pymatgen.io.lammps.data — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.lammps.data

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    This module implements a core class LammpsData for generating/parsing
    LAMMPS data file, and other bridging classes to build LammpsData from
    molecules. This module also implements a subclass CombinedData for
    merging LammpsData object.

    Only point particle styles are supported for now (atom_style in angle,
    atomic, bond, charge, full and molecular only). See the pages below for
    more info.

        http://lammps.sandia.gov/doc/atom_style.html
        http://lammps.sandia.gov/doc/read_data.html

    """

    from collections import OrderedDict
    from io import StringIO
    import itertools
    import re
    import warnings

    import numpy as np
    import pandas as pd
    from pathlib import Path
    from monty.json import MSONable
    from monty.dev import deprecated
    from monty.serialization import loadfn
    from ruamel.yaml import YAML

    from pymatgen.util.io_utils import clean_lines
    from pymatgen import Molecule, Element, Lattice, Structure, SymmOp

    __author__ = "Kiran Mathew, Zhi Deng, Tingzheng Hou"
    __copyright__ = "Copyright 2018, The Materials Virtual Lab"
    __version__ = "1.0"
    __maintainer__ = "Zhi Deng"
    __email__ = "z4deng@eng.ucsd.edu"
    __date__ = "Aug 1, 2018"

    MODULE_DIR = Path(__file__).resolve().parent

    SECTION_KEYWORDS = {"atom": ["Atoms", "Velocities", "Masses",
                                 "Ellipsoids", "Lines", "Triangles", "Bodies"],
                        "topology": ["Bonds", "Angles", "Dihedrals", "Impropers"],
                        "ff": ["Pair Coeffs", "PairIJ Coeffs", "Bond Coeffs",
                               "Angle Coeffs", "Dihedral Coeffs",
                               "Improper Coeffs"],
                        "class2": ["BondBond Coeffs", "BondAngle Coeffs",
                                   "MiddleBondTorsion Coeffs",
                                   "EndBondTorsion Coeffs", "AngleTorsion Coeffs",
                                   "AngleAngleTorsion Coeffs",
                                   "BondBond13 Coeffs", "AngleAngle Coeffs"]}

    CLASS2_KEYWORDS = {"Angle Coeffs": ["BondBond Coeffs", "BondAngle Coeffs"],
                       "Dihedral Coeffs": ["MiddleBondTorsion Coeffs",
                                           "EndBondTorsion Coeffs",
                                           "AngleTorsion Coeffs",
                                           "AngleAngleTorsion Coeffs",
                                           "BondBond13 Coeffs"],
                       "Improper Coeffs": ["AngleAngle Coeffs"]}

    SECTION_HEADERS = {"Masses": ["mass"],
                       "Velocities": ["vx", "vy", "vz"],
                       "Bonds": ["type", "atom1", "atom2"],
                       "Angles": ["type", "atom1", "atom2", "atom3"],
                       "Dihedrals": ["type", "atom1", "atom2", "atom3", "atom4"],
                       "Impropers": ["type", "atom1", "atom2", "atom3", "atom4"]}

    ATOMS_HEADERS = {"angle": ["molecule-ID", "type", "x", "y", "z"],
                     "atomic": ["type", "x", "y", "z"],
                     "bond": ["molecule-ID", "type", "x", "y", "z"],
                     "charge": ["type", "q", "x", "y", "z"],
                     "full": ["molecule-ID", "type", "q", "x", "y", "z"],
                     "molecular": ["molecule-ID", "type", "x", "y", "z"]}

    class LammpsBox(MSONable):
        """
        Object for representing a simulation box in LAMMPS settings.
        """

        def __init__(self, bounds, tilt=None):
            """

            Args:
                bounds: A (3, 2) array/list of floats setting the
                    boundaries of simulation box.
                tilt: A (3,) array/list of floats setting the tilt of
                    simulation box. Default to None, i.e., use an
                    orthogonal box.

            """
            bounds_arr = np.array(bounds)
            assert bounds_arr.shape == (3, 2), \
                "Expecting a (3, 2) array for bounds," \
                " got {}".format(bounds_arr.shape)
            self.bounds = bounds_arr.tolist()
            matrix = np.diag(bounds_arr[:, 1] - bounds_arr[:, 0])

            self.tilt = None
            if tilt is not None:
                tilt_arr = np.array(tilt)
                assert tilt_arr.shape == (3,), \
                    "Expecting a (3,) array for box_tilt," \
                    " got {}".format(tilt_arr.shape)
                self.tilt = tilt_arr.tolist()
                matrix[1, 0] = tilt_arr[0]
                matrix[2, 0] = tilt_arr[1]
                matrix[2, 1] = tilt_arr[2]
            self._matrix = matrix

        def __str__(self):
            return self.get_string()

        def __repr__(self):
            return self.get_string()

        @property
        def volume(self):
            """
            Volume of simulation box.

            """
            m = self._matrix
            return np.dot(np.cross(m[0], m[1]), m[2])

        def get_string(self, significant_figures=6):
            """
            Returns the string representation of simulation box in LAMMPS
            data file format.

            Args:
                significant_figures (int): No. of significant figures to
                    output for box settings. Default to 6.

            Returns:
                String representation

            """
            ph = "{:.%df}" % significant_figures
            lines = []
            for bound, d in zip(self.bounds, "xyz"):
                fillers = bound + [d] * 2
                bound_format = " ".join([ph] * 2 + [" {}lo {}hi"])
                lines.append(bound_format.format(*fillers))
            if self.tilt:
                tilt_format = " ".join([ph] * 3 + [" xy xz yz"])
                lines.append(tilt_format.format(*self.tilt))
            return "\n".join(lines)

        def get_box_shift(self, i):
            """
            Calculates the coordinate shift due to PBC.

            Args:
                i: A (n, 3) integer array containing the labels for box
                images of n entries.

            Returns:
                Coorindate shift array with the same shape of i

            """
            return np.inner(i, self._matrix.T)

        def to_lattice(self):
            """
            Converts the simulation box to a more powerful Lattice backend.
            Note that Lattice is always periodic in 3D space while a
            simulation box is not necessarily periodic in all dimensions.

            Returns:
                Lattice

            """
            return Lattice(self._matrix)

    def lattice_2_lmpbox(lattice, origin=(0, 0, 0)):
        """
        Converts a lattice object to LammpsBox, and calculates the symmetry
        operation used.

        Args:
            lattice (Lattice): Input lattice.
            origin: A (3,) array/list of floats setting lower bounds of
                simulation box. Default to (0, 0, 0).

