/usr/share/pyshared/ase/io/dacapo.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 | import numpy as np
from ase.calculators.singlepoint import SinglePointCalculator
from ase.atom import Atom
from ase.atoms import Atoms
def read_dacapo_text(fileobj):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
i = lines.index(' Structure: A1 A2 A3\n')
cell = np.array([[float(w) for w in line.split()[2:5]]
for line in lines[i + 1:i + 4]]).transpose()
i = lines.index(' Structure: >> Ionic positions/velocities ' +
'in cartesian coordinates <<\n')
atoms = []
for line in lines[i + 4:]:
words = line.split()
if len(words) != 9:
break
Z, x, y, z = words[2:6]
atoms.append(Atom(int(Z), [float(x), float(y), float(z)]))
atoms = Atoms(atoms, cell=cell.tolist())
try:
i = lines.index(
' DFT: CPU time Total energy\n')
except ValueError:
pass
else:
column = lines[i + 3].split().index('selfcons') - 1
try:
i2 = lines.index(' ANALYSIS PART OF CODE\n', i)
except ValueError:
pass
else:
while i2 > i:
if lines[i2].startswith(' DFT:'):
break
i2 -= 1
energy = float(lines[i2].split()[column])
atoms.set_calculator(SinglePointCalculator(energy, None, None,
None, atoms))
return atoms
def read_dacapo(filename):
from ase.io.pupynere import NetCDFFile
nc = NetCDFFile(filename)
dims = nc.dimensions
vars = nc.variables
cell = vars['UnitCell'][-1]
try:
magmoms = vars['InitialAtomicMagneticMoment'][:]
except KeyError:
magmoms = None
try:
tags = vars['AtomTags'][:]
except KeyError:
tags = None
atoms = Atoms(scaled_positions=vars['DynamicAtomPositions'][-1],
symbols=[(a + b).strip()
for a, b in vars['DynamicAtomSpecies'][:]],
cell=cell,
magmoms=magmoms,
tags=tags,
pbc=True)
try:
energy = vars['TotalEnergy'][-1]
force = vars['DynamicAtomForces'][-1]
except KeyError:
energy = None
force = None
calc = SinglePointCalculator(energy,force,None, None, atoms) ### Fixme magmoms
atoms.set_calculator(calc)
return atoms
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