Source code for MDAnalysis.topology.LAMMPSParser

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# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787


Parses data_ or dump_ files produced by LAMMPS_.

.. _data: DATA file format: :
.. _dump:

.. versionchanged:: 1.0.0
   Deprecated :class:`LAMMPSDataConverter` has now been removed.

.. _atom_style_kwarg:

Atom styles

By default parsers and readers for Lammps data files expect either an
*atomic* or *full* `atom_style`_.  This can be customised by passing
the `atom_style` keyword argument.  This should be a space separated
string indicating the position of the `id`, `type`, `resid`, `charge`,
`x`, `y` and `z` fields.  The `resid` and `charge` fields are optional
and any other specified field will be ignored.

For example to read a file with the following format, where there is no resid::

  Atoms # atomic

  1 1 3.7151744275286681e+01 1.8684434743140471e+01 1.9285127961842125e+01 0 0 0

The following code could be used::

  >>> import MDAnalysis as mda
  >>> u = mda.Universe('', atom_style='id type x y z')

.. _`atom_style`:


.. autoclass:: DATAParser

.. autoclass:: LammpsDumpParser

from __future__ import absolute_import, print_function

from six.moves import range
from six import raise_from

import numpy as np
import logging
import string
import functools
import warnings

from . import guessers
from ..lib.util import openany, conv_float
from ..lib.mdamath import triclinic_box
from .base import TopologyReaderBase, squash_by
from ..core.topology import Topology
from ..core.topologyattrs import (

logger = logging.getLogger("MDAnalysis.topology.LAMMPS")

# Sections will all start with one of these words
# and run until the next section title
SECTIONS = set([
    'Atoms',  # Molecular topology sections
    'Bonds',  # Forcefield sections
    'Pair LJCoeffs',
    'Bond Coeffs',
    'Angle Coeffs',
    'Dihedral Coeffs',
    'Improper Coeffs',
    'BondBond Coeffs',  # Class 2 FF sections
    'BondAngle Coeffs',
    'MiddleBondTorsion Coeffs',
    'EndBondTorsion Coeffs',
    'AngleTorsion Coeffs',
    'AngleAngleTorsion Coeffs',
    'BondBond13 Coeffs',
    'AngleAngle Coeffs',
# We usually check by splitting around whitespace, so check
# if any SECTION keywords will trip up on this
# and add them
for val in list(SECTIONS):
    if len(val.split()) > 1:

HEADERS = set([
    'atom types',
    'bond types',
    'angle types',
    'dihedral types',
    'improper types',
    'extra bond per atom',
    'extra angle per atom',
    'extra dihedral per atom',
    'extra improper per atom',
    'extra special per atom',
    'xlo xhi',
    'ylo yhi',
    'zlo zhi',
    'xy xz yz',