        Returns:
            LammpsBox, SymmOp

        """
        a, b, c = lattice.abc
        xlo, ylo, zlo = origin
        xhi = a + xlo
        m = lattice.matrix
        xy = np.dot(m[1], m[0] / a)
        yhi = np.sqrt(b ** 2 - xy ** 2) + ylo
        xz = np.dot(m[2], m[0] / a)
        yz = (np.dot(m[1], m[2]) - xy * xz) / (yhi - ylo)
        zhi = np.sqrt(c ** 2 - xz ** 2 - yz ** 2) + zlo
        tilt = None if lattice.is_orthogonal else [xy, xz, yz]
        rot_matrix = np.linalg.solve([[xhi - xlo, 0, 0],
                                      [xy, yhi - ylo, 0],
                                      [xz, yz, zhi - zlo]], m)
        bounds = [[xlo, xhi], [ylo, yhi], [zlo, zhi]]
        symmop = SymmOp.from_rotation_and_translation(rot_matrix, origin)
        return LammpsBox(bounds, tilt), symmop

    class LammpsData(MSONable):
        """
        Object for representing the data in a LAMMPS data file.

        """

        def __init__(self, box, masses, atoms, velocities=None, force_field=None,
                     topology=None, atom_style="full"):
            """
            This is a low level constructor designed to work with parsed
            data or other bridging objects (ForceField and Topology). Not
            recommended to use directly.

            Args:
                box (LammpsBox): Simulation box.
                masses (pandas.DataFrame): DataFrame with one column
                    ["mass"] for Masses section.
                atoms (pandas.DataFrame): DataFrame with multiple columns
                    for Atoms section. Column names vary with atom_style.
                velocities (pandas.DataFrame): DataFrame with three columns
                    ["vx", "vy", "vz"] for Velocities section. Optional
                    with default to None. If not None, its index should be
                    consistent with atoms.
                force_field (dict): Data for force field sections. Optional
                    with default to None. Only keywords in force field and
                    class 2 force field are valid keys, and each value is a
                    DataFrame.
                topology (dict): Data for topology sections. Optional with
                    default to None. Only keywords in topology are valid
                    keys, and each value is a DataFrame.
                atom_style (str): Output atom_style. Default to "full".

            """

            if velocities is not None:
                assert len(velocities) == len(atoms), \
                    "Inconsistency found between atoms and velocities"

            if force_field:
                all_ff_kws = SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]
                force_field = {k: v for k, v in force_field.items()
                               if k in all_ff_kws}

            if topology:
                topology = {k: v for k, v in topology.items()
                            if k in SECTION_KEYWORDS["topology"]}

            self.box = box
            self.masses = masses
            self.atoms = atoms
            self.velocities = velocities
            self.force_field = force_field
            self.topology = topology
            self.atom_style = atom_style

        def __str__(self):
            return self.get_string()

        def __repr__(self):
            return self.get_string()

        @property
        def structure(self):
            """
            Exports a periodic structure object representing the simulation
            box.

            Return:
                Structure

            """
            masses = self.masses
            atoms = self.atoms.copy()
            if "nx" in atoms.columns:
                atoms.drop(["nx", "ny", "nz"], axis=1, inplace=True)
            atoms["molecule-ID"] = 1
            ld_copy = self.__class__(self.box, masses, atoms)
            topologies = ld_copy.disassemble()[-1]
            molecule = topologies[0].sites
            coords = molecule.cart_coords - np.array(self.box.bounds)[:, 0]
            species = molecule.species
            latt = self.box.to_lattice()
            site_properties = {}
            if "q" in atoms:
                site_properties["charge"] = atoms["q"].values
            if self.velocities is not None:
                site_properties["velocities"] = self.velocities.values
            return Structure(latt, species, coords, coords_are_cartesian=True,
                             site_properties=site_properties)

        def get_string(self, distance=6, velocity=8, charge=4):
            """
            Returns the string representation of LammpsData, essentially
            the string to be written to a file. Support hybrid style
            coeffs read and write.

            Args:
                distance (int): No. of significant figures to output for
                    box settings (bounds and tilt) and atomic coordinates.
                    Default to 6.
                velocity (int): No. of significant figures to output for
                    velocities. Default to 8.
                charge (int): No. of significant figures to output for
                    charges. Default to 3.

            Returns:
                String representation

            """
            file_template = """Generated by pymatgen.io.lammps.data.LammpsData

    {stats}

    {box}

    {body}
    """
            box = self.box.get_string(distance)

            body_dict = OrderedDict()
            body_dict["Masses"] = self.masses
            types = OrderedDict()
            types["atom"] = len(self.masses)
            if self.force_field:
                all_ff_kws = SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]
                ff_kws = [k for k in all_ff_kws if k in self.force_field]
                for kw in ff_kws:
                    body_dict[kw] = self.force_field[kw]
                    if kw in SECTION_KEYWORDS["ff"][2:]:
                        types[kw.lower()[:-7]] = len(self.force_field[kw])

            body_dict["Atoms"] = self.atoms
            counts = OrderedDict()
            counts["atoms"] = len(self.atoms)
            if self.velocities is not None:
                body_dict["Velocities"] = self.velocities
            if self.topology:
                for kw in SECTION_KEYWORDS["topology"]:
                    if kw in self.topology:
                        body_dict[kw] = self.topology[kw]
                        counts[kw.lower()] = len(self.topology[kw])

            all_stats = list(counts.values()) + list(types.values())
            stats_template = "{:>%d}  {}" % len(str(max(all_stats)))
            count_lines = [stats_template.format(v, k) for k, v in counts.items()]
            type_lines = [stats_template.format(v, k + " types")
                          for k, v in types.items()]
            stats = "\n".join(count_lines + [""] + type_lines)

            def map_coords(q):
                return ("{:.%df}" % distance).format(q)

            def map_velos(q):
                return ("{:.%df}" % velocity).format(q)

            def map_charges(q):
                return ("{:.%df}" % charge).format(q)
            float_format = '{:.9f}'.format
            float_format_2 = '{:.1f}'.format
            int_format = '{:.0f}'.format
            default_formatters = {"x": map_coords, "y": map_coords, "z": map_coords,
                                  "vx": map_velos, "vy": map_velos, "vz": map_velos,
                                  "q": map_charges}
            coeffsdatatype = loadfn(str(MODULE_DIR / "CoeffsDataType.yaml"))
            coeffs = {}
            for style, types in coeffsdatatype.items():
                coeffs[style] = {}
                for type, formatter in types.items():
                    coeffs[style][type] = {}
                    for coeff, datatype in formatter.items():
                        if datatype == 'int_format':
                            coeffs[style][type][coeff] = int_format
                        elif datatype == 'float_format_2':
                            coeffs[style][type][coeff] = float_format_2
                        else:
                            coeffs[style][type][coeff] = float_format

