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# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
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# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
"""
LAMMPSParser
============
Parses data_ or dump_ files produced by LAMMPS_.
.. note::
By default, masses will be guessed on Universe creation if they are not
read from the input file. This may change in release 3.0.
See :ref:`Guessers` for more information.
.. _LAMMPS: http://lammps.sandia.gov/
.. _data: DATA file format: :http://lammps.sandia.gov/doc/2001/data_format.html
.. _dump: http://lammps.sandia.gov/doc/dump.html
.. 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('myfile.data', atom_style='id type x y z')
.. _`atom_style`: http://lammps.sandia.gov/doc/atom_style.html
Classes
-------
.. autoclass:: DATAParser
:members:
:inherited-members:
.. autoclass:: LammpsDumpParser
:members:
"""
import numpy as np
import logging
import string
import functools
import warnings
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 (
Atomtypes,
Atomids,
Angles,
Bonds,
Charges,
Dihedrals,
Impropers,
Masses,
Resids,
Resnums,
Segids,
)
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
'Velocities',
'Masses',
'Ellipsoids',
'Lines',
'Triangles',
'Bodies',
'Bonds', # Forcefield sections
'Angles',
'Dihedrals',
'Impropers',
'Pair',
'Pair LJCoeffs',
'PairIJ Coeffs',
'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:
SECTIONS.add(val.split()[0])
HEADERS = set([
'atoms',
'bonds',
'angles',
'dihedrals',
'impropers',
'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',
'ellipsoids',
'lines',
'triangles',
'bodies',
'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
.. versionchanged:: 2.8.0
Removed mass guessing (attributes guessing takes place now
through universe.guess_TopologyAttrs() API).
"""
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:
errmsg = (
"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')")
raise ValueError(errmsg) from 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:
errmsg = f"Position information not found: {err}"
raise IOError(errmsg) from 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
http://lammps.sandia.gov/doc/atom_style.html
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
"""
logger.info("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))
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
"""
logger.info("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.
Sets all masses to 1.0.
.. versionchanged:: 2.0.0
.. 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)
atomline = fin.readline() # ITEM ATOMS
attrs = atomline.split()[2:] # attributes on coordinate line
col_ids = {attr: i for i, attr in enumerate(attrs)} # column ids
for i in range(natoms):
fields = fin.readline().split()
indices[i] = fields[col_ids["id"]]
types[i] = fields[col_ids["type"]]
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
self.name = 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]))