This module is a python based extension of the E-CAM PI-hydration software module which was written in the lammps scripting language. The UCD based authors are Ali Zeinlabidin Jaafar, Shrinath Kumar, and Donal MacKernan. It consists of a complete rewrite of that module into python; the use of pylammps as a pyton wrapper ofLAMMPS which greatly enhances its adaptability, and is combined with PLUMED, in particular, metadynamics, and allows modification of forecfields and particle insertion or deletion during the course of sampling, such as changes in hydration levels in the context of thermodynamic perturbation. This greatly enhances the speed at which optimal hydration levels can be searched facilitating high throughput optimization.
Module verification checklist (for reviewers)
Checklist when the module is first submitted
- Have the relevant labels been added to the MR
- If submitted on someone elses behalf, has the software author been referenced (if they have a GitLab account)
Checklist when module is no longer "WIP"
- Is the module documentation sufficiently detailed?
- Is it mergeable? (i.e., there should be no merge conflicts)
- Are the build instructions sufficient - source code locations, build instructions, etc.? (If not the MR should be updated)
- Did it pass the tests that were described? (Are there unit/regression tests? Do they pass?)
- Are the tests sufficient?
- If the module introduces new functionality, is it tested? (Unit/regression tests?)
- Is the associated source code well formatted? (typos, line length, brackets,...it should be consistent with existing source)
- Is all new source code sufficiently documented? (functions, their arguments,...)
- Is there a description of any applications the module has? (This is a hard requirement for E-CAM PDRAs)
- Make sure the module appears in a toctree
- Add a link to the final result on https://e-cam.readthedocs.io