pymatgen.command_line.mcsqs_caller — pymatgen 2020.7.3 documentation

# Source code for pymatgen.command_line.mcsqs_caller

    """
    Module to call mcsqs, distributed with AT-AT
    https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/
    """

    import os
    import warnings
    from subprocess import Popen, TimeoutExpired
    from typing import Dict, Union, List, NamedTuple, Optional
    from pathlib import Path

    from monty.dev import requires
    from monty.os.path import which
    import tempfile

    from pymatgen import Structure

    class Sqs(NamedTuple):
        """
        Return type for run_mcsqs.
        """

        bestsqs: Structure
        objective_function: Union[float, str]
        allsqs: List
        directory: str

    @requires(
        which("mcsqs") and which("str2cif"),
        "run_mcsqs requires first installing AT-AT, "
        "see https://www.brown.edu/Departments/Engineering/Labs/avdw/atat/",
    )
    def run_mcsqs(
        structure: Structure,
        clusters: Dict[int, float],
        scaling: Union[int, List[int]],
        search_time: float = 60,
        directory: Optional[str] = None,
        instances: Optional[int] = None,
        temperature: Union[int, float] = 1,
        wr: float = 1,
        wn: float = 1,
        wd: float = 0.5,
        tol: float = 1e-3,
    ) -> Sqs:
        """
        Helper function for calling mcsqs with different arguments
        Args:
            structure (Structure): Disordered pymatgen Structure object
            clusters (dict): Dictionary of cluster interactions with entries in the form
                number of atoms: cutoff in angstroms
            scaling (int or list): Scaling factor to determine supercell. Two options are possible:
                    a. (preferred) Scales number of atoms, e.g., for a structure with 8 atoms,
                       scaling=4 would lead to a 32 atom supercell
                    b. A sequence of three scaling factors, e.g., [2, 1, 1], which
                       specifies that the supercell should have dimensions 2a x b x c
        Keyword Args:
            search_time (float): Time spent looking for the ideal SQS in minutes (default: 60)
            directory (str): Directory to run mcsqs calculation and store files (default: None
                runs calculations in a temp directory)
            instances (int): Specifies the number of parallel instances of mcsqs to run
                (default: number of cpu cores detected by Python)
            temperature (int or float): Monte Carlo temperature (default: 1), "T" in atat code
            wr (int or float): Weight assigned to range of perfect correlation match in objective
                function (default = 1)
            wn (int or float): Multiplicative decrease in weight per additional point in cluster (default: 1)
            wd (int or float): Exponent of decay in weight as function of cluster diameter (default: 0.5)
            tol (int or float): Tolerance for matching correlations (default: 1e-3)

        Returns:
            Tuple of Pymatgen structure SQS of the input structure, the mcsqs objective function,
                list of all SQS structures, and the directory where calculations are run
        """

        num_atoms = len(structure)

        if structure.is_ordered:
            raise ValueError("Pick a disordered structure")

        if instances is None:
            # os.cpu_count() can return None if detection fails
            instances = os.cpu_count()

        original_directory = os.getcwd()
        if not directory:
            directory = tempfile.mkdtemp()
        os.chdir(directory)

        if isinstance(scaling, (int, float)):

            if scaling % 1:
                raise ValueError("Scaling should be an integer, not {}".format(scaling))
            mcsqs_find_sqs_cmd = ["mcsqs", "-n {}".format(scaling * num_atoms)]

        else:

            # Set supercell to identity (will make supercell with pymatgen)
            with open("sqscell.out", "w") as f:
                f.write("1\n1 0 0\n0 1 0\n0 0 1\n")
            structure = structure * scaling
            mcsqs_find_sqs_cmd = ["mcsqs", "-rc", "-n {}".format(num_atoms)]

        structure.to(filename="rndstr.in")

        # Generate clusters
        mcsqs_generate_clusters_cmd = ["mcsqs"]
        for num in clusters:
            mcsqs_generate_clusters_cmd.append("-" + str(num) + "=" + str(clusters[num]))

