/modules/formats.py - Diff - DockOnSurf - Forge du Centre Blaise Pascal

Révision 1d8c374e modules/formats.py

         force_eval = cp2k.CP2K_INPUT.FORCE_EVAL_list[0]
         raw_coords = force_eval.SUBSYS.COORD.Default_keyword
         symbols = [atom.split()[0] for atom in raw_coords]
         positions = np.array([atom.split()[1:] for atom in raw_coords])
         positions = np.array([[float(coord) for coord in atom.split()[1:]]
                               for atom in raw_coords])
         if len(spec_atoms) > 0:
             add_special_atoms(spec_atoms)
         return Atoms(symbols=symbols, positions=positions)
-...
         return ase.io.read(file)
     def collect_coords(conf_list, code, run_type, spec_atms=tuple()):
         """Directs the reading of coordinates on a set of subdirectories.
         Given a dockonsurf directory hierarchy: project/run_type/conf_X
         (run_type = ['isolated', 'screening' or 'refinement']) with finished
         calculations produced by a given code, stored in every conf_X subdirectory,
         it collects the coordinates of the specified conf_X subdirectories in a
         single run_type by calling the adequate function (depending on the code) and
         returns a list of ase.Atoms objects.
         @param conf_list: List of directories where to read the coords from.
         @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.
         @param spec_atms: List of tuples containing pairs of new/traditional
             chemical symbols.
         @return: list of ase.Atoms objects.
         """
         from glob import glob
         atoms_list = []
         for conf in conf_list:
             if code == 'cp2k':
                 atoms_list.append(read_coords_cp2k(glob(f"{run_type}/{conf}/*-1"
                                                         f".restart")[0], spec_atms))
             elif code == 'vasp':
                 atoms_list.append(read_coords_vasp(f"{run_type}/{conf}/OUTCAR",
                                                    spec_atms))
             else:
                 err_msg = f"Collect coordinates not implemented for '{code}'."
                 logger.error(err_msg)
                 raise NotImplementedError(err_msg)
         return atoms_list
     def read_energy_cp2k(file):
         """Reads the CP2K out file and returns its final energy.
         """Reads the CP2K output file and returns its final energy.
         @param file: The file from which the energy should be read.
         @return: The last energy on the out file.
         @return: The last energy on the out file in eV.
         """
         out_fh = open(file, 'r')
         energy = None
-...
         return energy
     def collect_energies(conf_list, code, run_type):
         """Directs the reading of energies on a set of subdirectories.
     def collect_confs(dir_list, code, run_type, spec_atms=tuple()):
         """Reads the coordinates and energies of a list of finished calculations.
         Given a dockonsurf directory hierarchy: project/run_type/conf_X
         (run_type = ['isolated', 'screening' or 'refinement']) with finished
         calculations produced by a given code, stored in every conf_X subdirectory,
         it collects the energies of the specified conf_X subdirectories in a
         single run_type by calling the adequate function (depending on the code) and
         returns a list of energies.
         @param conf_list: List of directories where to read the energy.
         @param code: The code that produced the calculation output files.
         @param run_type: The type of calculation (and also the name of the folder)
                          containing the calculation subdirectories.
         @return: List of energies
         (run_type = ['isolated', 'screening' or 'refinement']) it reads the
         coordinates of each conf_X, it assigns its total energy from the calculation
         and assigns the conf_X label to track its origin. Finally it returns the
         ase.Atoms object.
         @param dir_list: List of directories where to read the coords from.
         @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.
         @param spec_atms: List of tuples containing pairs of new/traditional
             chemical symbols.
         @return: list of ase.Atoms objects.
         """
         from glob import glob
         import numpy as np
         energies = []
         for conf in conf_list:
         import os
         from modules.utilities import is_binary
         atoms_list = []
         for conf_dir in dir_list:
             conf_path = f"{run_type}/{conf_dir}/"
             if code == 'cp2k':
                 energies.append(read_energy_cp2k(
                     glob(f"{run_type}/{conf}/*.out")[0]))
                 ase_atms = read_coords_cp2k(glob(f"{conf_path}/*-1.restart")[0],
                                             spec_atms)
                 # Assign energy
                 for fil in os.listdir(conf_path):
                     if is_binary(conf_path+fil):
                         continue
                     conf_energy = read_energy_cp2k(conf_path+fil)
                     if conf_energy is not None:
                         ase_atms.info["energy"] = conf_energy
                         break
                 ase_atms.info[run_type[:3]] = conf_dir
                 atoms_list.append(ase_atms)
             elif code == 'vasp':
                 ase_atms = read_coords_vasp(f"{conf_path}/OUTCAR", spec_atms)
                 ase_atms.info["energy"] = ase_atms.get_total_energy() * 27.2113845
                 ase_atms.info[run_type[:3]] = conf_dir
                 atoms_list.append(ase_atms)
             else:
                 err_msg = f"Collect energies not implemented for '{code}'."
                 err_msg = f"Collect coordinates not implemented for '{code}'."
                 logger.error(err_msg)
                 raise NotImplementedError(err_msg)
         return atoms_list
         if len(energies) == 0:
             err = f"No results found on {run_type}"
             logger.error(err)
             raise FileNotFoundError(err)
         return np.array(energies)

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Chimie Théorique » scripts_chimie4psmn » DockOnSurf

Révision 1d8c374e modules/formats.py