pymatgen.io.lammps.outputs — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.lammps.outputs

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

    """
    This module implements classes and methods for processing LAMMPS output
    files (log and dump).
    """

    import re
    import glob
    from io import StringIO

    import numpy as np
    import pandas as pd

    from monty.json import MSONable
    from monty.io import zopen

    from pymatgen.io.lammps.data import LammpsBox

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

    class LammpsDump(MSONable):
        """
        Object for representing dump data for a single snapshot.
        """

        def __init__(self, timestep, natoms, box, data):
            """
            Base constructor.

            Args:
                timestep (int): Current timestep.
                natoms (int): Total number of atoms in the box.
                box (LammpsBox): Simulation box.
                data (pd.DataFrame): Dumped atomic data.

            """
            self.timestep = timestep
            self.natoms = natoms
            self.box = box
            self.data = data

        @classmethod
        def from_string(cls, string):
            """
            Constructor from string parsing.

            Args:
                string (str): Input string.

            """
            lines = string.split("\n")
            timestep = int(lines[1])
            natoms = int(lines[3])
            box_arr = np.loadtxt(StringIO("\n".join(lines[5:8])))
            bounds = box_arr[:, :2]
            tilt = None
            if "xy xz yz" in lines[4]:
                tilt = box_arr[:, 2]
                x = (0, tilt[0], tilt[1], tilt[0] + tilt[1])
                y = (0, tilt[2])
                bounds -= np.array([[min(x), max(x)], [min(y), max(y)], [0, 0]])
            box = LammpsBox(bounds, tilt)
            data_head = lines[8].replace("ITEM: ATOMS", "").split()
            data = pd.read_csv(StringIO("\n".join(lines[9:])), names=data_head,
                               delim_whitespace=True)
            return cls(timestep, natoms, box, data)

        @classmethod
        def from_dict(cls, d):
            """
            Args:
                d (dict): Dict representation

            Returns:
                LammpsDump
            """
            items = {"timestep": d["timestep"], "natoms": d["natoms"]}
            items["box"] = LammpsBox.from_dict(d["box"])
            items["data"] = pd.read_json(d["data"], orient="split")
            return cls(**items)

        def as_dict(self):
            """
            Returns: MSONable dict
            """
            d = dict()
            d["@module"] = self.__class__.__module__
            d["@class"] = self.__class__.__name__
            d["timestep"] = self.timestep
            d["natoms"] = self.natoms
            d["box"] = self.box.as_dict()
            d["data"] = self.data.to_json(orient="split")
            return d

    def parse_lammps_dumps(file_pattern):
        """
        Generator that parses dump file(s).

        Args:
            file_pattern (str): Filename to parse. The timestep wildcard
                (e.g., dump.atom.'*') is supported and the files are parsed
                in the sequence of timestep.

        Yields:
            LammpsDump for each available snapshot.

        """
        files = glob.glob(file_pattern)
        if len(files) > 1:
            pattern = r"%s" % file_pattern.replace("*", "([0-9]+)")
            pattern = pattern.replace("\\", "\\\\")
            files = sorted(files,
                           key=lambda f: int(re.match(pattern, f).group(1)))

        for fname in files:
            with zopen(fname, "rt") as f:
                dump_cache = []
                for line in f:
                    if line.startswith("ITEM: TIMESTEP"):
                        if len(dump_cache) > 0:
                            yield LammpsDump.from_string("".join(dump_cache))
                        dump_cache = [line]
                    else:
                        dump_cache.append(line)
                yield LammpsDump.from_string("".join(dump_cache))

    def parse_lammps_log(filename="log.lammps"):
        """
        Parses log file with focus on thermo data. Both one and multi line
        formats are supported. Any incomplete runs (no "Loop time" marker)
        will not be parsed.

        Notes:
            SHAKE stats printed with thermo data are not supported yet.
            They are ignored in multi line format, while they may cause
            issues with dataframe parsing in one line format.

        Args:
            filename (str): Filename to parse.

        Returns:
            [pd.DataFrame] containing thermo data for each completed run.

        """
        with open(filename) as f:
            lines = f.readlines()
        begin_flag = ("Memory usage per processor =",
                      "Per MPI rank memory allocation (min/avg/max) =")
        end_flag = "Loop time of"
        begins, ends = [], []
        for i, l in enumerate(lines):
            if l.startswith(begin_flag):
                begins.append(i)
            elif l.startswith(end_flag):
                ends.append(i)

        def _parse_thermo(lines):
            multi_pattern = r"-+\s+Step\s+([0-9]+)\s+-+"
            # multi line thermo data
            if re.match(multi_pattern, lines[0]):
                timestep_marks = [i for i, l in enumerate(lines)
                                  if re.match(multi_pattern, l)]
                timesteps = np.split(lines, timestep_marks)[1:]
                dicts = []
                kv_pattern = r"([0-9A-Za-z_\[\]]+)\s+=\s+([0-9eE\.+-]+)"
                for ts in timesteps:
                    data = {}
                    data["Step"] = int(re.match(multi_pattern, ts[0]).group(1))
                    data.update({k: float(v) for k, v
                                 in re.findall(kv_pattern, "".join(ts[1:]))})
                    dicts.append(data)
                df = pd.DataFrame(dicts)
                # rearrange the sequence of columns
                columns = ["Step"] + [k for k, v in
                                      re.findall(kv_pattern,
                                                 "".join(timesteps[0][1:]))]
                df = df[columns]
            # one line thermo data
            else:
                df = pd.read_csv(StringIO("".join(lines)), delim_whitespace=True)
            return df

        runs = []
        for b, e in zip(begins, ends):
            runs.append(_parse_thermo(lines[b + 1:e]))
        return runs