v0.4.0 (Orion Release 2020.3)¶
- Psi4 QM UI Atom Selection Torsion Scanning performs a torsion scan in the same way as other Floes (i.e. Psi4 QM SMARTS Torsion Scan). In this Floe, the atoms for the torsion scan are selected with the Orion 2D sketcher.
- Psi4 QM Interaction Energy computes the interaction energy between two or more molecules.
- Psi4 QM Atom Indices Torsion Scanning was updated to use atom indices starting at 0 instead of 1. The atom indices shown in the Orion 3D Viewer also start at 0 beginning in this release.
- Psi4 QM Property Calculation and Psi4 QM Geometry Optimization Floes have been updated to improve their handling of multi-conformer molecules.
- Psi4 QM Property Calculation now includes dipole moment as a calculation option.
- Psi4 QM Vacuum Entropy Floe has been updated to handle vacuum entropies for multiple molecules assuming the records associated with each molecule have an identifier field.
- The Cubes Split complex into individual molecules and Rejoin complex components and compute interaction energies were added to facilitate interaction energy calculations. These Cubes handle bookkeeping while the QM energies are computed with the Psi4 Property Calculation Cube.
- The Psi4 Property Calculation Cube was updated to include dipole moment as an option. It was also refactored to make adding new properties simpler.
Psi4MCEnergyFilterCubewere deprecated in the last release and have been deleted.
v0.3.0 (Orion Release 2020.2)¶
- Psi4 QM Complete Molecule Torsion Scan is a QM version of the Floe that used to be in the Scientific Floes package which was redistributed. This Floe identifies all rotatable bonds in a molecule and then performs a torsion scan round each bond. As with our other torsion scan Floes, QM single point energies or geometry optimizations can optionally be performed on the force field optimized structures.
- Psi4 QM Fragmentation and Torsion Scanning generates custom torsion rules which can be used in conformer generation. It begins by fragmenting the molecule around each rotatable bond. Then, a torsion scan with QM geometry optimization is performed for each rotatable bond. Lastly, these torsion scan results are analyzed to generate rules for conformer generation. The output from this Floe can be used as input for the Psi4 QM Conformer Ensemble Floe which will use the custom sampling rules for each rotatable bond.
- Psi4 QM Tautomer Floe enumerates tautomers of the input molecule and performs a local minima search for each. The final report for this Floe shows the relative energy of each tautomer including a distribution of their conformer energies.
- Psi4 QM Vacuum Entropy Floe expects an ensemble of optimized conformers such as output from the Psi4 QM Local Minima Search and generates a finite difference Hessian for each input conformer. Then, a gas phase entropy at room temperature is calculated for the ensemble.
- The new Psi4 Logs Report Cube was added to all QM Floes. When Psi4 log files are saved to a record during computation, this Cube will convert those fields to a Floe report to make accessing and reading the log files on Orion more straight forward.
- Cubes from the Snowball package for counting successful records and handling failures and exceptions were added to all Floes. This structure includes better communication of failures and exceptions with the user.
- A conformer splitter Cube was add to the Psi4 QM Property Calculation and Psi4 QM Geometry Optimization Floes to allow multiple conformer molecules to be used in these Floes. In both cases, the conformers are split, the Psi4 calculation is performed and the output contains one conformer per record. That is, the conformers are not re-merged.
- Promoted parameters have been updated for almost all Floes to make running Floes simpler.
The following Cubes have been added during this release, primarily to facilitate the new Floes and generate Floe reports.
- The Psi4 Logs Report Cube takes a field containing Psi4 log file strings and generates a Floe report for easier access to these log files for users who wish to save them.
- The Fragment Molecule for Torsion Scans Cube fragments molecules around each rotatable bond. There is a parent output port so that fragments can be recombined later if necessary.
- The Create Custom Torsion Rules Cube gathers fragmented molecules and analyzes their torsion scans to generate torsion rules for conformer generation. This Cube also generates a Floe report showing the torsion scans and rules for each fragment.
- The Tautomer Floe Report was created to analyze local minima search results for multiple tautomers of the same molecule. The tautomer enumeration Cube comes from the Snowball package.
- The Psi4 Finite Difference Hessian Cube was added to calculate finite difference Hessians single point gradients. This Cube is intended to be used in combination with the Psi4 Property Calculation Cube to compute the gradients.
- The Psi4 Vacuum Entropy Cube computes configurational entropy using previously calculated energies and Hessians for a conformer ensemble. It assumes the energies and Hessians were computed at the same level of theory.
- All Cubes were updated to use the same exception handling that is used in Classic Floes. This allows exceptions and individual failures to be communicated more clearly with the user.
Psi4MCEnergyFilterCubeCubes have been deprecated in favor of Cubes from the Snowball package. None of these Cubes are used in Floes for this release and a Deprecation Warning was added. In the next released version, these Cubes will be removed entirely.
- The Psi4 Strain and Energy Filter Cube was moved from the Crystal Math package to this one.
- The Exact Conformer Deduplicator Cube was updated to handle conformers from different molecule allowing for more diverse Floes to use this Cube. The description was also updated to make it clear that this Cube is only intended to deduplicate exact conformers within a very small RMSD.
v0.2.0 (Orion Release 2020.1)¶
Constraints were refactored out of the geometry optimization Cube. This allows for more geometry optimization options, including fixing only the relevant torsion in the torsion drive Floes.
Psi4 QM SMARTS Torsion Scan
is a new Floe which uses the
SMARTSMapCube from snowball to tag atoms in a torsion
using a SMARTS pattern rather than indices.
The torsion Floes were updated to use new constraint Cubes, meaning only the torsion being
scanned is held fixed. Additionally, the
Psi4 QM Torsion Scanning Floe was renamed
Psi4 QM Atom Indices Torsion Scanning
to distinguish from the SMARTS based torsion floe. Similarly, The
Psi4 QM Geometry Optimization,
Psi4 QM Conformer Ensemble, and
Psi4 Local Minima Search
Floes were updated to use the new constraint Cubes.
The following Cubes have been added in order to increase the variety of constraints which can be applied during optimizations
- Psi4 Constrain All Torsions assigns constraints to fix all torsions in a molecule.
- Psi4 Assign Constraints generates constraints for the tagged atoms in a molecule. The current implementation supports distances (two tagged atoms) or dihedral torsions (four bonded atoms)
- Tag atoms by Indices allows the user to tag atoms based on indices, this allows us to replicate the old torsion drive Floe.
- Torsion Scan Report Cube generates a Floe report showing MM and/or QM torsion scans.
The ability to constrain all torsions was removed from the Psi4 Geometry Optimization to allow for more general optimization parameters
Psi4 Torsion Driver was removed, the torsion scan Floes have been updated to use
the snowball torsion scan Cube instead.