Source code for htesp.crystal

#!/usr/bin/env python
#"""Writen by Niraj K. Nepal, Ph.D."""
"""Module to extract information about systems for running calculations"""
import sys
from pymatgen.core import structure
from pymatgen.io.pwscf import PWInput
from htesp.htepc import MpConnect as mpc
from htesp.element_extract import plain_value


def crystal_extract(filename):
    """
    Function to extract lattice parameters from Quantum Espresso (QE) input files using ASE package.

    Parameters:
    -----------
    filename : str
        QE input file or VASP POSCAR.

    Returns:
    --------
    None

    Prints lattice parameters including cell parameters, cell volume, crystal system, and spacegroup.
    """
    if 'scf' in filename:
        cell_inp = PWInput.from_file(filename).structure
    elif 'POSCAR' in filename or 'CONTCAR' in filename:
        cell_inp = structure.Structure.from_file(filename)
    else:
        # ``cell_inp`` would otherwise be unbound and the next line would raise
        # an unhelpful NameError.
        raise ValueError(
            "cannot tell what {} is: expected a QE 'scf' input or a VASP "
            "POSCAR/CONTCAR".format(filename))
    vol = cell_inp.lattice.volume
    cellpar = cell_inp.lattice.parameters
    sg_info = cell_inp.get_space_group_info()
    print("************ Printing structural parameters *****************\n")
    print("*         Cell par: {}".format(cellpar))
    print('*         Cell volume: {} '.format(round(vol,4)) + r'$\AA^3$')
    print("*         Spacegroup: {}              ".format(sg_info))
    print("************************************************************\n")




def convex_hull(comp):
    """
    Function to extract energy above hull from the Materials Project database.

    Parameters:
    -----------
    comp : str
        Compound name.

    Returns:
    --------
    tuple
        A tuple containing the energy above hull, formation energy per atom, and magnetic ordering information.
    """
    obj = mpc()
    print(comp)
    obj.setting(comp)
    # FIX(28): emmet's Ordering is a plain Enum, so the caller comparing
    # this against 'NM' needs the value, not the member.
    order = plain_value(obj.data['ordering'])
    return obj.data['energy_above_hull'],obj.data['formation_energy_per_atom'],order



def main(filename=None, argv=None):
    """
    Main function to extract properties from Materials Project and relaxed outputs.

    Usage:
    ------
    python script.py filename comp cond

    filename : str
        Name of the QE input file.

    comp : str
        Compound name.

    cond : str
        Condition indicator.

    Returns:
    --------
    None
    """
    # FIX(21): ``main`` is the entry point htesp.workflow.run_helper() calls;
    # the file name may also be passed directly.
    if filename is None:
        argv = list(sys.argv[1:] if argv is None else argv)
        if not argv:
            raise SystemExit("usage: crystal.py <scf input | POSCAR | CONTCAR>")
        filename = argv[0]
    #comp = sys.argv[2]
    #ehull,form_e,order=convex_hull(comp)
    #cond = sys.argv[3]
    #if cond == "initial":
    #    print("\n")
    #    print("******* Extracting properties from materials project and relaxed outputs *********\n")
    #    print("*         FE (eV/atom): {}                 ".format(round(form_e,4)))
    #    print("*         e_above_hull (eV/atom): {}                 ".format(ehull))
    #    print("*         Ordering: {}                   ".format(order) + "\n")
    crystal_extract(filename)

if __name__ == "__main__":
    main()