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""" write gromos96 geometry files
(the exact file format is copied from the freely available
gromacs package, http://www.gromacs.org
its procedure src/gmxlib/confio.c (write_g96_conf)
"""
import numpy as np
from ase import Atoms
from ase.data import chemical_symbols
from ase.utils import reader, writer
@reader
def read_gromos(fileobj):
"""Read gromos geometry files (.g96).
Reads:
atom positions,
and simulation cell (if present)
tries to set atom types
"""
lines = fileobj.readlines()
read_pos = False
read_box = False
tmp_pos = []
symbols = []
mycell = None
for line in lines:
if (read_pos and ('END' in line)):
read_pos = False
if (read_box and ('END' in line)):
read_box = False
if read_pos:
symbol, dummy, x, y, z = line.split()[2:7]
tmp_pos.append((10 * float(x), 10 * float(y), 10 * float(z)))
if (len(symbol) != 2):
symbols.append(symbol[0].lower().capitalize())
else:
symbol2 = symbol[0].lower().capitalize() + \
symbol[1]
if symbol2 in chemical_symbols:
symbols.append(symbol2)
else:
symbols.append(symbol[0].lower().capitalize())
if symbols[-1] not in chemical_symbols:
raise RuntimeError("Symbol '{}' not in chemical symbols"
.format(symbols[-1]))
if read_box:
try:
grocell = list(map(float, line.split()))
except ValueError:
pass
else:
mycell = np.diag(grocell[:3])
if len(grocell) >= 9:
mycell.flat[[1, 2, 3, 5, 6, 7]] = grocell[3:9]
mycell *= 10.
if ('POSITION' in line):
read_pos = True
if ('BOX' in line):
read_box = True
gmx_system = Atoms(symbols=symbols, positions=tmp_pos, cell=mycell)
if mycell is not None:
gmx_system.pbc = True
return gmx_system
@writer
def write_gromos(fileobj, atoms):
"""Write gromos geometry files (.g96).
Writes:
atom positions,
and simulation cell (if present)
"""
from ase import units
natoms = len(atoms)
try:
gromos_residuenames = atoms.get_array('residuenames')
except KeyError:
gromos_residuenames = []
for idum in range(natoms):
gromos_residuenames.append('1DUM')
try:
gromos_atomtypes = atoms.get_array('atomtypes')
except KeyError:
gromos_atomtypes = atoms.get_chemical_symbols()
pos = atoms.get_positions()
pos = pos / 10.0
vel = atoms.get_velocities()
if vel is None:
vel = pos * 0.0
else:
vel *= 1000.0 * units.fs / units.nm
fileobj.write('TITLE\n')
fileobj.write('Gromos96 structure file written by ASE \n')
fileobj.write('END\n')
fileobj.write('POSITION\n')
count = 1
rescount = 0
oldresname = ''
for resname, atomtype, xyz in zip(gromos_residuenames,
gromos_atomtypes,
pos):
if resname != oldresname:
oldresname = resname
rescount = rescount + 1
okresname = resname.lstrip('0123456789 ')
fileobj.write('%5d %-5s %-5s%7d%15.9f%15.9f%15.9f\n' %
(rescount, okresname, atomtype, count,
xyz[0], xyz[1], xyz[2]))
count = count + 1
fileobj.write('END\n')
if atoms.get_pbc().any():
fileobj.write('BOX\n')
mycell = atoms.get_cell()
grocell = mycell.flat[[0, 4, 8, 1, 2, 3, 5, 6, 7]] * 0.1
fileobj.write(''.join(['{:15.9f}'.format(x) for x in grocell]))
fileobj.write('\nEND\n')
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