"""
read and write gromacs geometry files
"""
from ase.atoms import Atoms
from ase.parallel import paropen
from ase.utils import basestring
import numpy as np
from ase.data import atomic_numbers
from ase import units
[docs]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)
"""
atoms = Atoms()
filed = open(filename, 'r')
lines = filed.readlines()
filed.close()
positions = []
gromacs_velocities = []
symbols = []
tags = []
gromacs_residuenumbers = []
gromacs_residuenames = []
gromacs_atomtypes = []
sym2tag = {}
tag = 0
for line in (lines[2:-1]):
#print line[0:5]+':'+line[5:11]+':'+line[11:15]+':'+line[15:20]
# it is not a good idea to use the split method with gromacs input
# since the fields are defined by a fixed column number. Therefore,
# they may not be space between the fields
#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)
# read velocities
velocities = np.array([0.0, 0.0, 0.0])
vx = line[44:52].strip()
vy = line[52:60].strip()
vz = line[60:68].strip()
for iv, vxyz in enumerate([vx, vy, vz]):
if len(vxyz) > 0:
try:
velocities[iv] = float(vxyz)
except ValueError:
raise ValueError("can not convert velocity to float")
else:
velocities = None
if velocities is not None:
# velocities from nm/ps to ase units
velocities *= units.nm / (1000.0 * units.fs)
gromacs_velocities.append(velocities)
gromacs_residuenumbers.append(int(line[0:5]))
gromacs_residuenames.append(line[5:11].strip())
symbol_read = line[11:16].strip()[0:2]
if symbol_read not in sym2tag.keys():
sym2tag[symbol_read] = tag
tag += 1
tags.append(sym2tag[symbol_read])
if symbol_read in atomic_numbers:
symbols.append(symbol_read)
elif symbol_read[0] in atomic_numbers:
symbols.append(symbol_read[0])
elif symbol_read[-1] in atomic_numbers:
symbols.append(symbol_read[-1])
else:
# not an atomic symbol
# if we can not determine the symbol, we use
# the dummy symbol X
symbols.append("X")
gromacs_atomtypes.append(line[11:16].strip())
line = lines[-1]
atoms = Atoms(symbols, positions, tags=tags)
if len(gromacs_velocities) == len(atoms):
atoms.set_velocities(gromacs_velocities)
elif len(gromacs_velocities) != 0:
raise ValueError("Some atoms velocities were not specified!")
if not atoms.has('residuenumbers'):
atoms.new_array('residuenumbers', gromacs_residuenumbers, int)
atoms.set_array('residuenumbers',gromacs_residuenumbers, int)
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
[docs]def write_gromacs(fileobj, images):
"""Write gromacs geometry files (.gro).
Writes:
* atom positions,
* velocities (if present, otherwise 0)
* simulation cell (if present)
"""
if isinstance(fileobj, basestring):
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()
try:
residuenumbers = images[-1].get_array('residuenumbers')
except (KeyError):
residuenumbers = np.ones(natoms, int)
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
# No "#" in the first line to prevent read error in VMD
fileobj.write('A Gromacs structure file written by ASE \n')
fileobj.write('%5d\n' % len(images[-1]))
count = 1
# gromac line see http://manual.gromacs.org/documentation/current/user-guide/file-formats.html#gro
# 1WATER OW1 1 0.126 1.624 1.679 0.1227 -0.0580 0.0434
for resnb, resname, atomtype, xyz, vxyz in zip\
(residuenumbers, gromacs_residuenames, gromacs_atomtypes, pos, vel):
# THIS SHOULD BE THE CORRECT, PYTHON FORMATTING, EQUIVALENT TO THE
# C FORMATTING GIVEN IN THE GROMACS DOCUMENTATION:
# >>> %5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f <<<
line = ("{0:>5d}{1:<5s}{2:>5s}{3:>5d}{4:>8.3f}{5:>8.3f}{6:>8.3f}"
"{7:>8.4f}{8:>8.4f}{9:>8.4f}\n"
.format(resnb, resname, atomtype, count,
xyz[0], xyz[1], xyz[2], vxyz[0], vxyz[1], vxyz[2]))
fileobj.write(line)
count += 1
# write box geometry
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))
else:
# When we do not have a cell, the cell is specified as an empty line
fileobj.write("\n")