0.3.2

What's Changed

• 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 favor 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 a relaxed surface scan.
  • Added neb_ci method to perform climbing image nudged elastic band calculations.
  • Added neb_ts method to perform a transition state search based on a nudged elastic band calculation.
  • Update to the output parser to avoid crashes 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 the comment of the orca-formatted multiple .xyz files.
  • Added option to remove temporary .xyz files used during parsing.
  • Added engine field to properly store computed properties 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.

Full Changelog: 0.3.1...0.3.2

0.3.1

Version 0.3.1

New/updated features highlights

• 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)

What's Changed

• Job failure monitoring by @GES-ppravatto in #92
• Bugfix in orca e dftbplus by @GES-ppravatto in #94
• Added command calls for engines/wrappers in logger at debug level by @GES-lbabetto in #95
• Buried volumes implementation by @GES-ppravatto in #97
• Bugfix in __check_engine function in Properties class by @GES-lbabetto in #96
• Error correction in merging by @GES-ppravatto in #98
• Added test to fukui functions + bugfix by @GES-ppravatto in #99
• Spectroscopy tools early implementation by @GES-ppravatto in #102
• New test for non-inplace calculations + removed charge and spin from engines by @GES-ppravatto in #103
• Early version of the mogli-based viewer by @GES-ppravatto in #101
• Last changes + version bump to 0.3.1 by @GES-ppravatto in #104

Full Changelog: 0.3.0...0.3.1

0.3.0

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)

• 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 Sysyem 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

0.2.1

Merge pull request #61 from GES-lbabetto/main

minor bugfixes and improvements

0.2.0

Merge pull request #60 from GES-lbabetto/main

Finalized DFTB+ implementation and added documentation

0.1.38a

Merge pull request #54 from GES-lbabetto/main

fixed typo in orca input generation

0.1.37a

Merge pull request #53 from GES-lbabetto/main

added highest protonation state search in oneeloxidation module

0.1.36a

Merge pull request #52 from GES-lbabetto/main

included dummy maxcore variable for xTB calculations + added support for charged molecules in oneeloxidation

0.1.35a

Merge pull request #51 from GES-lbabetto/main

moved get_ncores() call to inside spe/opt/etc. functions

0.1.34a

Merge pull request #49 from GES-lbabetto/main

switched to Config class in compechem.config for setting number of cores