Release Notes¶

v0.5.0 July 2024¶

This package is built using OpenEye-orionplatform==6.2.0, OpenEye-toolkits==2024.1.1, and OpenEye-Snowball==0.28.0.

Infrastructure has been added to support more robust checkpointing during the QM calculations. While calculations are running, a checkpoint file is saved to a collection which can be accessed if a calculation runs out of time or a spot instance is taken away. This change was implemented in all floes that perform geometry optimizations or single point energy calculations.
The Gaussian QM Conformer Ensemble Floe now uses the Omega Conformation Cube from Snowball by default. The more dense conformer generation used in previous releases is optionally available as well.

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

The Gaussian QM Parallel Run Input Files floe runs Gaussian input files in parallel taking advantage of the scalability of Orion parallel cubes. Due to AWS limitations, these calculations have a strict 10 hour time limit. Unfinished calculations will be saved to the failure output and can be restarted or the Gaussian QM Run Input Files floe can be used with serial cubes and no time limit.

The checkpointing capability in Gaussian has been leveraged to make parallel cubes for geometry optimization and single point energy calculations. All Gaussian floes use these parallel cubes which improves their scalability and overall cost.
All floes which use torsion scanning (Gaussian QM SMARTS Torsion Scan, Gaussian QM UI Torsion Scan, and Gaussian QM Fragmentation and Torsion Scan) are improved by the improvements in the Szybki TK in the 2023.1.0 toolkit release.
The Gaussian QM Fragmentation and Torsion Scan floe has been updated to support larger dataset 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.

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

Gaussian QM Conformer Ensemble Floe now includes the option to compare results to known conformers of a molecule. See Gaussian QM Conformer Ensemble Tutorial for more details.
Gaussian QM SMARTS Torsion Scan, Gaussian QM UI Torsion Scan, and Gaussian QM Fragmentation and Torsion Scan Floes include references to the input conformer in their Floe reports. See gaussian_tutorial_smarts_torsion_scan for one example.
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.

This package is built using OpenEye-orionplatform==4.4.0, OpenEye-toolkits==2022.1.1, and OpenEye-Snowball==0.24.0.
This release includes the new classification scheme and brief Floe descriptions.

Gaussian QM Conformer Ensemble Floe generates a dense conformer ensemble with a geometry optimization followed by a single point energy calculation at a higher level of theory.
Gaussian QM SMARTS Torsion Scan and Gaussian QM UI Torsion Scan Floes perform a force field torsion scan followed by a QM geometry optimization or single point energy.
Gaussian QM Fragmentation and Torsion Scan Floe fragments input molecules around each rotatable bond and then performs a torsion scan on each.

Gaussian log files generated in the Gaussian QM Run Input Files Floe can now be saved as a Floe Report to read on Orion before downloading results.
More methods, including semi-empirical and dispersion corrected options, were added as options for all Floes.
All Floes now have more options for solvents (water, DMSO, and Octanol) and solvent models (IEFPCM, CPCM, and SMD).

This is the first release of the Orion Gaussian Module so all Floes and Cubes are new.
Tutorials and frequently asked questions are included in this documentation.
This package is built using OpenEye-orionplatform==4.3.1, OpenEye-toolkits==2021.2.0, and OpenEye-Snowball==0.23.0.

Gaussian QM Run Input Files Floe allows users to run any Gaussian input file(s) or an archive file with multiple input files.
Gaussian QM Single Point Energy Floe calculates the QM single point energy on molecules or conformers in an Orion dataset.
Gaussian QM Geometry Optimization Floe performs a QM geometry optimization on molecules or conformers in an Orion dataset.

Gaussian Directory Archive File Reader Cube processes input files for Gaussian calculations.
Gaussian Archive File Writer Cube processes output from Gaussian calculations and saves them to one archive file.
Run Gaussian Input Directories Cube runs Gaussian calculations based on processed input files.
Gaussian Single Point Energy uses Gaussian to compute a QM single point energy on one conformer.
Gaussian Geometry Optimization Cube uses Gaussian to perform a geometry optimization on one conformer.
cube_QMSplitOutputs splits up input records across ten output ports to allow parallelization of multiple serial cubes.