Chimie Théorique » scripts_chimie4psmn » DockOnSurf

    subdirectory, it reads, from each subirectory, the final coordinates

    resulting from the calculation and returns a list of objects adequate to the

    required library.

    @param code: the code that produced the calculation results files.

    @param req: The required library object type to make the list of (eg. rdkit,

                ase)

def read_energies(code, run_type):

    """Reads the energies resulting from finished calculations.

    Given a run_type ('isolated', 'screening' or 'refinement') directory

    containing different subdirectories with finished calculations in every

    subdirectory, it reads the final energies of calculations inside each

    subdirectory.

    @param code: the code that produced the calculation results files.

    @param run_type: the type of calculation (and also the name of the folder)

                     containing the calculation subdirectories.

    @return: list of energies

    """

    import os

    import numpy as np

    from utilities import tail

    energies = []

    if code == 'cp2k':

        pattern = '-pos-1.xyz'

        for conf in os.listdir(run_type):

            for fil in os.listdir(f"{run_type}/{conf}"):

                if pattern in fil:

                    traj_fh = open(f"{run_type}/{conf}/{fil}", 'rb')

                    num_atoms = int(traj_fh.readline().strip())

                    last_geo = tail(traj_fh, num_atoms + 2).splitlines()

                    for line in last_geo:

                        if 'E =' in line:

                            energies.append(float(line.split('E =')[1]))

    return np.array(energies)