            section_template = "{kw}\n\n{df}\n"
            parts = []
            for k, v in body_dict.items():
                index = True if k != "PairIJ Coeffs" else False
                if k in ['Bond Coeffs', 'Angle Coeffs', 'Dihedral Coeffs', 'Improper Coeffs']:
                    listofdf = np.array_split(v, len(v.index))
                    df_string = ''
                    for i, df in enumerate(listofdf):
                        if isinstance(df.iloc[0]['coeff1'], str):
                            try:
                                formatters = {**default_formatters, **coeffs[k][df.iloc[0]['coeff1']]}
                            except KeyError:
                                formatters = default_formatters
                            line_string = \
                                df.to_string(header=False, formatters=formatters,
                                             index_names=False, index=index, na_rep='')
                        else:
                            line_string = \
                                v.to_string(header=False, formatters=default_formatters,
                                            index_names=False, index=index,
                                            na_rep='').splitlines()[i]
                        df_string += line_string.replace('nan', '').rstrip() + '\n'
                else:
                    df_string = v.to_string(header=False, formatters=default_formatters,
                                            index_names=False, index=index, na_rep='')
                parts.append(section_template.format(kw=k, df=df_string))
            body = "\n".join(parts)

            return file_template.format(stats=stats, box=box, body=body)

        def write_file(self, filename, distance=6, velocity=8, charge=4):
            """
            Writes LammpsData to file.

            Args:
                filename (str): Filename.
                distance (int): No. of significant figures to output for
                    box settings (bounds and tilt) and atomic coordinates.
                    Default to 6.
                velocity (int): No. of significant figures to output for
                    velocities. Default to 8.
                charge (int): No. of significant figures to output for
                    charges. Default to 3.

            """
            with open(filename, "w") as f:
                f.write(self.get_string(distance=distance, velocity=velocity,
                                        charge=charge))

        def disassemble(self, atom_labels=None, guess_element=True,
                        ff_label="ff_map"):
            """
            Breaks down LammpsData to building blocks
            (LammpsBox, ForceField and a series of Topology).
            RESTRICTIONS APPLIED:

            1. No complex force field defined not just on atom
                types, where the same type or equivalent types of topology
                may have more than one set of coefficients.
            2. No intermolecular topologies (with atoms from different
                molecule-ID) since a Topology object includes data for ONE
                molecule or structure only.

            Args:
                atom_labels ([str]): List of strings (must be different
                    from one another) for labelling each atom type found in
                    Masses section. Default to None, where the labels are
                    automaticaly added based on either element guess or
                    dummy specie assignment.
                guess_element (bool): Whether to guess the element based on
                    its atomic mass. Default to True, otherwise dummy
                    species "Qa", "Qb", ... will be assigned to various
                    atom types. The guessed or assigned elements will be
                    reflected on atom labels if atom_labels is None, as
                    well as on the species of molecule in each Topology.
                ff_label (str): Site property key for labeling atoms of
                    different types. Default to "ff_map".

            Returns:
                LammpsBox, ForceField, [Topology]

            """
            atoms_df = self.atoms.copy()
            if "nx" in atoms_df.columns:
                atoms_df[["x", "y", "z"]] += \
                    self.box.get_box_shift(atoms_df[["nx", "ny", "nz"]].values)
            atoms_df = pd.concat([atoms_df, self.velocities], axis=1)

            mids = atoms_df.get("molecule-ID")
            if mids is None:
                unique_mids = [1]
                data_by_mols = {1: {"Atoms": atoms_df}}
            else:
                unique_mids = np.unique(mids)
                data_by_mols = {}
                for k in unique_mids:
                    df = atoms_df[atoms_df["molecule-ID"] == k]
                    data_by_mols[k] = {"Atoms": df}

            masses = self.masses.copy()
            masses["label"] = atom_labels
            unique_masses = np.unique(masses["mass"])
            if guess_element:
                ref_masses = [el.atomic_mass.real for el in Element]
                diff = np.abs(np.array(ref_masses) - unique_masses[:, None])
                atomic_numbers = np.argmin(diff, axis=1) + 1
                symbols = [Element.from_Z(an).symbol for an in atomic_numbers]
            else:
                symbols = ["Q%s" % a for a in
                           map(chr, range(97, 97 + len(unique_masses)))]
            for um, s in zip(unique_masses, symbols):
                masses.loc[masses["mass"] == um, "element"] = s
            if atom_labels is None:  # add unique labels based on elements
                for el, vc in masses["element"].value_counts().iteritems():
                    masses.loc[masses["element"] == el, "label"] = \
                        ["%s%d" % (el, c) for c in range(1, vc + 1)]
            assert masses["label"].nunique(dropna=False) == len(masses), \
                "Expecting unique atom label for each type"
            mass_info = [tuple([r["label"], r["mass"]])
                         for _, r in masses.iterrows()]

            nonbond_coeffs, topo_coeffs = None, None
            if self.force_field:
                if "PairIJ Coeffs" in self.force_field:
                    nbc = self.force_field["PairIJ Coeffs"]
                    nbc = nbc.sort_values(["id1", "id2"]).drop(["id1", "id2"], axis=1)
                    nonbond_coeffs = [list(t) for t in nbc.itertuples(False, None)]
                elif "Pair Coeffs" in self.force_field:
                    nbc = self.force_field["Pair Coeffs"].sort_index()
                    nonbond_coeffs = [list(t) for t in nbc.itertuples(False, None)]

                topo_coeffs = {k: [] for k in SECTION_KEYWORDS["ff"][2:]
                               if k in self.force_field}
                for kw in topo_coeffs.keys():
                    class2_coeffs = {k: list(v.itertuples(False, None))
                                     for k, v in self.force_field.items()
                                     if k in CLASS2_KEYWORDS.get(kw, [])}
                    ff_df = self.force_field[kw]
                    for t in ff_df.itertuples(True, None):
                        d = {"coeffs": list(t[1:]), "types": []}
                        if class2_coeffs:
                            d.update({k: list(v[t[0] - 1])
                                      for k, v in class2_coeffs.items()})
                        topo_coeffs[kw].append(d)

            if self.topology:
                def label_topo(t):
                    return tuple(masses.loc[atoms_df.loc[t, "type"], "label"])
                for k, v in self.topology.items():
                    ff_kw = k[:-1] + " Coeffs"
                    for topo in v.itertuples(False, None):
                        topo_idx = topo[0] - 1
                        indices = topo[1:]
                        mids = atoms_df.loc[indices, "molecule-ID"].unique()
                        assert len(mids) == 1, \
                            "Do not support intermolecular topology formed " \
                            "by atoms with different molecule-IDs"
                        label = label_topo(indices)
                        topo_coeffs[ff_kw][topo_idx]["types"].append(label)
                        if data_by_mols[mids[0]].get(k):
                            data_by_mols[mids[0]][k].append(indices)
                        else:
                            data_by_mols[mids[0]][k] = [indices]

            if topo_coeffs:
                for v in topo_coeffs.values():
                    for d in v:
                        d["types"] = list(set(d["types"]))

            ff = ForceField(mass_info=mass_info, nonbond_coeffs=nonbond_coeffs,
                            topo_coeffs=topo_coeffs)

