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Reaction studies: smoke test, clearer names, and what replaces DirDyVTST (2008)

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#330 3 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
4/5
Tiempo estimado
Más de una semana
Aptitud para principiantes
15/100
Tipo de issue
Refactorización
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
c
Área
desktop

Línea de trabajo

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).

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

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

  1. 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.
  2. Names that say what is computed, e.g. "Reaction Rates (VTST)" and "Reaction in Solution (Metadynamics)".
  3. 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).

Lenguaje dominante
C
Estrellas
10
Forks
8
Merge medio
21 min
PR fusionados (30 d)
1

Preparar el entorno

Este proyecto no incluye contenedor de desarrollo, Dockerfile ni guía de contribución, así que la configuración corre por tu cuenta: empieza por su README y consulta nuestra guía para la primera contribución para los pasos generales.

Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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