Source code for pymatgen.io.shengbte

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

"""
This module implements reading and writing of ShengBTE CONTROL files.
"""

import warnings
from typing import Dict, List, Optional, Union, Any

import numpy as np
from monty.dev import requires
from monty.json import MSONable

from pymatgen import Structure
from pymatgen.io.vasp import Kpoints

try:
    import f90nml
except ImportError:
    f90nml = None

__author__ = "Rees Chang, Alex Ganose"
__copyright__ = "Copyright 2019, The Materials Project"
__version__ = "0.1"
__email__ = "rc564@cornell.edu, aganose@lbl.gov"
__date__ = "June 27, 2019"


[docs]class Control(MSONable, dict): """ Class for reading, updating, and writing ShengBTE CONTROL files. See https://bitbucket.org/sousaw/shengbte/src/master/ for more detailed description and default values of CONTROL arguments. """ required_params = [ "nelements", "natoms", "ngrid", "lattvec", "types", "elements", "positions", "scell", ] allocations_keys = ["nelements", "natoms", "ngrid", "norientations"] crystal_keys = [ "lfactor", "lattvec", "types", "elements", "positions", "masses", "gfactors", "epsilon", "born", "scell", "orientations", ] params_keys = [ "t", "t_min", "t_max", "t_step", "omega_max", "scalebroad", "rmin", "rmax", "dr", "maxiter", "nticks", "eps", ] flags_keys = [ "nonanalytic", "convergence", "isotopes", "autoisotopes", "nanowires", "onlyharmonic", "espresso", ] def __init__( self, ngrid: Optional[List[int]] = None, temperature: Union[float, Dict[str, float]] = 300, **kwargs ): """ Args: ngrid: Reciprocal space grid density as a list of 3 ints. temperature: The temperature to calculate the lattice thermal conductivity for. Can be given as a single float, or a dictionary with the keys "min", "max", "step". **kwargs: Other ShengBTE parameters. Several parameters are required for ShengBTE to run - we have listed these parameters below: - nelements (int): number of different elements in the compound - natoms (int): number of atoms in the unit cell - lattvec (size 3x3 array): real-space lattice vectors, in units of lfactor - lfactor (float): unit of measurement for lattice vectors (nm). I.e., set to 0.1 if lattvec given in Angstrom. - types (size natom list): a vector of natom integers, ranging from 1 to nelements, assigning an element to each atom in the system - elements (size natom list): a vector of element names - positions (size natomx3 array): atomic positions in lattice coordinates - scell (size 3 list): supercell sizes along each crystal axis used for the 2nd-order force constant calculation """ super().__init__() if ngrid is None: ngrid = [25, 25, 25] self["ngrid"] = ngrid if isinstance(temperature, (int, float)): self["t"] = temperature elif isinstance(temperature, dict): self["t_min"] = temperature["min"] self["t_max"] = temperature["max"] self["t_step"] = temperature["step"] else: raise ValueError( "Unsupported temperature type, must be float or dict" ) self.update(kwargs)
[docs] @classmethod @requires( f90nml, "ShengBTE Control object requires f90nml to be installed. " "Please get it at https://pypi.org/project/f90nml.", ) def from_file(cls, filepath: str): """ Read a CONTROL namelist file and output a 'Control' object Args: filepath: Path of the CONTROL file. Returns: 'Control' object with parameters instantiated. """ nml = f90nml.read(filepath) sdict = nml.todict() all_dict: Dict[str, Any] = {} all_dict.update(sdict["allocations"]) all_dict.update(sdict["crystal"]) all_dict.update(sdict["parameters"]) all_dict.update(sdict["flags"]) all_dict.pop("_start_index") # remove unnecessary cruft return cls.from_dict(all_dict)
[docs] @classmethod def from_dict(cls, control_dict: Dict): """ Write a CONTROL file from a Python dictionary. Description and default parameters can be found at https://bitbucket.org/sousaw/shengbte/src/master/. Note some parameters are mandatory. Optional parameters default here to None and will not be written to file. Args: control_dict: A Python dictionary of ShengBTE input parameters. """ return cls(**control_dict)
[docs] @requires( f90nml, "ShengBTE Control object requires f90nml to be installed. " "Please get it at https://pypi.org/project/f90nml.", ) def to_file(self, filename: str = "CONTROL"): """ Writes ShengBTE CONTROL file from 'Control' object Args: filename: A file name. """ for param in self.required_params: if param not in self.as_dict(): warnings.warn( "Required parameter '{}' not specified!".format(param) ) alloc_dict = _get_subdict(self, self.allocations_keys) alloc_nml = f90nml.Namelist({"allocations": alloc_dict}) control_str = str(alloc_nml) + "\n" crystal_dict = _get_subdict(self, self.crystal_keys) crystal_nml = f90nml.Namelist({"crystal": crystal_dict}) control_str += str(crystal_nml) + "\n" params_dict = _get_subdict(self, self.params_keys) params_nml = f90nml.Namelist({"parameters": params_dict}) control_str += str(params_nml) + "\n" flags_dict = _get_subdict(self, self.flags_keys) flags_nml = f90nml.Namelist({"flags": flags_dict}) control_str += str(flags_nml) + "\n" with open(filename, "w") as file: file.write(control_str)
[docs] @classmethod def from_structure( cls, structure: Structure, reciprocal_density: Optional[int] = 50000, **kwargs ): """ Get a ShengBTE control object from a structure. Args: structure: A structure object. reciprocal_density: If not None, the q-point grid ("ngrid") will be set using this density. kwargs: Additional options to be passed to the Control constructor. See the docstring of the __init__ method for more details Returns: A ShengBTE control object. """ elements = list(map(str, structure.composition.elements)) unique_nums = np.unique(structure.atomic_numbers) types_dict = dict(zip(unique_nums, range(len(unique_nums)))) types = [types_dict[i] + 1 for i in structure.atomic_numbers] control_dict = { "nelements": structure.ntypesp, "natoms": structure.num_sites, "norientations": 0, "lfactor": 0.1, "lattvec": structure.lattice.matrix.tolist(), "elements": elements, "types": types, "positions": structure.frac_coords.tolist(), } if reciprocal_density: kpoints = Kpoints.automatic_density(structure, reciprocal_density) control_dict["ngrid"] = kpoints.kpts[0] control_dict.update(**kwargs) return Control(**control_dict)
[docs] def get_structure(self) -> Structure: """ Get a pymatgen Structure from a ShengBTE control object. The control object must have the "lattvec", "types", "elements", and "positions" settings otherwise an error will be thrown. Returns: The structure. """ required = ["lattvec", "types", "elements", "positions"] if not all([r in self for r in required]): raise ValueError( "All of ['lattvec', 'types', 'elements', 'positions'] must be " "in control object" ) unique_elements = self["elements"] n_unique_elements = len(unique_elements) element_map = dict( zip(range(1, n_unique_elements + 1), unique_elements) ) species = [element_map[i] for i in self["types"]] cell = np.array(self["lattvec"]) if "lfactor" in self: cell *= self["lfactor"] * 10 # to nm then to Angstrom return Structure(cell, species, self["positions"])
[docs] def as_dict(self): """ Returns: MSONAble dict """ return dict(self)
def _get_subdict(master_dict, subkeys): """Helper method to get a set of keys from a larger dictionary""" return { k: master_dict[k] for k in subkeys if k in master_dict and master_dict[k] is not None }