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electrochemistry/echem/io_data/interphon.py
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227
electrochemistry/echem/io_data/interphon.py
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import os
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import re
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import shutil
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from typing import Callable
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from echem.io_data.jdftx import Ionpos, Lattice
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from echem.io_data.vasp import Poscar
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from echem.core.structure import Structure
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from echem.core.constants import THz2eV
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from echem.core.thermal_properties import ThermalProperties
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from InterPhon.core import PreProcess, PostProcess
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from nptyping import NDArray, Shape, Number
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from typing import Union
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from pathlib import Path
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class InterPhonInterface(ThermalProperties):
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def __init__(self,
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folder_to_jdftx_files: Union[str, Path],
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folder_files_to_copy: Union[str, Path] = None,
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select_fun: Callable[[Structure], list[list[str]]] = None,
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user_args: dict = None,
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sym_flag: bool = True):
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if isinstance(folder_to_jdftx_files, str):
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folder_to_jdftx_files = Path(folder_to_jdftx_files)
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if isinstance(folder_files_to_copy, str):
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folder_files_to_copy = Path(folder_files_to_copy)
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self.folder_to_jdftx_files = folder_to_jdftx_files
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self.folder_files_to_copy = folder_files_to_copy
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self.select_fun = select_fun
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self.user_args = user_args
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self.sym_flag = sym_flag
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self.post_process = None
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self.eigen_freq = None
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self.weights = None
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def _create_poscar_for_interphon(self,
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folder_to_jdftx_files: Path,
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select_fun: Callable[[Structure], list[list[str]]] = None) -> None:
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"""
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Function creates POSCAR with unitcell for InterPhon adding selective dynamics data
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Args:
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folder_to_jdftx_files (str): path to folder with jdft.ionpos and jdft.lattice files
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select_fun (Callable, optional): function that take Structure as input and provides list with
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selective dynamics data for POSCAR class. All atoms are allowed to move in default.
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"""
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ionpos = Ionpos.from_file(folder_to_jdftx_files / 'jdft.ionpos')
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lattice = Lattice.from_file(folder_to_jdftx_files / 'jdft.lattice')
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poscar = ionpos.convert('vasp', lattice)
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if select_fun is not None:
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sd_data = select_fun(poscar.structure)
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else:
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sd_data = [['T', 'T', 'T'] for _ in range(poscar.structure.natoms)]
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poscar.sdynamics_data = sd_data
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poscar.to_file(folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon')
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def _make_preprocess(self,
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poscar_unitcell: Path,
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folder_to_disps: Path,
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folder_files_to_copy: Path = None,
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user_args: dict = None,
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sym_flag: bool = True) -> None:
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"""
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Function creates folders with POSCARs with displaced atoms and all other necessary files for calculation
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Args:
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poscar_unitcell (str): path to the POSCAR file that contains the unitcell for IterPhon
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with defined sd dynamics
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folder_to_disps (str): path to a folder where all new folders with corresponding POSCARs with
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displaced atoms will be created
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folder_files_to_copy (str, optional): path to a folder from which all files will be copied to each
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new folder with new POSCARs
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user_args (dict, optional): dist with all necessary information for the InterPhon PreProcess class.
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Only 2D periodicity is supported. If you want switch off symmetries, you have to define 'periodicity'
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in user_args and set sym_flag=False
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Example and default value: user_args = {'dft_code': 'vasp', 'displacement': 0.05,
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'enlargement': "1 1 1", 'periodicity': "1 1 0"}
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sym_flag (bool, optional): if True the symmetry will be applied. Only 2D symmetries are supported
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"""
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if user_args is None:
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user_args = {'dft_code': 'vasp',
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'displacement': 0.05,
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'enlargement': '1 1 1',
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'periodicity': '1 1 0'}
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if poscar_unitcell != folder_to_disps / 'POSCAR_unitcell_InterPhon':
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shutil.copyfile(poscar_unitcell, folder_to_disps / 'POSCAR_unitcell_InterPhon')
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pre_process = PreProcess()
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pre_process.set_user_arg(user_args)
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pre_process.set_unit_cell(in_file=str(poscar_unitcell),
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code_name='vasp')
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pre_process.set_super_cell(out_file=str(folder_to_disps / 'POSCAR_supercell_InterPhon'),
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code_name='vasp')
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pre_process.write_displace_cell(out_file=str(folder_to_disps / 'POSCAR'),
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code_name='vasp',
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sym_flag=sym_flag)
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poscars_disp = [f for f in folder_to_disps.iterdir() if f.is_file() and bool(re.search(r'POSCAR-\d{4}$',
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f.name))]
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for poscar_disp in poscars_disp:
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poscar = Poscar.from_file(poscar_disp)
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ionpos, lattice = poscar.convert('jdftx')
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subfolder_to_disp = folder_to_disps / poscar_disp.name[-4:]
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if not os.path.isdir(subfolder_to_disp):
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os.mkdir(subfolder_to_disp)
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ionpos.to_file(subfolder_to_disp / 'jdft.ionpos')
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lattice.to_file(subfolder_to_disp / 'jdft.lattice')
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shutil.copyfile(folder_to_disps / poscar_disp, subfolder_to_disp / 'POSCAR')
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if folder_files_to_copy is not None:
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files_to_copy = [f for f in folder_files_to_copy.iterdir() if f.is_file()]
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for file in files_to_copy:
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shutil.copyfile(file, subfolder_to_disp / file.name)
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with open(folder_to_disps / 'user_args_InterPhon', 'w') as file:
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for key, value in user_args.items():
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file.write(f'{key}: {value}\n')
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def _make_postprocess(self,
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folder_to_disps: Path,
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filepath_unitcell: Path,
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filepath_supercell: Path,
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filepath_kpoints: Path,
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user_args: dict = None,
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sym_flag: bool = True) -> None:
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"""
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Function process the output files after all calculations with displaced atoms are finished
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Args:
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folder_to_disps (str): path to the folder contains all folders with performed calculations with
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atom displacements
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filepath_unitcell (str): path to the POSCAR file that contains the unitcell for IterPhon
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with defined sd dynamics
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filepath_supercell (str): path to the POSCAR file produced by InterPhon with proper enlargement
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filepath_kpoints (str): path to the KPOINTS file. The phonons will be assessed in the given k-points
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user_args (dict, optional): dist with all necessary information for the InterPhon PreProcess class.
