equi: write average position in out.lmp when if_dump_avg_posi=True by Yi-FanLi · Pull Request #90 · deepmodeling/dpti

Yi-FanLi · 2025-03-15T19:43:29Z

When the user sets if_dump_avg_posi=True, write the average position in out.lmp.

Summary by CodeRabbit

Refactor
- Streamlined simulation ensemble configuration to improve how simulation details are managed.
- Updated the command‐line interface by removing legacy options, resulting in a clearer and more consistent simulation setup experience.

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coderabbitai · 2025-03-15T19:44:09Z

📝 Walkthrough

Walkthrough

The changes update the function signatures in dpti/equi.py. The gen_equi_ensemble_settings function now accepts an extra parameter (if_dump_avg_posi) to conditionally append specific commands to its output. In contrast, the gen_equi_lammps_input function has removed the if_dump_avg_posi parameter and now calls gen_equi_ensemble_settings with the updated interface. Additionally, the make_task function no longer accepts if_dump_avg_posi and now includes a new parameter (npt_dir), while the command-line argument --avg-posi has been removed.

Changes

File	Change Summary
`dpti/equi.py`	- `gen_equi_ensemble_settings`: Added `if_dump_avg_posi` parameter to conditionally append commands. - `gen_equi_lammps_input`: Removed `if_dump_avg_posi` parameter and updated its call to `gen_equi_ensemble_settings`. - `make_task`: Removed `if_dump_avg_posi` parameter and added new parameter `npt_dir`. - Removed command-line argument `--avg-posi` from the argument parser.

Sequence Diagram(s)

sequenceDiagram
    participant U as User/CLI
    participant L as gen_equi_lammps_input
    participant E as gen_equi_ensemble_settings
    participant T as make_task

    U->>L: Provide simulation configuration (no --avg-posi)
    L->>E: Call gen_equi_ensemble_settings(ens, if_dump_avg_posi)
    E-->>L: Return ensemble settings string
    L->>T: Call make_task(..., npt_dir)
    T-->>L: Confirm task creation
    L-->>U: Return simulation input configuration

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📥 Commits

Reviewing files that changed from the base of the PR and between 7009516 and 8769790.

📒 Files selected for processing (1)

dpti/equi.py (3 hunks)

🔇 Additional comments (2)

dpti/equi.py (2)

134-164: Correctly implemented feature to write average positions when if_dump_avg_posi=True

The modification to the gen_equi_ensemble_settings function adds support for writing average atom positions to the output file by updating the function signature and adding the necessary LAMMPS commands. The added code correctly:

Undumps the previously dumped data

Removes the average position fix

Reads the average positions from the dump file before writing to out.lmp

This implementation achieves the PR objective of writing average positions to out.lmp when if_dump_avg_posi is True.

🧰 Tools

🪛 Ruff (0.8.2)

153-153: Use format specifiers instead of percent format

(UP031)

206-208: Properly updated function call to include if_dump_avg_posi parameter

The call to gen_equi_ensemble_settings has been correctly updated to pass the if_dump_avg_posi parameter, ensuring that the new functionality is accessible when needed.

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…eepmodeling#90) * avoid reading --avg-posi from cmd line; only read it from json * write average position in out.lmp if if_dump_avg_posi=True * support writing average position in out.lmp if if_dump_avg_posi=True * improve indentation * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Yi-FanLi and others added 5 commits March 15, 2025 15:17

avoid reading --avg-posi from cmd line; only read it from json

428d337

write average position in out.lmp if if_dump_avg_posi=True

183aa83

support writing average position in out.lmp if if_dump_avg_posi=True

c246ddb

improve indentation

7234224

[pre-commit.ci] auto fixes from pre-commit.com hooks

8769790

for more information, see https://pre-commit.ci

Yi-FanLi merged commit ceea761 into deepmodeling:devel Mar 15, 2025
3 of 7 checks passed

coderabbitai bot mentioned this pull request Jun 11, 2025

And example CLI command and fix small bugs #91

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equi: write average position in out.lmp when if_dump_avg_posi=True#90

equi: write average position in out.lmp when if_dump_avg_posi=True#90
Yi-FanLi merged 5 commits intodeepmodeling:develfrom
Yi-FanLi:avg_posi

Yi-FanLi commented Mar 15, 2025 •

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Yi-FanLi commented Mar 15, 2025 •

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