Release Notes¶

v1.2.0 July 2023¶

This package is built using OpenEye-orionplatform==5.1.0, OpenEye-toolkits==2023.1.0, and OpenEye-Snowball==0.26.0.

Floe Updates¶

The GeomeTRIC optimization engine has been exposed for all geometry optimizations. It is set as the default engine for torsion scans and is optionally available for all other Floes with geometry optimizations.
All Floes which use torsion scanning (Psi4 QM Complete Molecule Torsion Scan, Psi4 QM SMARTS Torsion Scan, Psi4 QM UI Atom Selection Torsion Scanning, and Psi4 QM Fragmentation and Torsion Scanning) are improved by the improvements in Szybki TK in the 2023.1.0 toolkit release.
The Psi4 QM Fragmentation and Torsion Scanning Floe has been updated to support larger datasets of molecules by removing duplicate fragments. This has improved efficiency of the Floe up to 60% for larger datasets with similar chemistry. In addition, the Floe report now includes force field energies to allow for better understanding of the results.

v1.1.4 December 2022¶

This package is built using OpenEye-orionplatform==4.5.4, OpenEye-toolkits==2022.2.1, and OpenEye-Snowball==0.25.1.

Floe Updates¶

The method WB97X-V was removed as an option from all Psi4 Floes. The gradients for this correction are computed numerically and are prohibitively slow for any practical applications and cause problems with parallel cube time limits on Orion.vi
Psi4 QM Conformer Ensemble Floe now includes the option to compare results to known conformers of a molecule. This includes a computed RMSD and more information in the Floe Report.
Psi4 QM UI Atom Selection Torsion Scanning, Psi4 QM SMARTS Torsion Scan, and Psi4 QM Fragmentation and Torsion Scanning Floes include references to the input conformer in their Floe reports.
More clear descriptions have been added to all Floes to highlight the importance of considering hardware requirements (memory, number of CPUs, and disk space) when changing the method and basis set for a calculation. Multiple FAQ answers also address this topic.

v1.0.0 (Orion Release 2022.2)¶

The major change in this release was to upgrade to Psi4 1.5 which improves performance for some functionals and will allow for new features in future releases.

Floe Updates¶

All Floes use the new Orion categories and include brief descriptions.
Force field torsion scans are performed in gas phase (instead of water) in the Psi4 QM Complete Molecule Torsion Scan, Psi4 QM SMARTS Torsion Scan, Psi4 QM UI Atom Selection Torsion Scanning, and Psi4 QM Fragmentation and Torsion Scanning Floes.
Records which fail the Psi4 QM Conformer Ensemble and Psi4 QM Local Minima Search Floes due to high energy now include conformer strain energy.

Deleted Floes¶

The deprecated Psi4 QM Atom Indices Torsion Scanning Floe was removed.

Cube Updates¶

Many Cubes were moved to a new QM Support Cubes package, to be used in multiple Floe packages. They are still importable from the Psi4 package during this release.

v0.6.0 (Orion Release 2021.2)¶

The How-To Guides and Frequently Asked Questions sections were added to the documentation.

Floe Updates¶

The Psi4 QM Property Calculation has the new property option of HOMO-LUMO Gap energy.
The cubes in Psi4 QM Fragmentation and Torsion Scanning were refactored, but all results should remain the same.

New Cubes¶

Create Custom Torsion Rules was created to separate the process of creating custom torsion libraries from generating a Floe Report. This was a refactoring in Psi4 QM Fragmentation and Torsion Scanning that did not change its behavior.
Summarize Tautomer Enumeration and Fragmentation Scanning Results was created to generate reports for Floes, which enumerate tautomers, create custom torsion sampling rules, and generate conformer ensembles.

Cube Updates¶

Psi4 Property Calculation was updated to include HOMO-LUMO Gap energy as a property option. In addition, it now has 6-31G and LanL2DZ as basis set options.
Psi4 Geometry Optimization now has 6-31G and LanL2DZ as basis set options.
Fragment Molecule for Torsion Scans was updated to include conjugated single bonds – such as amides – in its definition of rotatable bonds for torsion scans.
Create Floe Report for Fragmentation now only generates the Floe report about torsion scans for custom torsion libraries, using the data processed in Create Custom Torsion Rules.
Psi4 Conformer Sub-Sampling now allows for sampling of multiple tautomers of the same molecule.

v0.5.1 (Orion Release 2021.1)¶

New Floes¶

The floe Psi4 HF3c Dipole Moment was added for the analyze page. It computes the dipole moment at HF-3c level and updates the record.

Floe Updates¶

All Floes were updated to use promoted parameter groups.
The Psi4 QM Conformer Ensemble now has an option to include polar hydrogens when constraining rotatable bonds.
Floe Reports were added to the Psi4 QM Conformer Ensemble and Psi4 QM Local Minima Search Floes.
The Psi4 QM Vacuum Entropy Floe now checks that input conformers are within a local minimum at the set level of theory before computing the parallel Hessian.

New Cubes¶

Conformer Floe Report was introduced to display conformer energy ensembles in a Floe Report.
Psi4 Torsion Driver was returned to the package to drive torsions without moving the rest of a conformer. It may be added to Floes in the future.

Cube Updates¶

The Psi4 Conformer Generation now fails for molecules with no stereochemistry specified.
If no reference conformers are sent to the Psi4 Conformer Sub-Sampling, then it passes all records. This helps facilitate updates in Floes in the Crystal Math Package.
Fragment Molecule for Torsion Scans was updated to handle rare corner cases for fragmenting certain ring systems.
Psi4 Constrain All Torsions optionally includes polar hydrogen bonds when constraining polar hydrogens.
Parameters to set Psi4 SCF convergence thresholds are now exposed in Psi4 Property Calculation.
Psi4 Logs Report was updated to more efficiently handle a large number of records with log data.

v0.4.0 (Orion Release 2020.3)¶

New Floes¶

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.

Floe Updates¶

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. There are improved checks to fail gracefully if into conformers are not fully optimized.

New Cubes¶

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.

Cube Updates¶

The Psi4 Property Calculation Cube was updated to include dipole moment as an option. It was also refactored to make adding new properties simpler.

Deleted Cubes¶

The Psi4MCSplitterCube, Psi4MCMergerCube, and Psi4MCEnergyFilterCube were deprecated in the last release and have been deleted.

v0.3.0 (Orion Release 2020.2)¶

New Floes¶

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.

Floe Updates¶

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.

New Cubes¶

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.

Cube Updates¶

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.
The Psi4MCSplitterCube, Psi4MCMergerCube, and Psi4MCEnergyFilterCube Cubes 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)¶

General Notice¶

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.

New 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.

Floe Updates¶

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 QM Local Minima Search Floes were updated to use the new constraint Cubes.

New 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.

Cube Updates¶

The ability to constrain all torsions was removed from the Psi4 Geometry Optimization to allow for more general optimization parameters

Removed Cubes¶

Psi4 Torsion Driver was removed, the torsion scan Floes have been updated to use the snowball torsion scan Cube instead.