/usr/share/pyshared/ase/io/lammps.py is in python-ase 3.6.0.2515-1.1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 | from ase.atoms import Atoms
from ase.quaternions import Quaternions
from ase.parallel import paropen
def read_lammps_dump(fileobj, index=-1):
"""Method which reads a LAMMPS dump file."""
if isinstance(fileobj, str):
f = paropen(fileobj)
else:
f = fileobj
# load everything into memory
lines = f.readlines()
natoms = 0
images = []
while len(lines) > natoms:
line = lines.pop(0)
if 'ITEM: TIMESTEP' in line:
n_atoms = 0
lo = [] ; hi = [] ; tilt = []
id = [] ; type = []
positions = []
velocities = []
forces = []
quaternions = []
if 'ITEM: NUMBER OF ATOMS' in line:
line = lines.pop(0)
natoms = int(line.split()[0])
if 'ITEM: BOX BOUNDS' in line:
# save labels behind "ITEM: BOX BOUNDS" in triclinic case (>=lammps-7Jul09)
tilt_items = line.split()[3:]
for i in range(3):
line = lines.pop(0)
fields = line.split()
lo.append(float(fields[0]))
hi.append(float(fields[1]))
if (len(fields) >= 3):
tilt.append(float(fields[2]))
# determine cell tilt (triclinic case!)
if (len(tilt) >= 3):
# for >=lammps-7Jul09 use labels behind "ITEM: BOX BOUNDS" to assign tilt (vector) elements ...
if (len(tilt_items) >= 3):
xy = tilt[tilt_items.index('xy')]
xz = tilt[tilt_items.index('xz')]
yz = tilt[tilt_items.index('yz')]
# ... otherwise assume default order in 3rd column (if the latter was present)
else:
xy = tilt[0]
xz = tilt[1]
yz = tilt[2]
else:
xy = xz = yz = 0
xhilo = (hi[0] - lo[0]) - xy - xz
yhilo = (hi[1] - lo[1]) - yz
zhilo = (hi[2] - lo[2])
cell = [[xhilo,0,0],[xy,yhilo,0],[xz,yz,zhilo]]
def add_quantity(fields, var, labels):
for label in labels:
if label not in atom_attributes:
return
var.append([float(fields[atom_attributes[label]])
for label in labels])
if 'ITEM: ATOMS' in line:
# (reliably) identify values by labels behind "ITEM: ATOMS" - requires >=lammps-7Jul09
# create corresponding index dictionary before iterating over atoms to (hopefully) speed up lookups...
atom_attributes = {}
for (i, x) in enumerate(line.split()[2:]):
atom_attributes[x] = i
for n in range(natoms):
line = lines.pop(0)
fields = line.split()
id.append( int(fields[atom_attributes['id']]) )
type.append( int(fields[atom_attributes['type']]) )
add_quantity(fields, positions, ['x', 'y', 'z'])
add_quantity(fields, velocities, ['vx', 'vy', 'vz'])
add_quantity(fields, forces, ['fx', 'fy', 'fz'])
add_quantity(fields, quaternions, ['c_q[1]', 'c_q[2]',
'c_q[3]', 'c_q[4]'])
if len(quaternions):
images.append(Quaternions(symbols=type,
positions=positions,
cell=cell,
quaternions=quaternions))
else:
images.append(Atoms(symbols=type,
positions=positions,
cell=cell))
return images[index]
|