            topo_list = []
            for mid in unique_mids:
                data = data_by_mols[mid]
                atoms = data["Atoms"]
                shift = min(atoms.index)
                type_ids = atoms["type"]
                species = masses.loc[type_ids, "element"]
                labels = masses.loc[type_ids, "label"]
                coords = atoms[["x", "y", "z"]]
                m = Molecule(species.values, coords.values,
                             site_properties={ff_label: labels.values})
                charges = atoms.get("q")
                velocities = atoms[["vx", "vy", "vz"]] if "vx" in atoms.columns \
                    else None
                topologies = {}
                for kw in SECTION_KEYWORDS["topology"]:
                    if data.get(kw):
                        topologies[kw] = (np.array(data[kw]) - shift).tolist()
                topologies = None if not topologies else topologies
                topo_list.append(Topology(sites=m, ff_label=ff_label,
                                          charges=charges, velocities=velocities,
                                          topologies=topologies))

            return self.box, ff, topo_list

        @classmethod
        def from_file(cls, filename, atom_style="full", sort_id=False):
            """
            Constructor that parses a file.

            Args:
                filename (str): Filename to read.
                atom_style (str): Associated atom_style. Default to "full".
                sort_id (bool): Whether sort each section by id. Default to
                    True.

            """
            with open(filename) as f:
                lines = f.readlines()
            kw_pattern = r"|".join(itertools.chain(*SECTION_KEYWORDS.values()))
            section_marks = [i for i, l in enumerate(lines)
                             if re.search(kw_pattern, l)]
            parts = np.split(lines, section_marks)

            float_group = r"([0-9eE.+-]+)"
            header_pattern = dict()
            header_pattern["counts"] = r"^\s*(\d+)\s+([a-zA-Z]+)$"
            header_pattern["types"] = r"^\s*(\d+)\s+([a-zA-Z]+)\s+types$"
            header_pattern["bounds"] = r"^\s*{}$".format(r"\s+".join(
                [float_group] * 2 + [r"([xyz])lo \3hi"]))
            header_pattern["tilt"] = r"^\s*{}$".format(r"\s+".join(
                [float_group] * 3 + ["xy xz yz"]))

            header = {"counts": {}, "types": {}}
            bounds = {}
            for l in clean_lines(parts[0][1:]):  # skip the 1st line
                match = None
                for k, v in header_pattern.items():
                    match = re.match(v, l)
                    if match:
                        break
                    else:
                        continue
                if match and k in ["counts", "types"]:
                    header[k][match.group(2)] = int(match.group(1))
                elif match and k == "bounds":
                    g = match.groups()
                    bounds[g[2]] = [float(i) for i in g[:2]]
                elif match and k == "tilt":
                    header["tilt"] = [float(i) for i in match.groups()]
            header["bounds"] = [bounds.get(i, [-0.5, 0.5]) for i in "xyz"]
            box = LammpsBox(header["bounds"], header.get("tilt"))

            def parse_section(sec_lines):
                title_info = sec_lines[0].split("#", 1)
                kw = title_info[0].strip()
                sio = StringIO("".join(sec_lines[2:]))  # skip the 2nd line
                if kw.endswith("Coeffs") and not kw.startswith("PairIJ"):
                    df_list = [pd.read_csv(StringIO(line), header=None, comment="#",
                                           delim_whitespace=True) for line in sec_lines[2:] if line.strip()]
                    df = pd.concat(df_list, ignore_index=True)
                    names = ["id"] + ["coeff%d" % i
                                      for i in range(1, df.shape[1])]
                else:
                    df = pd.read_csv(sio, header=None, comment="#",
                                     delim_whitespace=True)
                    if kw == "PairIJ Coeffs":
                        names = ["id1", "id2"] + ["coeff%d" % i
                                                  for i in range(1, df.shape[1] - 1)]
                        df.index.name = None
                    elif kw in SECTION_HEADERS:
                        names = ["id"] + SECTION_HEADERS[kw]
                    elif kw == "Atoms":
                        names = ["id"] + ATOMS_HEADERS[atom_style]
                        if df.shape[1] == len(names):
                            pass
                        elif df.shape[1] == len(names) + 3:
                            names += ["nx", "ny", "nz"]
                        else:
                            raise ValueError("Format in Atoms section inconsistent"
                                             " with atom_style %s" % atom_style)
                    else:
                        raise NotImplementedError("Parser for %s section"
                                                  " not implemented" % kw)
                df.columns = names
                if sort_id:
                    sort_by = "id" if kw != "PairIJ Coeffs" else ["id1", "id2"]
                    df.sort_values(sort_by, inplace=True)
                if "id" in df.columns:
                    df.set_index("id", drop=True, inplace=True)
                    df.index.name = None
                return kw, df

            err_msg = "Bad LAMMPS data format where "
            body = {}
            seen_atoms = False
            for part in parts[1:]:
                name, section = parse_section(part)
                if name == "Atoms":
                    seen_atoms = True
                if name in ["Velocities"] + SECTION_KEYWORDS["topology"] and \
                        not seen_atoms:  # Atoms must appear earlier than these
                    raise RuntimeError(err_msg + "%s section appears before"
                                                 " Atoms section" % name)
                body.update({name: section})

            err_msg += "Nos. of {} do not match between header and {} section"
            assert len(body["Masses"]) == header["types"]["atom"], \
                err_msg.format("atom types", "Masses")
            atom_sections = ["Atoms", "Velocities"] \
                if "Velocities" in body else ["Atoms"]
            for s in atom_sections:
                assert len(body[s]) == header["counts"]["atoms"], \
                    err_msg.format("atoms", s)
            for s in SECTION_KEYWORDS["topology"]:
                if header["counts"].get(s.lower(), 0) > 0:
                    assert len(body[s]) == header["counts"][s.lower()], \
                        err_msg.format(s.lower(), s)

            items = {k.lower(): body[k] for k in ["Masses", "Atoms"]}
            items["velocities"] = body.get("Velocities")
            ff_kws = [k for k in body if k
                      in SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]]
            items["force_field"] = {k: body[k] for k in ff_kws} if ff_kws \
                else None
            topo_kws = [k for k in body if k in SECTION_KEYWORDS["topology"]]
            items["topology"] = {k: body[k] for k in topo_kws} \
                if topo_kws else None
            items["atom_style"] = atom_style
            items["box"] = box
            return cls(**items)

        @classmethod
        def from_ff_and_topologies(cls, box, ff, topologies, atom_style="full"):
            """
            Constructor building LammpsData from a ForceField object and a
            list of Topology objects. Do not support intermolecular
            topologies since a Topology object includes data for ONE
            molecule or structure only.

            Args:
                box (LammpsBox): Simulation box.
                ff (ForceField): ForceField object with data for Masses and
                    force field sections.
                topologies ([Topology]): List of Topology objects with data
                    for Atoms, Velocities and topology sections.
                atom_style (str): Output atom_style. Default to "full".

