Source code for pychemia.code.codes

from abc import ABCMeta, abstractmethod
import os
import subprocess


class Codes:
    __metaclass__ = ABCMeta

    def __init__(self):
        self.stdin_file = None
        self.stdout_file = None
        self.stderr_file = None
        self.stdin_filename = None
        self.stdout_filename = None
        self.stderr_filename = None
        self.binary = None
        self.runner = None
        self.workdir = None

    @abstractmethod
    def initialize(self, structure, workdir=None, kpoints=None, binary=None):
        pass

    @abstractmethod
    def set_inputs(self):
        pass

    @abstractmethod
    def get_outputs(self):
        pass

    @abstractmethod
    def finalize(self):
        pass

    def run(self, use_mpi=False, omp_max_threads=0, mpi_num_procs=1):
        """
        Execute the binary and return a reference to the subprocess
        created

        :param use_mpi: If mpirun will be called to execute the binary
        :param omp_max_threads: Number of OpenMP threads to be created
                                by default the environment variable
                                OMP_NUM_THREADS is not changed
        :param mpi_num_procs: Number of MPI processes
        :return:
        """
        cwd = os.getcwd()
        os.chdir(self.workdir)
        if omp_max_threads > 0:
            os.environ["OMP_NUM_THREADS"] = str(omp_max_threads)
        if self.stdin_filename is not None:
            self.stdin_file = open(self.stdin_filename, 'r')
        if self.stdout_filename is not None:
            self.stdout_file = open(self.stdout_filename, 'w')
        if self.stderr_filename is not None:
            self.stderr_file = open(self.stderr_filename, 'w')
        if use_mpi:
            sp = subprocess.Popen(['mpirun', '-n', str(mpi_num_procs), self.binary],
                                  stdout=self.stdout_file, stderr=self.stderr_file, stdin=self.stdin_file)
        else:
            sp = subprocess.Popen(self.binary, stdout=self.stdout_file, stderr=self.stderr_file, stdin=self.stdin_file)
        os.chdir(cwd)
        self.runner = sp
        return sp