/usr/share/pyshared/ase/io/dftb.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 | from ase.atoms import Atoms
def read_dftb(filename='dftb_in.hsd'):
"""Method to read coordinates form DFTB+ input file dftb_in.hsd
additionally read information about fixed atoms
and periodic boundary condition
"""
from ase import Atoms
if isinstance(filename, str):
myfile = open(filename)
lines = myfile.readlines()
atoms_pos = []
atom_symbols = []
type_names = []
my_pbc = False
mycell = []
for iline, line in enumerate(lines):
if (line.strip().startswith('#')):
pass
else:
if ('TypeNames' in line):
col = line.split()
for i in range(3, len(col)-1):
type_names.append(col[i].strip("\""))
elif ('Periodic' in line):
if ('Yes' in line):
my_pbc = True
elif ('LatticeVectors' in line):
for imycell in range(3):
extraline = lines[iline+imycell+1]
cols = extraline.split()
mycell.append(\
[float(cols[0]),float(cols[1]),float(cols[2])])
else:
pass
start_reading_coords = False
stop_reading_coords = False
for line in lines:
if (line.strip().startswith('#')):
pass
else:
if ('TypesAndCoordinates' in line):
start_reading_coords = True
if start_reading_coords:
if ('}' in line):
stop_reading_coords = True
if (start_reading_coords and not(stop_reading_coords)
and not 'TypesAndCoordinates' in line):
typeindexstr, xxx, yyy, zzz = line.split()[:4]
typeindex = int(typeindexstr)
symbol = type_names[typeindex-1]
atom_symbols.append(symbol)
atoms_pos.append([float(xxx), float(yyy), float(zzz)])
if type(filename) == str:
myfile.close()
atoms = Atoms(positions = atoms_pos, symbols = atom_symbols,
cell = mycell, pbc = my_pbc)
return atoms
def write_dftb(filename, atoms):
"""Method to write atom structure in DFTB+ format
(gen format)
"""
import numpy as np
#sort
atoms.set_masses()
masses = atoms.get_masses()
indexes = np.argsort(masses)
atomsnew = Atoms()
for i in indexes:
atomsnew = atomsnew + atoms[i]
if isinstance(filename, str):
myfile = open(filename, 'w')
else: # Assume it's a 'file-like object'
myfile = filename
ispbc = atoms.get_pbc()
box = atoms.get_cell()
if (any(ispbc)):
myfile.write('%8d %2s \n' %(len(atoms), 'S'))
else:
myfile.write('%8d %2s \n' %(len(atoms), 'C'))
chemsym = atomsnew.get_chemical_symbols()
allchem = ''
for i in chemsym:
if i not in allchem:
allchem = allchem + i + ' '
myfile.write(allchem+' \n')
coords = atomsnew.get_positions()
itype = 1
for iatom, coord in enumerate(coords):
if iatom > 0:
if chemsym[iatom] != chemsym[iatom-1]:
itype = itype+1
myfile.write('%5i%5i %19.16f %19.16f %19.16f \n' \
%(iatom+1, itype,
coords[iatom][0], coords[iatom][1], coords[iatom][2]))
# write box
if (any(ispbc)):
#dftb dummy
myfile.write(' %19.16f %19.16f %19.16f \n' %(0, 0, 0))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[0][0], box[0][1], box[0][2]))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[1][0], box[1][1], box[1][2]))
myfile.write(' %19.16f %19.16f %19.16f \n'
%( box[2][0], box[2][1], box[2][2]))
if type(filename) == str:
myfile.close()
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