Reaction studies: smoke test, clearer names, and what replaces DirDyVTST (2008)
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评估
调研方向
Start with the GUI suite, which only checks that the Gas Phase and Condensed Phase study editors open, and with the DirDyVTST, Polyrate and MetaDyn task editors the issue names. Create each study, open every task editor, generate the input, and run a small case only where a code is installed. Done means both study types run end to end, and the DirDyVTST keep/rebuild/hide decision is recorded on the issue (see #221 and #62).
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描述
The two reaction study types have not been run end to end in this fork; the GUI suite only checks that their editors open.
- Gas Phase Reaction Study: reactants, products and transition state, DirDyVTST (
dirdyed) with NWChem, and the Polyrate editor for rate constants. - Condensed Phase Reaction Study: one Solvate task (Solvation Editor), then chained Metadynamics tasks (the MetaDyn registration: NWChem plane-wave PSPW, Car-Parrinello only).
Status of the external programs
- DirDyVTST: last version 2008, and it is listed among the programs no longer distributed from the University of Minnesota.
- Polyrate 17-C (2018, manual 2022): Apache 2.0. It reaches electronic-structure codes through interface programs (Gaussrate, Nwchemrate, ...). There is none for ORCA, and interfaces from before 2016 do not work with it.
- Pilgrim 2.0 (2020): MIT, Python, the same group. It does VTST with SCT tunnelling, multi-structural VTST, dual-level ISPE and kinetic Monte Carlo. Which codes it reads still has to be checked.
To do
- Smoke test of both study types: create the study, open each task's editor, generate the input, and run a small case where a code is available.
- Names that say what is computed, e.g. "Reaction Rates (VTST)" and "Reaction in Solution (Metadynamics)".
- Decide between keeping DirDyVTST, rebuilding the study on Pilgrim or on Polyrate with Gaussrate (ORCA/Gaussian instead of NWChem), or hiding it. The condensed phase study could take CP2K AIMD/metadynamics as a second code (#329).
Related: #221 (DirDyVTST editor redesign), #62 (DirDyGauss).
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