            """
            atom_types = set.union(*[t.species for t in topologies])
            assert atom_types.issubset(ff.maps["Atoms"].keys()), \
                "Unknown atom type found in topologies"

            items = dict(box=box, atom_style=atom_style, masses=ff.masses,
                         force_field=ff.force_field)

            mol_ids, charges, coords, labels = [], [], [], []
            v_collector = [] if topologies[0].velocities else None
            topo_collector = {"Bonds": [], "Angles": [], "Dihedrals": [],
                              "Impropers": []}
            topo_labels = {"Bonds": [], "Angles": [], "Dihedrals": [],
                           "Impropers": []}
            for i, topo in enumerate(topologies):
                if topo.topologies:
                    shift = len(labels)
                    for k, v in topo.topologies.items():
                        topo_collector[k].append(np.array(v) + shift + 1)
                        topo_labels[k].extend([tuple([topo.type_by_sites[j]
                                                      for j in t]) for t in v])
                if isinstance(v_collector, list):
                    v_collector.append(topo.velocities)
                mol_ids.extend([i + 1] * len(topo.sites))
                labels.extend(topo.type_by_sites)
                coords.append(topo.sites.cart_coords)
                q = [0.0] * len(topo.sites) if not topo.charges else topo.charges
                charges.extend(q)

            atoms = pd.DataFrame(np.concatenate(coords), columns=["x", "y", "z"])
            atoms["molecule-ID"] = mol_ids
            atoms["q"] = charges
            atoms["type"] = list(map(ff.maps["Atoms"].get, labels))
            atoms.index += 1
            atoms = atoms[ATOMS_HEADERS[atom_style]]

            velocities = None
            if v_collector:
                velocities = pd.DataFrame(np.concatenate(v_collector),
                                          columns=SECTION_HEADERS["Velocities"])
                velocities.index += 1

            topology = {k: None for k, v in topo_labels.items() if len(v) > 0}
            for k in topology:
                df = pd.DataFrame(np.concatenate(topo_collector[k]),
                                  columns=SECTION_HEADERS[k][1:])
                df["type"] = list(map(ff.maps[k].get, topo_labels[k]))
                if any(pd.isnull(df["type"])):  # Throw away undefined topologies
                    warnings.warn("Undefined %s detected and removed" % k.lower())
                    df.dropna(subset=["type"], inplace=True)
                    df.reset_index(drop=True, inplace=True)
                df.index += 1
                topology[k] = df[SECTION_HEADERS[k]]
            topology = {k: v for k, v in topology.items() if not v.empty}

            items.update({"atoms": atoms, "velocities": velocities,
                          "topology": topology})
            return cls(**items)

        @classmethod
        def from_structure(cls, structure, ff_elements=None, atom_style="charge",
                           is_sort=False):
            """
            Simple constructor building LammpsData from a structure without
            force field parameters and topologies.

            Args:
                structure (Structure): Input structure.
                ff_elements ([str]): List of strings of elements that must
                    be present due to force field settings but not
                    necessarily in the structure. Default to None.
                atom_style (str): Choose between "atomic" (neutral) and
                    "charge" (charged). Default to "charge".
                is_sort (bool): whether to sort sites

            """
            if is_sort:
                s = structure.get_sorted_structure()
            else:
                s = structure.copy()
            box, symmop = lattice_2_lmpbox(s.lattice)
            coords = symmop.operate_multi(s.cart_coords)
            site_properties = s.site_properties
            if "velocities" in site_properties:
                velos = np.array(s.site_properties["velocities"])
                rot = SymmOp.from_rotation_and_translation(symmop.rotation_matrix)
                rot_velos = rot.operate_multi(velos)
                site_properties.update({"velocities": rot_velos})
            boxed_s = Structure(box.to_lattice(), s.species, coords,
                                site_properties=site_properties,
                                coords_are_cartesian=True)

            symbols = list(s.symbol_set)
            if ff_elements:
                symbols.extend(ff_elements)
            elements = sorted(Element(el) for el in set(symbols))
            mass_info = [tuple([i.symbol] * 2) for i in elements]
            ff = ForceField(mass_info)
            topo = Topology(boxed_s)
            return cls.from_ff_and_topologies(box=box, ff=ff, topologies=[topo],
                                              atom_style=atom_style)

        @classmethod
        def from_dict(cls, d):
            """
            Constructor that reads in a dictionary.

            Args:
                d (dict): Dictionary to read.
            """
            def decode_df(s):
                return pd.read_json(s, orient="split")
            items = dict()
            items["box"] = LammpsBox.from_dict(d["box"])
            items["masses"] = decode_df(d["masses"])
            items["atoms"] = decode_df(d["atoms"])
            items["atom_style"] = d["atom_style"]

            velocities = d["velocities"]
            if velocities:
                velocities = decode_df(velocities)
            items["velocities"] = velocities
            force_field = d["force_field"]
            if force_field:
                force_field = {k: decode_df(v) for k, v in force_field.items()}
            items["force_field"] = force_field
            topology = d["topology"]
            if topology:
                topology = {k: decode_df(v) for k, v in topology.items()}
            items["topology"] = topology
            return cls(**items)

        def as_dict(self):
            """
            Returns the LammpsData as a dict.

            """
            def encode_df(df):
                return df.to_json(orient="split")
            d = dict()
            d["@module"] = self.__class__.__module__
            d["@class"] = self.__class__.__name__
            d["box"] = self.box.as_dict()
            d["masses"] = encode_df(self.masses)
            d["atoms"] = encode_df(self.atoms)
            d["atom_style"] = self.atom_style

            d["velocities"] = None if self.velocities is None \
                else encode_df(self.velocities)
            d["force_field"] = None if not self.force_field \
                else {k: encode_df(v) for k, v in self.force_field.items()}
            d["topology"] = None if not self.topology \
                else {k: encode_df(v) for k, v in self.topology.items()}
            return d

    class Topology(MSONable):
        """
        Class carrying most data in Atoms, Velocities and molecular
        topology sections for ONE SINGLE Molecule or Structure
        object, or a plain list of Sites.

