Source code for ase.io.gromos

""" 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


[docs]@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
[docs]@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')