[Documentation] Add model_devi Variant gromacs with complete parameter specification #1796
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
This PR adds comprehensive parameter documentation for the GROMACS variant in
model_devi_args
, addressing the placeholder implementation that previously had an empty parameter list and "TODO: add doc" documentation.Changes Made
Added
model_devi_gromacs_args()
functionCreated a new function following the established pattern of
model_devi_lmp_args()
andmodel_devi_amber_args()
that includes:model_devi_jobs
- Standard job configuration (reused from existingmodel_devi_jobs_args()
)model_devi_dt
- Timestep for MD simulation (required parameter)gromacs_settings
- Dictionary containing 11 GROMACS-specific file and processing parameters:mdp_filename
,topol_filename
,conf_filename
,index_filename
,type_filename
ndx_filename
,ref_filename
,deffnm
,maxwarn
,traj_filename
,group_name
Updated GROMACS variant documentation
[]
with propermodel_devi_gromacs_args()
callParameter alignment with implementation
All documented parameters match the actual usage in
dpgen/generator/run.py
:jdata["gromacs_settings"]
with proper defaults_make_model_devi_native_gromacs()
functionBefore/After
Before:
After:
Now users have full parameter validation and documentation when configuring GROMACS model deviation tasks, bringing it in line with the LAMMPS and Amber engines.
Testing
Fixes #771.
💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.