        """

        def __init__(self, sites, ff_label=None, charges=None, velocities=None,
                     topologies=None):
            """

            Args:
                sites ([Site] or SiteCollection): A group of sites in a
                    list or as a Molecule/Structure.
                ff_label (str): Site property key for labeling atoms of
                    different types. Default to None, i.e., use
                    site.species_string.
                charges ([q, ...]): Charge of each site in a (n,)
                    array/list, where n is the No. of sites. Default to
                    None, i.e., search site property for charges.
                velocities ([[vx, vy, vz], ...]): Velocity of each site in
                    a (n, 3) array/list, where n is the No. of sites.
                    Default to None, i.e., search site property for
                    velocities.
                topologies (dict): Bonds, angles, dihedrals and improper
                    dihedrals defined by site indices. Default to None,
                    i.e., no additional topology. All four valid keys
                    listed below are optional.
                    {
                        "Bonds": [[i, j], ...],
                        "Angles": [[i, j, k], ...],
                        "Dihedrals": [[i, j, k, l], ...],
                        "Impropers": [[i, j, k, l], ...]
                    }

            """
            if not isinstance(sites, (Molecule, Structure)):
                sites = Molecule.from_sites(sites)

            if ff_label:
                type_by_sites = sites.site_properties.get(ff_label)
            else:
                type_by_sites = [site.specie.symbol for site in sites]
            # search for site property if not override
            if charges is None:
                charges = sites.site_properties.get("charge")
            if velocities is None:
                velocities = sites.site_properties.get("velocities")
            # validate shape
            if charges is not None:
                charge_arr = np.array(charges)
                assert charge_arr.shape == (len(sites),), \
                    "Wrong format for charges"
                charges = charge_arr.tolist()
            if velocities is not None:
                velocities_arr = np.array(velocities)
                assert velocities_arr.shape == (len(sites), 3), \
                    "Wrong format for velocities"
                velocities = velocities_arr.tolist()

            if topologies:
                topologies = {k: v for k, v in topologies.items()
                              if k in SECTION_KEYWORDS["topology"]}

            self.sites = sites
            self.ff_label = ff_label
            self.charges = charges
            self.velocities = velocities
            self.topologies = topologies
            self.type_by_sites = type_by_sites
            self.species = set(type_by_sites)

        @classmethod
        def from_bonding(cls, molecule, bond=True, angle=True, dihedral=True,
                         tol=0.1, **kwargs):
            """
            Another constructor that creates an instance from a molecule.
            Covalent bonds and other bond-based topologies (angles and
            dihedrals) can be automatically determined. Cannot be used for
            non bond-based topologies, e.g., improper dihedrals.

            Args:
                molecule (Molecule): Input molecule.
                bond (bool): Whether find bonds. If set to False, angle and
                    dihedral searching will be skipped. Default to True.
                angle (bool): Whether find angles. Default to True.
                dihedral (bool): Whether find dihedrals. Default to True.
                tol (float): Bond distance tolerance. Default to 0.1.
                    Not recommended to alter.
                **kwargs: Other kwargs supported by Topology.

            """
            real_bonds = molecule.get_covalent_bonds(tol=tol)
            bond_list = [list(map(molecule.index, [b.site1, b.site2]))
                         for b in real_bonds]
            if not all((bond, bond_list)):
                # do not search for others if not searching for bonds or no bonds
                return cls(sites=molecule, **kwargs)
            else:
                angle_list, dihedral_list = [], []
                dests, freq = np.unique(bond_list, return_counts=True)
                hubs = dests[np.where(freq > 1)].tolist()
                bond_arr = np.array(bond_list)
                if len(hubs) > 0:
                    hub_spokes = {}
                    for hub in hubs:
                        ix = np.any(np.isin(bond_arr, hub), axis=1)
                        bonds = np.unique(bond_arr[ix]).tolist()
                        bonds.remove(hub)
                        hub_spokes[hub] = bonds
                # skip angle or dihedral searching if too few bonds or hubs
                dihedral = False if len(bond_list) < 3 or len(hubs) < 2 \
                    else dihedral
                angle = False if len(bond_list) < 2 or len(hubs) < 1 else angle

                if angle:
                    for k, v in hub_spokes.items():
                        angle_list.extend([[i, k, j] for i, j in
                                           itertools.combinations(v, 2)])
                if dihedral:
                    hub_cons = bond_arr[np.all(np.isin(bond_arr, hubs), axis=1)]
                    for i, j in hub_cons.tolist():
                        ks = [k for k in hub_spokes[i] if k != j]
                        ls = [l for l in hub_spokes[j] if l != i]
                        dihedral_list.extend([[k, i, j, l] for k, l in
                                              itertools.product(ks, ls)
                                              if k != l])

                topologies = {k: v for k, v
                              in zip(SECTION_KEYWORDS["topology"][:3],
                                     [bond_list, angle_list, dihedral_list])
                              if len(v) > 0}
                topologies = None if len(topologies) == 0 else topologies
                return cls(sites=molecule, topologies=topologies, **kwargs)

    class ForceField(MSONable):
        """
        Class carrying most data in Masses and force field sections.

        Attributes:
            masses (pandas.DataFrame): DataFrame for Masses section.
            force_field (dict): Force field section keywords (keys) and
                data (values) as DataFrames.
            maps (dict): Dict for labeling atoms and topologies.

        """

        def _is_valid(self, df):
            return not pd.isnull(df).values.any()

        def __init__(self, mass_info, nonbond_coeffs=None, topo_coeffs=None):
            """

            Args:
                mass_into (list): List of atomic mass info. Elements,
                    strings (symbols) and floats are all acceptable for the
                    values, with the first two converted to the atomic mass
                    of an element. It is recommended to use
                    OrderedDict.items() to prevent key duplications.
                    [("C", 12.01), ("H", Element("H")), ("O", "O"), ...]
                nonbond_coeffs [coeffs]: List of pair or pairij
                    coefficients, of which the sequence must be sorted
                    according to the species in mass_dict. Pair or PairIJ
                    determined by the length of list. Optional with default
                    to None.
                topo_coeffs (dict): Dict with force field coefficients for
                    molecular topologies. Optional with default
                    to None. All four valid keys listed below are optional.
                    Each value is a list of dicts with non optional keys
                    "coeffs" and "types", and related class2 force field
                    keywords as optional keys.
                    {
                        "Bond Coeffs":
                            [{"coeffs": [coeff],
                              "types": [("C", "C"), ...]}, ...],
                        "Angle Coeffs":
                            [{"coeffs": [coeff],
                              "BondBond Coeffs": [coeff],
                              "types": [("H", "C", "H"), ...]}, ...],
                        "Dihedral Coeffs":
                            [{"coeffs": [coeff],
                              "BondBond13 Coeffs": [coeff],
                              "types": [("H", "C", "C", "H"), ...]}, ...],
                        "Improper Coeffs":
                            [{"coeffs": [coeff],
                              "AngleAngle Coeffs": [coeff],
                              "types": [("H", "C", "C", "H"), ...]}, ...],
                    }
                    Topology of same type or equivalent types (e.g.,
                    ("C", "H") and ("H", "C") bonds) are NOT ALLOWED to
                    be defined MORE THAN ONCE with DIFFERENT coefficients.

