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from __future__ import print_function
""" read and write gromacs geometry files
"""
from ase.atoms import Atoms
from ase.parallel import paropen
def read_gromacs(filename):
""" From:
http://manual.gromacs.org/current/online/gro.html
C format
"%5d%5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f"
python: starting from 0, including first excluding last
0:4 5:10 10:15 15:20 20:28 28:36 36:44 44:52 52:60 60:68
Import gromacs geometry type files (.gro).
Reads atom positions,
velocities(if present) and
simulation cell (if present)
"""
from ase.data import chemical_symbols
from ase import units
atoms = Atoms()
filed = open(filename, 'r')
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
gromacs_residuenames = []
gromacs_atomtypes = []
for line in (lines[2:-1]):
#print line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20]
inp = line.split()
floatvect = float(line[20:28]) * 10.0, \
float(line[28:36]) * 10.0, \
float(line[36:44]) * 10.0
positions.append(floatvect)
try:
#velocities from nm/ps to ase units
floatvect = \
float(line[44:52]) * units.nm / (1000.0 * units.fs), \
float(line[52:60]) * units.nm / (1000.0 * units.fs), \
float(line[60:68]) * units.nm / (1000.0 * units.fs)
except:
floatvect = 0.0, 0.0, 0.0
gromacs_velocities.append(floatvect)
symbols.append(inp[1][0:2])
gromacs_residuenames.append(inp[0])
gromacs_atomtypes.append(inp[1])
line = lines[-1]
symbols_ok = []
for isymbol in symbols:
if isymbol in chemical_symbols:
#ok atom name
symbols_ok.append(isymbol)
else:
#not ok atom name
symbols_ok.append(isymbol[0])
atoms = Atoms(symbols_ok, positions)
atoms.set_velocities(gromacs_velocities)
if not atoms.has('residuenames'):
atoms.new_array('residuenames', gromacs_residuenames, str)
atoms.set_array('residuenames', gromacs_residuenames, str)
if not atoms.has('atomtypes'):
atoms.new_array('atomtypes', gromacs_atomtypes, str)
atoms.set_array('atomtypes', gromacs_atomtypes, str)
try:
line = lines[-1]
inp = line.split()
floatvect0 = \
float(inp[0]) * 10.0, \
float(inp[1]) * 10.0, \
float(inp[2]) * 10.0
try:
floatvect1 = \
float(inp[3]) * 10.0, \
float(inp[4]) * 10.0, \
float(inp[5]) * 10.0
floatvect2 = \
float(inp[6]) * 10.0, \
float(inp[7]) * 10.0, \
float(inp[8]) * 10.0
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
#
#v1(x) v2(y) v3(z) fv0[0 1 2] v1(x) v2(x) v3(x)
#v1(y) v1(z) v2(x) fv1[0 1 2] v1(y) v2(y) v3(y)
#v2(z) v3(x) v3(y) fv2[0 1 2] v1(z) v2(z) v3(z)
mycell += [[floatvect0[0], floatvect1[2], floatvect2[1]]]
mycell += [[floatvect1[0], floatvect0[1], floatvect2[2]]]
mycell += [[floatvect1[1], floatvect2[0], floatvect0[2]]]
atoms.set_cell(mycell)
atoms.set_pbc(True)
except:
mycell = []
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
mycell += [[floatvect0[0], 0.0, 0.0]]
mycell += [[ 0.0, floatvect0[1], 0.0]]
mycell += [[ 0.0, 0.0, floatvect0[2]]]
atoms.set_cell(floatvect0)
atoms.set_pbc(True)
except:
atoms.set_pbc(False)
return atoms
def write_gromacs(fileobj, images):
"""Write gromacs geometry files (\*.gro).
Writes:
atom positions,
velocities (if present, otherwise 0)
and simulation cell (if present)
"""
from ase import units
if isinstance(fileobj, str):
fileobj = paropen(fileobj, 'w')
if not isinstance(images, (list, tuple)):
images = [images]
natoms = len(images[-1])
try:
gromacs_residuenames = images[-1].get_array('residuenames')
except:
gromacs_residuenames = []
for idum in range(natoms):
gromacs_residuenames.append('1DUM')
try:
gromacs_atomtypes = images[-1].get_array('atomtypes')
except:
gromacs_atomtypes = images[-1].get_chemical_symbols()
pos = images[-1].get_positions()
pos = pos / 10.0
try:
vel = images[-1].get_velocities()
vel = vel * 1000.0 * units.fs / units.nm
except:
vel = pos
vel = pos * 0.0
fileobj.write('#A Gromacs structure file written by ASE \n')
fileobj.write('%5d \n' % len(images[-1]))
count = 1
for resname, atomtype, xyz, vxyz in zip\
(gromacs_residuenames, gromacs_atomtypes, pos, vel):
fileobj.write(\
' %5s %5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f\n' % \
(resname, atomtype, count, \
xyz[0], xyz[1], xyz[2], \
vxyz[0], vxyz[1], vxyz[2]))
count = count + 1
if images[-1].get_pbc().any():
mycell = images[-1].get_cell()
#gromacs manual (manual.gromacs.org/online/gro.html) says:
#v1(x) v2(y) v3(z) v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)
#
#cell[0,0] cell[1,0] cell[2,0] v1(x) v2(y) v3(z) fv0[0 1 2]
#cell[0,1] cell[1,1] cell[2,1] v1(y) v1(z) v2(x) fv1[0 1 2]
#cell[0,2] cell[1,2] cell[2,2] v2(z) v3(x) v3(y) fv2[0 1 2]
fileobj.write('%10.5f%10.5f%10.5f' \
% (mycell[0, 0] * 0.1, \
mycell[1, 1] * 0.1, \
mycell[2, 2] * 0.1))
fileobj.write('%10.5f%10.5f%10.5f' \
% (mycell[1, 0] * 0.1, \
mycell[2, 0] * 0.1, \
mycell[0, 1] * 0.1))
fileobj.write('%10.5f%10.5f%10.5f\n' \
% (mycell[2, 1] * 0.1, \
mycell[0, 2] * 0.1, \
mycell[1, 2] * 0.1))
return
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