Skip to content

Changelog

Sierra v2.0.0

  • New Feature - OrbNet model "Sky":
    • Sky expands chemical coverage to include the transition metals as well as As and Se.
  • New Feature - Calculate pairwise interaction energies with or without the counterpoise corrections using the InteractionEnergyInput.
  • New Feature - Added the option active to OptimizationInput, to complement constraints in cases where most of the molecule shall be held fixed.
  • Improved the conformer workflow to generate lower-energy conformers.
  • Improved handling of results:
    • Contracted fields, e.g. frequencies, normal_modes and infrared_intensities in Hessian calculations, have been moved out of extras.
    • Storage of non-contracted extras fields can be specified in inputs.
    • Existing flags for controlling optional output have been moved into details for consistency.
  • Improved EntosObjectIdentifiers by shortening the length and storing in binary format.
  • API Changes:
    • Input options that express "number of" now consistently start with n_. This includes the specification of the number of cores, which is now n_cores (in contrast to ncores).
    • Replaced SingleInput with EnergyInput, GradientInput and HessianInput.
  • General Fixes:
    • Fixed ExcitationResult to use Array[float] for consistency.
    • Fixed geometry optimization of charged molecules with OrbNetMethod.
    • Fixed issues with multi-threading in OrbNet.
    • Fixed Fermi occupations for large systems in the XTBMethod.
    • Fixed restricted open-shell in XTBMethod.
    • Fixed allowing tuples in py-qcore.
    • Fixed a rounding issue due to unit conversion in molecular geometries.
  • Notes:
    • Conversion from xyz files to sdf files is no longer supported - however, writing sdf files is still possible if an sdf file is provided as input.
    • A newline character has been added at the end of files when writing molecules to common formats e.g. .xyz.

Sierra v1.5.0

  • New OrbNet model "Denali"
    • Adds support for charged molecules
    • Adds support for Li, Mg, Ca, K, and Na ions and complexes
    • Improved geometry optimization stability for all OrbNet methods
    • Improved accuracy for small molecules and intermolecular complexes involving small molecules
  • New feature: Thermodynamic properties
  • New feature: Excited states via linear response can be run using the ExcitationInput
  • Improved solvation model
    • Solvation is now available for DFT with parameters optimized for the B97-3c functional
    • Significantly improved electrostatics due to reparameterization of Generalized-Born method
    • Solvation is now rotationally invariant
    • Automatic selection of suitable parameter set
    • Larger coverage of the periodic table
  • Improved conformer workflow
    • Total computation time approximately halved
    • On average, resulting conformers are lower in energy
  • Improved xTB robustness and speed for molecules with challenging electronic structure

  • Improved IAO populations

    • More robust algorithm
    • Available for spin-unrestricted calculations

  • API changes

    • Denali is now the default OrbNet method when creating a method with OrbNetMethod(); “Fuji” can still be accessed by calling OrbNetMethod(model=”fuji”)
    • time_step has been changed to step_size in StringInputDetails
    • The NMR attributes stored in NMRProperty have been changed from a plain Array type to Dict[int, Array], where each key in the dictionary corresponds to an atom index in the molecule. This change has been performed to better account for the sparsity in NMRProperties where all atoms do not have corresponding attributes.
    • The NMR attributes stored in NMRProperty now contain the coupling constants j_coupling and k_coupling, stored as a Dict[Tuple[int, int], Array] where the key is a pair of atom indices.