            """
            def map_mass(v):
                return v.atomic_mass.real if isinstance(v, Element) else Element(v).atomic_mass.real \
                    if isinstance(v, str) else v
            index, masses, self.mass_info, atoms_map = [], [], [], {}
            for i, m in enumerate(mass_info):
                index.append(i + 1)
                mass = map_mass(m[1])
                masses.append(mass)
                self.mass_info.append((m[0], mass))
                atoms_map[m[0]] = i + 1
            self.masses = pd.DataFrame({"mass": masses}, index=index)
            self.maps = {"Atoms": atoms_map}

            ff_dfs = {}

            self.nonbond_coeffs = nonbond_coeffs
            if self.nonbond_coeffs:
                ff_dfs.update(self._process_nonbond())

            self.topo_coeffs = topo_coeffs
            if self.topo_coeffs:
                self.topo_coeffs = {k: v for k, v in self.topo_coeffs.items()
                                    if k in SECTION_KEYWORDS["ff"][2:]}
                for k in self.topo_coeffs.keys():
                    coeffs, mapper = self._process_topo(k)
                    ff_dfs.update(coeffs)
                    self.maps.update(mapper)

            self.force_field = None if len(ff_dfs) == 0 else ff_dfs

        def _process_nonbond(self):
            pair_df = pd.DataFrame(self.nonbond_coeffs)
            assert self._is_valid(pair_df), \
                "Invalid nonbond coefficients with rows varying in length"
            npair, ncoeff = pair_df.shape
            pair_df.columns = ["coeff%d" % i for i in range(1, ncoeff + 1)]
            nm = len(self.mass_info)
            ncomb = int(nm * (nm + 1) / 2)
            if npair == nm:
                kw = "Pair Coeffs"
                pair_df.index = range(1, nm + 1)
            elif npair == ncomb:
                kw = "PairIJ Coeffs"
                ids = list(itertools.
                           combinations_with_replacement(range(1, nm + 1), 2))
                id_df = pd.DataFrame(ids, columns=["id1", "id2"])
                pair_df = pd.concat([id_df, pair_df], axis=1)
            else:
                raise ValueError("Expecting {} Pair Coeffs or "
                                 "{} PairIJ Coeffs for {} atom types,"
                                 " got {}".format(nm, ncomb, nm, npair))
            return {kw: pair_df}

        def _process_topo(self, kw):

            def find_eq_types(label, section):
                if section.startswith("Improper"):
                    label_arr = np.array(label)
                    seqs = [[0, 1, 2, 3], [0, 2, 1, 3],
                            [3, 1, 2, 0], [3, 2, 1, 0]]
                    return [tuple(label_arr[s]) for s in seqs]
                else:
                    return [label] + [label[::-1]]

            main_data, distinct_types = [], []
            class2_data = {k: [] for k in self.topo_coeffs[kw][0].keys()
                           if k in CLASS2_KEYWORDS.get(kw, [])}
            for i, d in enumerate(self.topo_coeffs[kw]):
                main_data.append(d["coeffs"])
                distinct_types.append(d["types"])
                for k in class2_data.keys():
                    class2_data[k].append(d[k])
            distinct_types = [set(itertools.
                                  chain(*[find_eq_types(t, kw)
                                          for t in dt])) for dt in distinct_types]
            type_counts = sum([len(dt) for dt in distinct_types])
            type_union = set.union(*distinct_types)
            assert len(type_union) == type_counts, "Duplicated items found " \
                                                   "under different coefficients in %s" % kw
            atoms = set(np.ravel(list(itertools.chain(*distinct_types))))
            assert atoms.issubset(self.maps["Atoms"].keys()), \
                "Undefined atom type found in %s" % kw
            mapper = {}
            for i, dt in enumerate(distinct_types):
                for t in dt:
                    mapper[t] = i + 1

            def process_data(data):
                df = pd.DataFrame(data)
                assert self._is_valid(df), \
                    "Invalid coefficients with rows varying in length"
                n, c = df.shape
                df.columns = ["coeff%d" % i for i in range(1, c + 1)]
                df.index = range(1, n + 1)
                return df

            all_data = {kw: process_data(main_data)}
            if class2_data:
                all_data.update({k: process_data(v) for k, v
                                 in class2_data.items()})
            return all_data, {kw[:-7] + "s": mapper}

        def to_file(self, filename):
            """
            Saves object to a file in YAML format.

            Args:
                filename (str): Filename.

            """
            d = {"mass_info": self.mass_info,
                 "nonbond_coeffs": self.nonbond_coeffs,
                 "topo_coeffs": self.topo_coeffs}
            yaml = YAML(typ="safe")
            with open(filename, "w") as f:
                yaml.dump(d, f)

        @classmethod
        def from_file(cls, filename):
            """
            Constructor that reads in a file in YAML format.

            Args:
                filename (str): Filename.

            """
            yaml = YAML(typ="safe")
            with open(filename, "r") as f:
                d = yaml.load(f)
            return cls.from_dict(d)

        @classmethod
        def from_dict(cls, d):
            """
            Constructor that reads in a dictionary.

            Args:
                d (dict): Dictionary to read.
            """
            d["mass_info"] = [tuple(m) for m in d["mass_info"]]
            if d.get("topo_coeffs"):
                for v in d["topo_coeffs"].values():
                    for c in v:
                        c["types"] = [tuple(t) for t in c["types"]]
            return cls(d["mass_info"], d["nonbond_coeffs"], d["topo_coeffs"])

    class CombinedData(LammpsData):
        """
        Object for a collective set of data for a series of LAMMPS data file.
        velocities not yet implementd.
        """

        def __init__(self, list_of_molecules, list_of_names, list_of_numbers, coordinates, atom_style="full"):
            """
            Args:
                list_of_molecules: a list of LammpsData of a single cluster.
                list_of_names: a list of name for each cluster.
                list_of_numbers: a list of Integer for counts of each molecule
                    coordinates (pandas.DataFrame): DataFrame with with four
                    columns ["atom", "x", "y", "z"] for coordinates of atoms.
                atom_style (str): Output atom_style. Default to "full".

            """

            max_xyz = coordinates[['x', 'y', 'z']].max().max()
            min_xyz = coordinates[['x', 'y', 'z']].min().min()
            self.box = LammpsBox(np.array(3*[[min_xyz - 0.5, max_xyz + 0.5]]))
            self.atom_style = atom_style
            self.n = sum(list_of_numbers)
            self.names = list_of_names
            self.mols = list_of_molecules
            self.nums = list_of_numbers
            self.masses = pd.concat([mol.masses.copy() for mol in self.mols], ignore_index=True)
            self.masses.index += 1
            all_ff_kws = SECTION_KEYWORDS["ff"] + SECTION_KEYWORDS["class2"]
            ff_kws = [k for k in all_ff_kws if k in self.mols[0].force_field]
            self.force_field = {}
            for kw in ff_kws:
                self.force_field[kw] = pd.concat([mol.force_field[kw].copy() for mol in self.mols
                                                  if kw in mol.force_field], ignore_index=True)
                self.force_field[kw].index += 1

