Release Notes

v2.7.1 December 2021

General Notice

  • This package is built using OpenEye-Snowball==0.23.0, OpenEye-Psi4==0.6.0 and the associated OpenEye-orionplatform

Floes in this package

  • Cost Estimate approximates CPU hours and $cost of performing parts of CSP protocol.

  • CIF Reader uploads CIF files and converts them into Orion records.

  • Psi4 QM Conformer Ensemble (Part I of CSP Protocol) generates conformers for CSP.

  • Psi4 Combined Tautomer and Torsion Sampling Conformer Floe generates conformers with tautomer and torsions sampling.

  • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering) generates a collection of IEFF crystal structures and performs filtering to find lowest energy structures.

  • Polymorph Filtering based on IEFF Energies (Part II’ of CSP Protocol: Filtering) filters existing collection of IEFF crystal structures.

  • Multi-level approach to conformer ensemble of crystal polymorphs (Parts I+II of CSP Protocol) generates conformers and crystal structure sampling with IEFF force field. Can be used iteratively to perform multi-level conformer sampling.

  • Force Field optimization of crystal structures in the dimer expansion approach (Part III of CSP Protocol) optimizes crystal structures with dimer expansion in the Force Field approach.

  • Loose quantum optimization of crystal structures (Part III of CSP Protocol) optimizes crystal structures with dimer expansion in the QM approach. The stoppage criterion is loose, which saves time and cost. The error on final energy usually within 2 kcal/mol.

  • Quantum optimization of crystal structures (Part III of CSP Protocol) optimizes crystal structures with dimer expansion in the QM approach. The stoppage criterion is tight for better convergence of final geometries and energies.

  • Force Field crystal entropy with a cluster expansion method (Part IV of CSP Protocol) computes finite temperature corrections in the dimer approach with Force Field energies.

  • QM crystal entropy with a cluster expansion method (Part IV of CSP Protocol) computes finite temperature corrections in the dimer approach with QM energies.

  • Force Field Solubility computes intrinsic thermodynamics equilibrium Solubility in Force Field dimer approach (sublimation enthalpy, sublimation entropy) and ZAP hydration free energy.

  • QM Solubility computes intrinsic thermodynamics equilibrium Solubility in QM dimer approach (sublimation enthalpy, sublimation entropy) and ZAP hydration free energy.

  • Water Sampling samples waters around input conformers to produce monohydrate conforer ensemble.

  • Filtering of crystal structures based on powder spectrum filters input crystal structures based on similarity with the input powder diffraction spectrum.

  • Crystal RMSD Floe compares reference and fit crystal structures with cluster RMSD approach.

Floe Updates

  • Psi4 Combined Tautomer and Torsion Sampling Conformer Floe is a new Floe in this package that generates conformer ensemble with torsions and tautomer sampling.

  • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering), Polymorph Filtering based on IEFF Energies (Part II’ of CSP Protocol: Filtering) those two floes have a number of improvements, that allow reduced wall clock times and costs: scaling to up to 100K CPUs (as opposed to 10K before), speedup in powder deduplication process.

  • Loose quantum optimization of crystal structures (Part III of CSP Protocol), Quantum optimization of crystal structures (Part III of CSP Protocol), Force Field optimization of crystal structures in the dimer expansion approach (Part III of CSP Protocol) have improvements in wall clock time via parallelization of the floe report (previously was wall clock time bottleneck for jobs at scale)

  • Other minor improvements and bug fixes in several Floes.

v2.5.0 November 2020

General Notice

  • This package is built using OpenEye-Snowball==0.20.0, OpenEye-Psi4==0.4.0 and the associated OpenEye-orionplatform

New Floes

  • Force Field optimization of crystal structures in the dimer expansion approach Floe optimizes crystal structures based on MMFF dimer energies

  • Crystal entropy with a cluster expansion method using Force Field Floe computes crystal entropy based on MMFF dimer energies

  • Crystal entropy with a cluster expansion method using Density Functional Theory Floe computes crystal entropy based on HF3C dimer energies

  • Crystal entropy post process Floe computes crystal entropy from pre-calculated supercell displacements and forces.

  • Solubility Floe computes Solubility from equilibrium sublimation thermodynamics. Needs input data with crystal enthalpy (part III Floe), crystal entropy, vacuum entropy and solvation free energy.

  • Automated Force Field Solubility Floe computes Solubility by first computing equilibrium sublimation thermodynamics (force field, MMFF)

  • Automated DFT Solubility Floe computes Solubility by first computing equilibrium sublimation thermodynamics (quantum, HF3C)

Floe Updates

  • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering) has several improvements, main is the parallelization of crystal RMSD deduplication process.

  • Polymorph Filtering based on IEFF Energies (Part II’ of CSP Protocol: Filtering) has several improvements, main is the parallelization of crystal RMSD deduplication process.

v2.0.0 August 2020

General Notice

  • This package is built using OpenEye-Snowball==0.19.0, OpenEye-Psi4==0.3.0 and the associated OpenEye-orionplatform

New Floes

  • Multi-level approach to conformer ensemble of crystal polymorphs

This workflow implements multi-level sampling of conformational ensemble of crystal polymorphs. Allows for treating very flexible molecules in a practical way.

  • Filtering of crystal structures based on powder spectrum

This workflow filters crystal structures based on powder similarity spectrum. Useful for example in cases when powder spectrum is known about the crystal polymorph, to filter Force Field predicted polymorphs and reduce the number of quantum calculations.

  • Loose quantum optimization of crystal structures (Part III of CSP Protocol)

This workflow optimizes crystal structure with quantum dimer level DFT energies, by using a loose convergence criteria, which allows for efficient cost/accuracy ballance. Useful for cases when many quantum optimizations are necessary.

Floe Updates

  • Psi4 QM Conformer Ensemble (Part I of CSP Protocol) has updated default paramters for better conformational sampling.

  • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering) has been improved by faster packing generation of crystal structures (10-20x speedup); some housekeeping improvements and bug fixes.

  • Polymorph Filtering based on IEFF Energies (Part II’ of CSP Protocol: Filtering) has been improved by a bug fix.

  • Quantum optimization of crystal structures (Part III of CSP Protocol) has been cost optimized in three ways: 1. single-point scoring with b3lyp method is now done only for short-range (6A) cluster, long-range energy with cheaper HF3C. This reduces number of expensive b3lyp dimer calculations by ~70%; 2. each single-point dimer is computed on an optimized for this purpose instance (r5.4xlarge), reduces cost per dimer by 2x; 3. each single-point dimer is computed with Psi4 single-point energy function, as opposed to single-point gradient, gives additional ~20% cost reduction. All these imrpovements translate into 40-45% reduction in cost per each crystal structure optimization.

v1.8.4 April 2020

General Notice

  • This package is built using OpenEye-Snowball==0.18.1, OpenEye-Psi4==0.2.1 and the associated OpenEye-orionplatform

Floe Updates

  • Psi4 QM Conformer Ensemble (Part I of CSP Protocol) has several bug fixes.

  • Polymorph Search with IEFF Crystal Force Field (Part II of CSP Protocol: Generation and Filtering) has been improved by faster deduplication method based on powder diffraction spectrum similarity; packing Cube has a new time-out parameter; cleaner processing of input conformers without strain field.

  • Polymorph Filtering based on IEFF Energies (Part II’ of CSP Protocol: Filtering) has been improved by faster deduplication method based on powder diffraction spectrum similarity.

  • Quantum optimization of crystal structures (Part III of CSP Protocol) now allows for counterpoise correction for both geometry and single point scoring stages. Minor improvements in error handling.