Release notes#

Version 0.3.2#

  • Refactoring of the orca module:

    • Introduced the OrcaJobInfo class to allow for a more easily readable and maintainable code.

    • Modified the write_input method of the OrcaInput class to allow for more complex input structures.

    • Added option for the user to add custom blocks both during a call of an OrcaInput method or during the construction of the engine class instance.

    • Removed the scf_block option in favour of the more general blocks option.

    • Added opt_ts method to perform transition state optimizations.

    • Added scan_ts method to perform transition state search based on relaxed surface scan.

    • Added neb_ci method to perform climbing image nudged elastic band calculations.

    • Added neb_ts method to perform a transition state seach based on a nudged elastic band calculation.

    • Update to the output parser to avoid crash when imaginary modes are detected or the Mulliken analysis is not performed

    • Added integration test for all the new features and update to the one using the scf_block option.

  • Update to the externalutilities module:

    • Added option to read energies stored in comment of the the orca-formatted multiple .xyz files.

    • Added option to remove temporary .xyz files used during parsing.

    • Added engine field to properly store computed properies in the output systems.

    • Added unit test to verify new functionalities.

  • Update to documentation to include new features and addition of examples to the OrcaInput docstrings.

Version 0.3.1#

  • Update of System and JSON format:

    • Defined extension-based identification of .xyz and .json file types in System class constructor.

    • Defined versioning of JSON files and auto-update routines to ensure retro-compatibility

  • Update to the engines classes behavior and testing:

    • Charge and spin cannot be changed from engine during calculation (Must be changed manually by the user acting on System)

    • Added test for non-inplace calculations after bugfix.

    • Added explicit option in OrcaInput to run frequency analysis when running optimization. Removed automatic switch to numerical frequencies when requiring analytical frequencies in solvent.

    • Added option to select the level of geometry convergence to be used during optimization in OrcaInput.

  • Added vibrational spectroscopy functions to OrcaInput parser:

    • Added VibrationalData object in properties to store vibrational informations and plot infrared and raman spectra.

    • Added option to compute Raman spectra when calling frequency analysis.

    • Added option to compute overtones and combination bands in infrared spectra when calling frequency analysis.

  • Implemented buried volume calculation from System geometry.

  • Added mogli tools to visualize molecule and use custom coloring (early)

Version 0.3.0#

  • Updated functions and added automatic routine for computing pKa

    • Added functional tests

    • Updated documentation

  • Properties class now accepts also levels of theory in string format and performs an early validation of the format

  • Added gibbs free energy parser to OrcaInput and XtbInput classes

  • Moved MPI_FLAGS to the config module as global variables

  • Various bugfixes and code uniformation

    • VMD based wrapper no longer strips characters at the beginning of filenames

    • Mulliken charges and spin populations are correctly parsed for coupled-cluster calculations

    • Removed forbidden characters to output files (e.g. partentheses and slash)

Version 0.3.0 - alpha#

  • Refactoring of System:

    • The geometry of the molecule has been moved to a MolecularGeometry class that is now an attribute of the System class.

    • The properties are now organized in a Properties class holding the reference to the electronic and vibronic levels of theory.

    • Added option to save and load System data in .json data format.

  • Differentiated engines from wrappers

    • Engines: take as argument a System object and update its properties

    • Wrappers: general wrappers around a software

  • Implemented early version of dependency search/check for wrappers and engines

  • Implemented VMD based tools to render Fukui functions

  • Implemented new parser for orca + added Hirshfeld charges

  • Moved constants to a separate file

  • Removed MDTrajectory class and velocities (will be re-implemented with NAMD engine)

  • Added some unit and integration tests