(fd, atoms):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
fd.write('Number of particles = %i\n' % len(atoms))
fd.write('A = 1.0 Angstrom\n')
cell = atoms.get_cell(complete=True)
for i in range(3):
for j in range(3):
fd.write('H0(%1.1i,%1.1i) = %f A\n' % (i + 1, j + 1, cell[i, j]))
entry_count = 3
for x in atoms.arrays.keys():
if x not in cfg_default_fields:
if len(atoms.get_array(x).shape) == 1:
entry_count += 1
else:
entry_count += atoms.get_array(x).shape[1]
vels = atoms.get_velocities()
if isinstance(vels, np.ndarray):
entry_count += 3
else:
fd.write('.NO_VELOCITY.\n')
fd.write('entry_count = %i\n' % entry_count)
i = 0
for name, aux in atoms.arrays.items():
if name not in cfg_default_fields:
if len(aux.shape) == 1:
fd.write('auxiliary[%i] = %s [a.u.]\n' % (i, name))
i += 1
else:
if aux.shape[1] == 3:
for j in range(3):
fd.write('auxiliary[%i] = %s_%s [a.u.]\n' %
(i, name, chr(ord('x') + j)))
i += 1
else:
for j in range(aux.shape[1]):
fd.write('auxiliary[%i] = %s_%1.1i [a.u.]\n' %
(i, name, j))
i += 1
# Distinct elements
spos = atoms.get_scaled_positions()
for i in atoms:
el = i.symbol
fd.write('%f\n' % ase.data.atomic_masses[chemical_symbols.index(el)])
fd.write(f'{el}\n')
x, y, z = spos[i.index, :]
s = f'{x:e} {y:e} {z:e} '
if isinstance(vels, np.ndarray):
vx, vy, vz = vels[i.index, :]
s = s + f' {vx:e} {vy:e} {vz:e} '
for name, aux in atoms.arrays.items():
if name not in cfg_default_fields:
if len(aux.shape) == 1:
s += ' %e' % aux[i.index]
else:
s += (aux.shape[1] * ' %e') % tuple(aux[i.index].tolist())
fd.write(f'{s}\n')
default_color = {
'H': [0.800, 0.800, 0.800],
'C': [0.350, 0.350, 0.350],
'O': [0.800, 0.200, 0.200]}
default_radius = {'H': 0.435, 'C': 0.655, 'O': 0.730}
def write_clr(fd, atoms):
"""Write extra color and radius code to a CLR-file (for use with AtomEye).
Hit F12 in AtomEye to use.
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
color = None
radius = None
if atoms.has('color'):
color = atoms.get_array('color')
if atoms.has('radius'):
radius = atoms.get_array('radius')
if color is None:
color = np.zeros([len(atoms), 3], dtype=float)
for a in atoms:
color[a.index, :] = default_color[a.symbol]
if radius is None:
radius = np.zeros(len(atoms), dtype=float)
for a in atoms:
radius[a.index] = default_radius[a.symbol]
radius.shape = (-1, 1)
for c1, c2, c3, r in np.append(color, radius, axis=1):
fd.write(f'{c1:f} {c2:f} {c3:f} {r:f}\n')
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@reader
def read_cfg(fd):
"""Read atomic configuration from a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
nat = None
naux = 0
aux = None
auxstrs = None
cell = np.zeros([3, 3])
transform = np.eye(3)
eta = np.zeros([3, 3])
current_atom = 0
current_symbol = None
current_mass = None
L = fd.readline()
while L:
L = L.strip()
if len(L) != 0 and not L.startswith('#'):
if L == '.NO_VELOCITY.':
vels = None
naux += 3
else:
s = L.split('=')
if len(s) == 2:
key, value = s
key = key.strip()
value = [x.strip() for x in value.split()]
if key == 'Number of particles':
nat = int(value[0])
spos = np.zeros([nat, 3])
masses = np.zeros(nat)
syms = [''] * nat
vels = np.zeros([nat, 3])
if naux > 0:
aux = np.zeros([nat, naux])
elif key == 'A':
pass # unit = float(value[0])
elif key == 'entry_count':
naux += int(value[0]) - 6
auxstrs = [''] * naux
if nat is not None:
aux = np.zeros([nat, naux])
elif key.startswith('H0('):
i, j = (int(x) for x in key[3:-1].split(','))
cell[i - 1, j - 1] = float(value[0])
elif key.startswith('Transform('):
i, j = (int(x) for x in key[10:-1].split(','))
transform[i - 1, j - 1] = float(value[0])
elif key.startswith('eta('):
i, j = (int(x) for x in key[4:-1].split(','))
eta[i - 1, j - 1] = float(value[0])
elif key.startswith('auxiliary['):
i = int(key[10:-1])
auxstrs[i] = value[0]
else:
# Everything else must be particle data.
# First check if current line contains an element mass or
# name. Then we have an extended XYZ format.
s = [x.strip() for x in L.split()]
if len(s) == 1:
if L in chemical_symbols:
current_symbol = L
else:
current_mass = float(L)
elif current_symbol is None and current_mass is None:
# Standard CFG format
masses[current_atom] = float(s[0])
syms[current_atom] = s[1]
spos[current_atom, :] = [float(x) for x in s[2:5]]
vels[current_atom, :] = [float(x) for x in s[5:8]]
current_atom += 1
elif (current_symbol is not None and
current_mass is not None):
# Extended CFG format
masses[current_atom] = current_mass
syms[current_atom] = current_symbol
props = [float(x) for x in s]
spos[current_atom, :] = props[0:3]
off = 3
if vels is not None:
off = 6
vels[current_atom, :] = props[3:6]
aux[current_atom, :] = props[off:]
current_atom += 1
L = fd.readline()
# Sanity check
if current_atom != nat:
raise RuntimeError('Number of atoms reported for CFG file (={}) and '
'number of atoms actually read (={}) differ.'
.format(nat, current_atom))
if np.any(eta != 0):
raise NotImplementedError('eta != 0 not yet implemented for CFG '
'reader.')
cell = np.dot(cell, transform)
if vels is None:
a = ase.Atoms(
symbols=syms,
masses=masses,
scaled_positions=spos,
cell=cell,
pbc=True)
else:
a = ase.Atoms(
symbols=syms,
masses=masses,
scaled_positions=spos,
momenta=masses.reshape(-1, 1) * vels,
cell=cell,
pbc=True)
i = 0
while i < naux:
auxstr = auxstrs[i]
if auxstr[-2:] == '_x':
a.set_array(auxstr[:-2], aux[:, i:i + 3])
i += 3
else:
a.set_array(auxstr, aux[:, i])
i += 1
return a