aalexmmaldonado/reptar: v0.0.3

• Main Author: Alex Maldonado
• Format: Software
• Language: unknown
• Published: 2022
• Subjects: Sphinx; Hartree; Orca
• Online Access: https://zenodo.org/record/7384564; https://doi.org/10.5281/zenodo.7384564

Added Ability to remove data with the File object. Option (missing_is_none) to return None from File.get() if the key does not exist. Saver with sampling. with_md5_update option for putting data in reptar files. File.copy() method to help copying data between groups. driverOPT and psi4_opt worker. reptar-write-xyz script for writing xyz files from command line. driverENERGY for just energy calculations. psi4_energy worker. Saver class for long calculations. Parse final electronic energies from ORCA. Support for CREST conformer and rotamer searches. Support for Atomic Simulation Environment (ASE) trajectories. Determine structure indices with respect to structure provenance specifications. Simple structural descriptors. Quick documentation for sampler. Example script for GDML npz files. Writer for standard XYZ files with optional comments. Writer for extended XYZ files used in the Gaussian approximation potentials (GAP) code. Documentation for writers. Method to store arrays in ASE and schnetpack databases. Changed Pylint and Black formatting; thus, lots of naming changes were made. Renamed creator class to Creator to avoid namespace conflicts. Moved reptar.calculators.save.Saver to reptar.Saver. Condensed and cleaned sampling routines into Sampler class. Use qcelemental.periodictable for atomic numbers, symbols, and masses instead of manual dictionaries. All drivers have a use_ray parameter that defaults to False. Calculators now use keyword arguments. Cleaned up ray calculations. Convert scf energies from cclib to Hartree by default. Moved example calculations to reptar-data. Manual api documents with sphinx-multiversion. Raise RuntimeError when key does not exist in exdir. PDB writer numbers each atom name. Renamed File.add() to File.put(). Return data from exdir as np.ndarray instead of np.memmap. creator.group is now creator.from_calc. Specify array dimensions in docstrings. Do not import every submodule in reptar. That way, optional calculation dependencies are not required when importing reptar. Upgrades ...