            self.atoms = pd.DataFrame()
            mol_count = 0
            type_count = 0
            for i, mol in enumerate(self.mols):
                atoms_df = mol.atoms.copy()
                atoms_df['molecule-ID'] += mol_count
                atoms_df['type'] += type_count
                for j in range(self.nums[i]):
                    self.atoms = self.atoms.append(atoms_df, ignore_index=True)
                    atoms_df['molecule-ID'] += 1
                type_count += len(mol.masses)
                mol_count += self.nums[i]
            self.atoms.index += 1
            assert len(self.atoms) == len(coordinates), 'Wrong number of coordinates.'
            self.atoms.update(coordinates)

            self.velocities = None
            assert self.mols[0].velocities is None, "Velocities not supported"

            self.topology = {}
            atom_count = 0
            count = {"Bonds": 0, "Angles": 0, "Dihedrals": 0, "Impropers": 0}
            for i, mol in enumerate(self.mols):
                for kw in SECTION_KEYWORDS["topology"]:
                    if kw in mol.topology:
                        if kw not in self.topology:
                            self.topology[kw] = pd.DataFrame()
                        topo_df = mol.topology[kw].copy()
                        topo_df['type'] += count[kw]
                        for col in topo_df.columns[1:]:
                            topo_df[col] += atom_count
                        for j in range(self.nums[i]):
                            self.topology[kw] = self.topology[kw].append(topo_df, ignore_index=True)
                            for col in topo_df.columns[1:]:
                                topo_df[col] += len(mol.atoms)
                        count[kw] += len(mol.force_field[kw[:-1]+" Coeffs"])
                atom_count += len(mol.atoms) * self.nums[i]
            for kw in SECTION_KEYWORDS["topology"]:
                if kw in self.topology:
                    self.topology[kw].index += 1

        @classmethod
        def parse_xyz(cls, filename):
            """
            load xyz file generated from packmol (for those who find it hard to install openbabel)

            Returns:
                pandas.DataFrame

            """
            with open(filename) as f:
                lines = f.readlines()

            sio = StringIO("".join(lines[2:]))  # skip the 2nd line
            df = pd.read_csv(sio, header=None, comment="#", delim_whitespace=True, names=['atom', 'x', 'y', 'z'])
            df.index += 1
            return df

        @classmethod
        def from_files(cls, coordinate_file, list_of_numbers, *filenames):
            """
            Constructor that parse a series of data file.

            Args:
                coordinate_file (str): The filename of xyz coordinates.
                list_of_numbers (list): A list of numbers specifying counts for each
                    clusters parsed from files.
                filenames (str): A series of filenames in string format.
            """
            names = []
            mols = []
            styles = []
            coordinates = cls.parse_xyz(filename=coordinate_file)
            for i in range(0, len(filenames)):
                exec("cluster%d = LammpsData.from_file(filenames[i])" % (i + 1))
                names.append("cluster%d" % (i + 1))
                mols.append(eval("cluster%d" % (i + 1)))
                styles.append(eval("cluster%d" % (i + 1)).atom_style)
            style = set(styles)
            assert len(style) == 1, "Files have different atom styles."
            return cls.from_lammpsdata(mols, names, list_of_numbers, coordinates, style.pop())

        @classmethod
        def from_lammpsdata(cls, mols, names, list_of_numbers, coordinates, atom_style=None):
            """
            Constructor that can infer atom_style.
            The input LammpsData objects are used non-destructively.

            Args:
                mols: a list of LammpsData of a single cluster.
                names: a list of name for each cluster.
                list_of_numbers: a list of Integer for counts of each molecule
                    coordinates (pandas.DataFrame): DataFrame with with four
                    columns ["atom", "x", "y", "z"] for coordinates of atoms.
                atom_style (str): Output atom_style. Default to "full".
            """
            styles = []
            for mol in mols:
                styles.append(mol.atom_style)
            style = set(styles)
            assert len(style) == 1, "Data have different atom_style."
            style_return = style.pop()
            if atom_style:
                assert atom_style == style_return, "Data have different atom_style as specified."
            return cls(mols, names, list_of_numbers, coordinates, style_return)

        def get_string(self, distance=6, velocity=8, charge=4):
            """
            Returns the string representation of CombinedData, essentially
            the string to be written to a file. Combination info is included.

            Args:
                distance (int): No. of significant figures to output for
                    box settings (bounds and tilt) and atomic coordinates.
                    Default to 6.
                velocity (int): No. of significant figures to output for
                    velocities. Default to 8.
                charge (int): No. of significant figures to output for
                    charges. Default to 3.

            Returns:
                String representation
            """
            lines = LammpsData.get_string(self, distance, velocity, charge).splitlines()
            info = '# ' + ' + '.join(str(a) + " " + b for a, b in zip(self.nums, self.names))
            lines.insert(1, info)
            return "\n".join(lines)

    @deprecated(LammpsData.from_structure,
                "structure_2_lmpdata has been deprecated "
                "in favor of LammpsData.from_structure")
    def structure_2_lmpdata(structure, ff_elements=None, atom_style="charge",
                            is_sort=False):
        """
        Converts a structure to a LammpsData object with no force field
        parameters and topologies.

        Args:
            structure (Structure): Input structure.
            ff_elements ([str]): List of strings of elements that must be
                present due to force field settings but not necessarily in
                the structure. Default to None.
            atom_style (str): Choose between "atomic" (neutral) and
                "charge" (charged). Default to "charge".
            is_sort (bool): whether to sort the structure sites
        Returns:
            LammpsData

        """
        if is_sort:
            s = structure.get_sorted_structure()
        else:
            s = structure.copy()

        a, b, c = s.lattice.abc
        m = s.lattice.matrix
        xhi = a
        xy = np.dot(m[1], m[0] / xhi)
        yhi = np.sqrt(b ** 2 - xy ** 2)
        xz = np.dot(m[2], m[0] / xhi)
        yz = (np.dot(m[1], m[2]) - xy * xz) / yhi
        zhi = np.sqrt(c ** 2 - xz ** 2 - yz ** 2)
        box_bounds = [[0.0, xhi], [0.0, yhi], [0.0, zhi]]
        box_tilt = [xy, xz, yz]
        box_tilt = None if not any(box_tilt) else box_tilt
        box = LammpsBox(box_bounds, box_tilt)
        new_latt = Lattice([[xhi, 0, 0], [xy, yhi, 0], [xz, yz, zhi]])
        s.lattice = new_latt

        symbols = list(s.symbol_set)
        if ff_elements:
            symbols.extend(ff_elements)
        elements = sorted(Element(el) for el in set(symbols))
        mass_info = [tuple([i.symbol] * 2) for i in elements]
        ff = ForceField(mass_info)
        topo = Topology(s)
        return LammpsData.from_ff_and_topologies(box=box, ff=ff, topologies=[topo],
                                                 atom_style=atom_style)