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Example and default value: user_args = {'dft_code': 'vasp', 'displacement': 0.05,
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'enlargement': "1 1 1", 'periodicity': "1 1 0"}
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sym_flag (bool, optional): if True the symmetry will be applied. Only 2D symmetries are supported
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"""
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if user_args is None:
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user_args = {'dft_code': 'vasp',
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'displacement': 0.05,
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'enlargement': '1 1 1',
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'periodicity': '1 1 0'}
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output_paths = [f / 'output.out' for f in folder_to_disps.iterdir()
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if f.is_dir() and bool(re.search(r'\d{4}$', f.name))]
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post_process = PostProcess(in_file_unit_cell=str(filepath_unitcell),
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in_file_super_cell=str(filepath_supercell),
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code_name='vasp')
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post_process.set_user_arg(user_args)
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post_process.set_reciprocal_lattice()
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post_process.set_force_constant(force_files=[str(f) for f in output_paths],
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code_name='jdftx',
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sym_flag=sym_flag)
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post_process.set_k_points(k_file=str(filepath_kpoints))
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post_process.eval_phonon()
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self.post_process = post_process
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ThermalProperties.__init__(self, self.post_process.w_q * THz2eV)
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def create_displacements_jdftx(self):
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self._create_poscar_for_interphon(folder_to_jdftx_files=self.folder_to_jdftx_files,
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select_fun=self.select_fun)
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self._make_preprocess(poscar_unitcell=self.folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon',
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folder_to_disps=self.folder_to_jdftx_files,
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folder_files_to_copy=self.folder_files_to_copy,
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user_args=self.user_args,
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sym_flag=self.sym_flag)
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def get_phonons(self) -> NDArray[Shape['Nkpts, Nfreq'], Number]:
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if self.post_process is None:
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self._make_postprocess(folder_to_disps=self.folder_to_jdftx_files,
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filepath_unitcell=self.folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon',
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filepath_supercell=self.folder_to_jdftx_files / 'POSCAR_supercell_InterPhon',
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filepath_kpoints=self.folder_to_jdftx_files / 'KPOINTS',
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user_args=self.user_args,
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sym_flag=self.sym_flag)
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return self.eigen_freq
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def get_Gibbs_ZPE(self) -> float:
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if self.eigen_freq is None:
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self._make_postprocess(folder_to_disps=self.folder_to_jdftx_files,
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filepath_unitcell=self.folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon',
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filepath_supercell=self.folder_to_jdftx_files / 'POSCAR_supercell_InterPhon',
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filepath_kpoints=self.folder_to_jdftx_files / 'KPOINTS',
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user_args=self.user_args,
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sym_flag=self.sym_flag)
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return ThermalProperties.get_Gibbs_ZPE(self)
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def get_enthalpy_vib(self,
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T: float) -> float:
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if self.eigen_freq is None:
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self._make_postprocess(folder_to_disps=self.folder_to_jdftx_files,
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filepath_unitcell=self.folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon',
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filepath_supercell=self.folder_to_jdftx_files / 'POSCAR_supercell_InterPhon',
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filepath_kpoints=self.folder_to_jdftx_files / 'KPOINTS',
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user_args=self.user_args,
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sym_flag=self.sym_flag)
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return ThermalProperties.get_enthalpy_vib(self, T)
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def get_TS_vib(self,
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T: float) -> float:
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if self.eigen_freq is None:
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self._make_postprocess(folder_to_disps=self.folder_to_jdftx_files,
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filepath_unitcell=self.folder_to_jdftx_files / 'POSCAR_unitcell_InterPhon',
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filepath_supercell=self.folder_to_jdftx_files / 'POSCAR_supercell_InterPhon',
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filepath_kpoints=self.folder_to_jdftx_files / 'KPOINTS',
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user_args=self.user_args,
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sym_flag=self.sym_flag)
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return ThermalProperties.get_TS_vib(self, T)
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