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Implemented read coordinates and energies for vasp calculation.
molec_file supports POSCAR/CONTCAR files.
Removed TODO
Removed warning when dealing with non-3D molecules.
Added log register to output the normal vector to the surface at the given site when calculated with asann. Added TODOs
Corrected bug: Coordinates were not stored in the list in formats.py. Refactored screening.py file.
Moved the change of units (Ha to eV) to read_energy_cp2k in formats.py
Change on function names and documentation.
Corrected bug: read_coords_cp2k expected a file as argument, and directory was parsed, now parsing file.
Corrected bug: missing and wrong arguments for read_coords_cp2k and read_energy_cp2k respectively.
Made the read_coords, read_energies function more general, robust and readable and transfered the actual work to be done by code-specific functions (read_coords_cp2k and read_energy_cp2k).
Made the read_coords function more robust and readable.
A maximum number of jobs can be set to, not only the pending ones, but now also the running ones.
Included extra arguments for the proper working of special atoms.
Implemented add_special_atoms which Allows to use custom elements with symbols not in the periodic table.
Added punctuation marks at the end of every log messages.
When a SDF mol file has no explicit hydrogen atoms it adds them before converting it to the adequate format.
Changed the import statement of internal libraries. Added logging to utilities.py
Implemented function to read energies of a set of finished calculations. Implemented auxiliary function equivalent to bash tail. Reformat blank spaces and add TODO lines
Added read_coords function to read coordinates resulting from finished calculations.
Allow to convert, to rdkit.Mol object, xyz files containing multiple geometries, taking into consideration only the last one.
Changed the number of conformers for which to warn the user to be greater than 1 and not 0
Added a warning when a mol object with more than one conformer is parsed to the rdkit_mol_to_ase_atoms function. Extended confs_to_mol_list documentation
Moved confs_to_mol_list function from isolated.py to formats.py module and generalised the calculations functions to be able to work with no matter which kind of calculation
Changed logging of formats.py from info to debug severity level.
Disabled the removal of hydrogens when using rdkit sdl mol file reader. Now, rdkit mol object contain hydrogens explicitly.
Moved logger to a global variable
Changed the read_coords.py module name to formats.py which states more clearly the purpose of the module.