[docs]class DATAParser(TopologyReaderBase): """Parse a LAMMPS DATA file for topology and coordinates. Note that LAMMPS DATA files can be used standalone. Both topology and coordinate parsing functionality is kept in this class as the topology and coordinate reader share many common functions By default the parser expects either *atomic* or *full* `atom_style` however this can be by passing an `atom_style` keyword argument, see :ref:`atom_style_kwarg`. .. versionadded:: 0.9.0 """ format = 'DATA' def iterdata(self): with openany(self.filename) as f: for line in f: line = line.partition('#')[0].strip() if line: yield line
[docs] def grab_datafile(self): """Split a data file into dict of header and sections Returns ------- header - dict of header section: value sections - dict of section name: content """ f = list(self.iterdata()) starts = [i for i, line in enumerate(f) if line.split()[0] in SECTIONS] starts += [None] header = {} for line in f[:starts[0]]: for token in HEADERS: if line.endswith(token): header[token] = line.split(token)[0] continue sects = {f[l]:f[l+1:starts[i+1]] for i, l in enumerate(starts[:-1])} return header, sects
@staticmethod def _interpret_atom_style(atom_style): """Transform a string description of atom style into a dict Required fields: id, type, x, y, z Optional fields: resid, charge eg: "id resid type charge x y z" {'id': 0, 'resid': 1, 'type': 2, 'charge': 3, 'x': 4, 'y': 5, 'z': 6, } """ style_dict = {} atom_style = atom_style.split() for attr in ['id', 'type', 'resid', 'charge', 'x', 'y', 'z']: try: location = atom_style.index(attr) except ValueError: pass else: style_dict[attr] = location reqd_attrs = ['id', 'type', 'x', 'y', 'z'] missing_attrs = [attr for attr in reqd_attrs if attr not in style_dict] if missing_attrs: raise ValueError("atom_style string missing required field(s): {}" "".format(', '.join(missing_attrs))) return style_dict
[docs] def parse(self, **kwargs): """Parses a LAMMPS_ DATA file. Returns ------- MDAnalysis Topology object. """ # Can pass atom_style to help parsing try: self.style_dict = self._interpret_atom_style(kwargs['atom_style']) except KeyError: self.style_dict = None head, sects = self.grab_datafile() try: masses = self._parse_masses(sects['Masses']) except KeyError: masses = None if 'Atoms' not in sects: raise ValueError("Data file was missing Atoms section") try: top = self._parse_atoms(sects['Atoms'], masses) except Exception: raise_from(ValueError( "Failed to parse atoms section. You can supply a description " "of the atom_style as a keyword argument, " "eg mda.Universe(..., atom_style='id resid x y z')" ), None) # create mapping of id to index (ie atom id 10 might be the 0th atom) mapping = {atom_id: i for i, atom_id in enumerate(top.ids.values)} for attr, L, nentries in [ (Bonds, 'Bonds', 2), (Angles, 'Angles', 3), (Dihedrals, 'Dihedrals', 4), (Impropers, 'Impropers', 4) ]: try: type, sect = self._parse_bond_section(sects[L], nentries, mapping) except KeyError: type, sect = [], [] top.add_TopologyAttr(attr(sect, type)) return top
[docs] def read_DATA_timestep(self, n_atoms, TS_class, TS_kwargs, atom_style=None): """Read a DATA file and try and extract x, v, box. - positions - velocities (optional) - box information Fills this into the Timestep object and returns it .. versionadded:: 0.9.0 .. versionchanged:: 0.18.0 Added atom_style kwarg """ if atom_style is None: self.style_dict = None else: self.style_dict = self._interpret_atom_style(atom_style) header, sects = self.grab_datafile() unitcell = self._parse_box(header) try: positions, ordering = self._parse_pos(sects['Atoms']) except KeyError as err: raise_from( IOError("Position information not found: {}".format(err)), None) if 'Velocities' in sects: velocities = self._parse_vel(sects['Velocities'], ordering) else: velocities = None ts = TS_class.from_coordinates(positions, velocities=velocities, **TS_kwargs) ts.dimensions = unitcell return ts
def _parse_pos(self, datalines): """Strip coordinate info into np array""" pos = np.zeros((len(datalines), 3), dtype=np.float32) # TODO: could maybe store this from topology parsing? # Or try to reach into Universe? # but ugly because assumes lots of things, and Reader should be standalone ids = np.zeros(len(pos), dtype=np.int32) if self.style_dict is None: if len(datalines[0].split()) in (7, 10): style_dict = {'id': 0, 'x': 4, 'y': 5, 'z': 6} else: style_dict = {'id': 0, 'x': 3, 'y': 4, 'z': 5} else: style_dict = self.style_dict for i, line in enumerate(datalines): line = line.split() ids[i] = line[style_dict['id']] pos[i, :] = [line[style_dict['x']], line[style_dict['y']], line[style_dict['z']]] order = np.argsort(ids) pos = pos[order] # return order for velocities return pos, order def _parse_vel(self, datalines, order): """Strip velocity info into np array Parameters ---------- datalines : list list of strings from file order : np.array array which rearranges the velocities into correct order (from argsort on atom ids) Returns ------- velocities : np.ndarray """ vel = np.zeros((len(datalines), 3), dtype=np.float32) for i, line in enumerate(datalines): line = line.split() vel[i] = line[1:4] vel = vel[order] return vel def _parse_bond_section(self, datalines, nentries, mapping): """Read lines and strip information Arguments --------- datalines : list the raw lines from the data file nentries : int number of integers per line mapping : dict converts atom_ids to index within topology Returns ------- types : tuple of strings type of the bond/angle/dihedral/improper indices : tuple of ints indices of atoms involved """ section = [] type = [] for line in datalines: line = line.split() # map to 0 based int section.append(tuple([mapping[int(x)] for x in line[2:2 + nentries]])) type.append(line[1]) return tuple(type), tuple(section) def _parse_atoms(self, datalines, massdict=None): """Creates a Topology object Adds the following attributes - resid - type - masses (optional) - charge (optional) Lammps atoms can have lots of different formats, and even custom formats Treated here are - atoms with 7 fields (with charge) "full" - atoms with 6 fields (no charge) "molecular" Arguments --------- datalines - the relevent lines from the data file massdict - dictionary relating type to mass Returns ------- top - Topology object """"Doing Atoms section") n_atoms = len(datalines) if self.style_dict is None: sd = {'id': 0, 'resid': 1, 'type': 2} # Fields per line n = len(datalines[0].split()) if n in (7, 10): sd['charge'] = 3 else: sd = self.style_dict has_charge = 'charge' in sd has_resid = 'resid' in sd # atom ids aren't necessarily sequential atom_ids = np.zeros(n_atoms, dtype=np.int32) types = np.zeros(n_atoms, dtype=object) if has_resid: resids = np.zeros(n_atoms, dtype=np.int32) else: resids = np.ones(n_atoms, dtype=np.int32) if has_charge: charges = np.zeros(n_atoms, dtype=np.float32) for i, line in enumerate(datalines): line = line.split() # these numpy array are already typed correctly, # so just pass the raw strings # and let numpy handle the conversion atom_ids[i] = line[sd['id']] if has_resid: resids[i] = line[sd['resid']] types[i] = line[sd['type']] if has_charge: charges[i] = line[sd['charge']] # at this point, we've read the atoms section, # but it's still (potentially) unordered # TODO: Maybe we can optimise by checking if we need to sort # ie `if np.any(np.diff(atom_ids) > 1)` but we want to search # in a generatorish way, np.any() would check everything at once order = np.argsort(atom_ids) atom_ids = atom_ids[order] types = types[order] if has_resid: resids = resids[order] if has_charge: charges = charges[order] attrs = [] attrs.append(Atomtypes(types)) if has_charge: attrs.append(Charges(charges)) if massdict is not None: masses = np.zeros(n_atoms, dtype=np.float64) for i, at in enumerate(types): masses[i] = massdict[at] attrs.append(Masses(masses)) else: # Guess them masses = guessers.guess_masses(types) attrs.append(Masses(masses, guessed=True)) residx, resids = squash_by(resids)[:2] n_residues = len(resids) attrs.append(Atomids(atom_ids)) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) attrs.append(Segids(np.array(['SYSTEM'], dtype=object))) top = Topology(n_atoms, n_residues, 1, attrs=attrs, atom_resindex=residx) return top def _parse_masses(self, datalines): """Lammps defines mass on a per atom type basis. This reads mass for each type and stores in dict """"Doing Masses section") masses = {} for line in datalines: line = line.split() masses[line[0]] = float(line[1]) return masses def _parse_box(self, header): x1, x2 = np.float32(header['xlo xhi'].split()) x = x2 - x1 y1, y2 = np.float32(header['ylo yhi'].split()) y = y2 - y1 z1, z2 = np.float32(header['zlo zhi'].split()) z = z2 - z1 if 'xy xz yz' in header: # Triclinic unitcell = np.zeros((3, 3), dtype=np.float32) xy, xz, yz = np.float32(header['xy xz yz'].split()) unitcell[0][0] = x unitcell[1][0] = xy unitcell[1][1] = y unitcell[2][0] = xz unitcell[2][1] = yz unitcell[2][2] = z unitcell = triclinic_box(*unitcell) else: # Orthogonal unitcell = np.zeros(6, dtype=np.float32) unitcell[:3] = x, y, z unitcell[3:] = 90., 90., 90. return unitcell
[docs]class LammpsDumpParser(TopologyReaderBase): """Parses Lammps ascii dump files in 'atom' format Only reads atom ids. Sets all masses to 1.0. .. versionadded:: 0.19.0 """ format = 'LAMMPSDUMP' def parse(self, **kwargs): with openany(self.filename) as fin: fin.readline() # ITEM TIMESTEP fin.readline() # 0 fin.readline() # ITEM NUMBER OF ATOMS natoms = int(fin.readline()) fin.readline() # ITEM BOX fin.readline() # x fin.readline() # y fin.readline() # z indices = np.zeros(natoms, dtype=int) types = np.zeros(natoms, dtype=object) fin.readline() # ITEM ATOMS for i in range(natoms): idx, atype, _, _, _ = fin.readline().split() indices[i] = idx types[i] = atype order = np.argsort(indices) indices = indices[order] types = types[order] attrs = [] attrs.append(Atomids(indices)) attrs.append(Atomtypes(types)) attrs.append(Masses(np.ones(natoms, dtype=np.float64), guessed=True)) warnings.warn('Guessed all Masses to 1.0') attrs.append(Resids(np.array([1], dtype=int))) attrs.append(Resnums(np.array([1], dtype=int))) attrs.append(Segids(np.array(['SYSTEM'], dtype=object))) return Topology(natoms, 1, 1, attrs=attrs)
@functools.total_ordering class LAMMPSAtom(object): # pragma: no cover __slots__ = ("index", "name", "type", "chainid", "charge", "mass", "_positions") def __init__(self, index, name, type, chain_id, charge=0, mass=1): self.index = index = repr(type) self.type = type self.chainid = chain_id self.charge = charge self.mass = mass def __repr__(self): return "<LAMMPSAtom " + repr(self.index + 1) + ": name " + repr(self.type) + " of chain " + repr( self.chainid) + ">" def __lt__(self, other): return self.index < other.index def __eq__(self, other): return self.index == other.index def __hash__(self): return hash(self.index) def __getattr__(self, attr): if attr == 'pos': return self._positions[self.index] else: super(LAMMPSAtom, self).__getattribute__(attr) def __iter__(self): pos = self.pos return iter((self.index + 1, self.chainid, self.type, self.charge, self.mass, pos[0], pos[1], pos[2]))