v1.2.0 July 2023¶
This package is built using
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
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.
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.
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.
Psi4 QM Atom Indices Torsion ScanningFloe was removed.
Many Cubes were moved to a new
QM Support Cubespackage, 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)¶
Create Custom Torsion Ruleswas 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 Resultswas created to generate reports for Floes, which enumerate tautomers, create custom torsion sampling rules, and generate conformer ensembles.
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 Scanswas updated to include conjugated single bonds – such as amides – in its definition of rotatable bonds for torsion scans.
Create Floe Report for Fragmentationnow only generates the Floe report about torsion scans for custom torsion libraries, using the data processed in
Create Custom Torsion Rules.
Psi4 Conformer Sub-Samplingnow allows for sampling of multiple tautomers of the same molecule.
v0.5.1 (Orion Release 2021.1)¶
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.
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.
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.
Conformer Floe Reportwas introduced to display conformer energy ensembles in a Floe Report.
Psi4 Torsion Driverwas returned to the package to drive torsions without moving the rest of a conformer. It may be added to Floes in the future.
Psi4 Conformer Generationnow 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 Scanswas updated to handle rare corner cases for fragmenting certain ring systems.
Psi4 Constrain All Torsionsoptionally includes polar hydrogen bonds when constraining polar hydrogens.
Parameters to set Psi4 SCF convergence thresholds are now exposed in Psi4 Property Calculation.
Psi4 Logs Reportwas updated to more efficiently handle a large number of records with log data.
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 Scanningwas 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 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.
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.
Psi4 Logs ReportCube 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.
Psi4 Logs ReportCube 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.
Fragment Molecule for Torsion ScansCube fragments molecules around each rotatable bond. There is a parent output port so that fragments can be recombined later if necessary.
Create Custom Torsion RulesCube 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.
Tautomer Floe Reportwas 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.
Psi4 Strain and Energy FilterCube was moved from the Crystal Math package to this one.
Exact Conformer DeduplicatorCube 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 QM 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 Torsionsassigns constraints to fix all torsions in a molecule.
Psi4 Assign Constraintsgenerates 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 Indicesallows the user to tag atoms based on indices, this allows us to replicate the old torsion drive Floe.
Torsion Scan Report Cubegenerates 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.