        # Run mcsqs to find clusters
        p = Popen(mcsqs_generate_clusters_cmd)
        p.communicate()

        # Generate SQS structures
        add_ons = [
            "-T {}".format(temperature),
            "-wr {}".format(wr),
            "-wn {}".format(wn),
            "-wd {}".format(wd),
            "-tol {}".format(tol),
        ]

        mcsqs_find_sqs_processes = []
        if instances and instances > 1:
            # if multiple instances, run a range of commands using "-ip"
            for i in range(instances):
                instance_cmd = ["-ip {}".format(i + 1)]
                cmd = mcsqs_find_sqs_cmd + add_ons + instance_cmd
                p = Popen(cmd)
                mcsqs_find_sqs_processes.append(p)
        else:
            # run normal mcsqs command
            cmd = mcsqs_find_sqs_cmd + add_ons
            p = Popen(cmd)
            mcsqs_find_sqs_processes.append(p)

        try:
            for idx, p in enumerate(mcsqs_find_sqs_processes):
                p.communicate(timeout=search_time * 60)

            if instances and instances > 1:
                p = Popen(["mcsqs", "-best"])
                p.communicate()

            if os.path.exists("bestsqs.out") and os.path.exists("bestcorr.out"):
                return _parse_sqs_path(".")

            raise RuntimeError("mcsqs exited before timeout reached")

        except TimeoutExpired:
            for p in mcsqs_find_sqs_processes:
                p.kill()
                p.communicate()

            # Find the best sqs structures
            if instances and instances > 1:

                if not os.path.exists("bestcorr1.out"):
                    raise RuntimeError(
                        "mcsqs did not generate output files, "
                        "is search_time sufficient or are number of instances too high?"
                    )

                p = Popen(["mcsqs", "-best"])
                p.communicate()

            if os.path.exists("bestsqs.out") and os.path.exists("bestcorr.out"):
                sqs = _parse_sqs_path(".")
                return sqs

            else:
                os.chdir(original_directory)
                raise TimeoutError("Cluster expansion took too long.")

    def _parse_sqs_path(path) -> Sqs:
        """
        Private function to parse mcsqs output directory
        Args:
            path: directory to perform parsing

        Returns:
            Tuple of Pymatgen structure SQS of the input structure, the mcsqs objective function,
                list of all SQS structures, and the directory where calculations are run
        """

        path = Path(path)

        # detected instances will be 0 if mcsqs was run in series, or number of instances
        detected_instances = len(list(path.glob("bestsqs*[0-9]*")))

        # Convert best SQS structure to cif file and pymatgen Structure
        p = Popen("str2cif < bestsqs.out > bestsqs.cif", shell=True, cwd=path)
        p.communicate()

        with warnings.catch_warnings():
            warnings.simplefilter("ignore")
            bestsqs = Structure.from_file(path / "bestsqs.cif")

        # Get best SQS objective function
        with open(path / "bestcorr.out", "r") as f:
            lines = f.readlines()

        objective_function_str = lines[-1].split("=")[-1].strip()
        objective_function: Union[float, str]
        if objective_function_str != "Perfect_match":
            objective_function = float(objective_function_str)
        else:
            objective_function = "Perfect_match"

        # Get all SQS structures and objective functions
        allsqs = []

        for i in range(detected_instances):
            sqs_out = "bestsqs{}.out".format(i + 1)
            sqs_cif = "bestsqs{}.cif".format(i + 1)
            corr_out = "bestcorr{}.out".format(i + 1)
            p = Popen("str2cif <" + sqs_out + ">" + sqs_cif, shell=True, cwd=path)
            p.communicate()
            with warnings.catch_warnings():
                warnings.simplefilter("ignore")
                sqs = Structure.from_file(sqs_cif)
            with open(path / corr_out, "r") as f:
                lines = f.readlines()

            objective_function_str = lines[-1].split("=")[-1].strip()
            obj: Union[float, str]
            if objective_function_str != "Perfect_match":
                obj = float(objective_function_str)
            else:
                obj = "Perfect_match"
            allsqs.append({"structure": sqs, "objective_function": obj})

        return Sqs(
            bestsqs=bestsqs,
            objective_function=objective_function,
            allsqs=allsqs,
            directory=str(path.resolve()),
        )