Example #1
0
    def __init__(self):
        self.control = Control()
        self.system = System()
        self.electrons = Electrons()
        self.ions = Ions()
        self.cell = Cell()

        self.atomic_species = AtomicSpecies()
        self.atomic_positions = AtomicPositions()
        self.k_points = KPoints()
        self.cell_parameters = CellParameters()
        # Not Implemented (Card not a class)
        #self.occupations = Card("OCCUPATIONS")
        #self.constrains = Card("CONTRAINTS")
        #self.atomicforces = Card("ATOMIC_FORCES")

        self.namelist_asoc = {
            "control": self.control,
            "system": self.system,
            "electrons": self.electrons,
            "ions": self.ions,
            "cell": self.cell
        }
Example #2
0
class PWBase:
    """
    PW Quantum Espresso Base

    From this class you can:
     - initialize the input
     - create inputfile
     - validate input
     - run pw.x
    """

    def __init__(self):
        self.control = Control()
        self.system = System()
        self.electrons = Electrons()
        self.ions = Ions()
        self.cell = Cell()

        self.atomic_species = AtomicSpecies()
        self.atomic_positions = AtomicPositions()
        self.k_points = KPoints()
        self.cell_parameters = CellParameters()
        # Not Implemented (Card not a class)
        #self.occupations = Card("OCCUPATIONS")
        #self.constrains = Card("CONTRAINTS")
        #self.atomicforces = Card("ATOMIC_FORCES")

        self.namelist_asoc = {
            "control": self.control,
            "system": self.system,
            "electrons": self.electrons,
            "ions": self.ions,
            "cell": self.cell
        }

    def add_keypairs_to_namelist(self, qe_keypairs):
        """ Adds the respective keys to each namelist 

        """
        for name, keypairs in qe_keypairs.items():
            namelist = self.namelist_asoc.get(name.lower())
            if namelist:
                namelist.add_keypairs(keypairs)
            else:
                error_str = "{0} is not valid namelist"
                raise Exception(error_str.format(name))

    def to_string(self, header=True):
        qe_str = ""

        if (header == True):
            qe_str += "! File Autogenerated from Python QE\n"

        ## NameLists
        qe_str += self.control.to_string()
        qe_str += self.system.to_string()
        qe_str += self.electrons.to_string()
        qe_str += self.ions.to_string()
        qe_str += self.cell.to_string()

        ## Cards
        qe_str += str(self.atomic_species)
        qe_str += str(self.atomic_positions)
        qe_str += str(self.k_points)

        # Only needed if unitcell is not defined
        # By ibrav
        if self.system.get_current_value("ibrav") == 0:
            qe_str += str(self.cell_parameters)

        # Not Implemented
        # qe_str += str(self.occupations)
        # qe_str += str(self.contraints)
        # qe_str += str(self.atomic_forces)
        return qe_str

    def to_file(self, filename, input_format="fortran"):
        """ Writes QE configuration to <filename> in format
        specified. Currently only supports the Fortran style. 

        """
        if input_format == "fortran":
            with open(filename, "w") as qefile:
                qefile.write(self.to_string())
        else:
            raise Exception("xml input specification not supported")

    def run(self, infile="", outfile="", errfile=""):
        """Runs QE pw.x.

        If stdin, stdout, stderr filenames are not defined
        no file is created for the given input or output.

        If 'infile' is defined the program will run from the
        file rather than stdin via '-i'.

        Notice:
        QE will still create the save files in the directory
        specified by 'outfile' and 'errfile' in control namelist
        """
        from subprocess import Popen, PIPE
        from time import time
        from pyqe import config

        start_time = time()
        if infile != "":
            self.to_file(infile)

            pw_command = config.prefix + ["pw.x", '-i', infile] + config.postfix
            proc = Popen(pw_command, stdout=PIPE, stderr=PIPE)
            pw_output = proc.communicate()
        else:
            pw_input = self.to_string()

            pw_command = config.prefix + ["pw.x"] + config.postfix
            proc = Popen(pw_command, stdin=PIPE, stdout=PIPE, stderr=PIPE)
            pw_output = proc.communicate(pw_input.encode())

        proc.wait()
        end_time = time()

        pw_out = pw_output[0].decode()
        pw_err = pw_output[1].decode()

        if outfile != "":
            with open(outfile, "w") as f:
                f.write(pw_out)

        if errfile != "":
            with open(errfile, "w") as f:
                f.write(pw_err)

        if proc.returncode != 0:
            with open("CRASH", "r") as f:
                print("Quantum Espresso CRASH FILE:\n{0}".format(f.read()))
            raise Exception("pw.x CRASHED")

        from pyqe.io import read_out_file, read_data_file
        results = read_out_file(pw_out)

        # Read save file output
        prefix = self.control.get_current_value("prefix")
        outdir = self.control.get_current_value("outdir")
        if outdir[-1] == '/':
            data_file = outdir + prefix + '.save/data-file.xml'
        else:
            data_file = outdir + '/' + prefix + '.save/data-file.xml'
        results.update({"data-file": read_data_file(data_file)})

        # Add run related info
        results.update({'time': end_time - start_time})

        return results

    def validate(self):
        """ Each Namelist and Card will validate its contents.
        Sometimes they will need access to global information.  (not
        sure how to handle this yet) """
        self.control.validate(self)
        self.system.validate(self)
        self.electrons.validate(self)
        self.ions.validate(self)
        self.cell.validate(self)

        self.atomic_species.validate()
        self.atomic_positions.validate()
        self.k_points.validate()
        self.cell_parameters.validate()