And example CLI command and fix small bugs

[felix5572]

Summary by CodeRabbit

• New Features

  • Added example workflows, configuration files, and scripts for Sn high-pressure and water phase diagram simulations, including step-by-step guides for running NPT, NVT, HTI, and TI simulations.
  • Introduced scripts to automate model downloads and simulation workflows.
  • Added new compressed model files and LAMMPS data/configuration files for water and ice systems.

• Bug Fixes

  • Improved compatibility in handling missing files and parameter key fallbacks in simulation setup and Gibbs free energy calculations.
  • Updated formatting for thermodynamic output in LAMMPS input scripts and tests for consistency.

• Documentation

  • Major README overhaul: clarified usage, simplified setup instructions, updated links, and removed outdated Airflow content.
  • Added a detailed (deprecated) workflow README for Airflow-based free energy calculations.

• Chores

  • Updated dependencies by commenting out Airflow and relaxing SQLAlchemy version constraints.
  • Enhanced test configuration and coverage with new hooks and updated test expectations.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

This update introduces new example files and scripts for molecular simulation workflows, adjusts parameter handling and output formatting in core modules, enhances test configuration and coverage, and revises documentation for clarity and current usage. The changes also improve compatibility with varying input conventions and simplify dependency management in the project configuration.

Changes

File(s)	Change Summary
dpti/equi.py	Updated gen_equi_ensemble_settings signature to set if_dump_avg_posi default to False.
dpti/hti_liq.py	Moved assignment to jdata["model"] inside conditional to avoid errors when model is None.
dpti/hti_water.py	Added fallback mechanism for sigma parameter keys in three functions, supporting alternate dictionary key names.
dpti/ti.py tests/benchmark_gdi/deepmd/0/in.lammps tests/benchmark_ti/path-p/in.lammps tests/benchmark_ti/path-p/task.000006/in.lammps tests/benchmark_ti/path-t/task.000006/in.lammps tests/benchmark_ti_water/new_job/task.000003/in.lammps tests/test_ti_gen_lammps_input.py	Changed LAMMPS thermo_modify format from 4*8 %20.6f to float %20.6f in code and tests.
dpti/hti.py	Added fallback to load equi_settings.json if jdata.json is missing when computing Gibbs free energy.
examples/Sn_High_Pressure/command.sh examples/water_SCAN/ice04/command.sh examples/download_models.sh	Added new shell scripts for running simulation workflows and downloading models.
examples/Sn_High_Pressure/conf.lmp examples/Sn_High_Pressure/hti.json	Added/modified configuration and reference files for Sn high-pressure example.
examples/water_SCAN/H2O-Phase-Diagram-model_compressed.pb examples/water_SCAN/ice04/ice04.lmp	Added compressed model and LAMMPS data files for water/ice example.
examples/water_SCAN/ice04/graph.pb examples/Sn_High_Pressure/conf.lmp	Added reference files pointing to model files.
examples/water_SCAN/ice04/hti_ice.json examples/water_SCAN/ice04/npt.json examples/water_SCAN/ice04/nvt.json examples/water_SCAN/ice04/path-p.json examples/water_SCAN/ice04/path-t.json	Added new configuration JSON files for water/ice simulation workflows.
pyproject.toml	Commented out apache-airflow dependency and removed sqlalchemy version constraint.
README.md	Major revision: updated links, directory overview, example CLI commands, removed Airflow workflow instructions, updated Docker usage, and clarified documentation.
workflow/README.md	Added detailed, deprecated Airflow workflow setup and usage documentation.
tests/conftest.py	Added pytest_configure to print environment info and adjust sys.path for test imports.
tests/graph.pb	Added comments with Huggingface model download URLs.
tests/test_hti_ff_spring.py	Moved and updated test method for multi-element spring constant, adjusting expected values.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant ShellScript
    participant dpti_CLI
    participant LAMMPS
    participant OutputFiles

    User->>ShellScript: Run command.sh
    ShellScript->>dpti_CLI: dpti generate NPT/NVT/HTI/TI input files
    dpti_CLI->>OutputFiles: Write simulation input files
    ShellScript->>LAMMPS: Submit simulation jobs
    LAMMPS->>OutputFiles: Produce simulation results
    ShellScript->>dpti_CLI: dpti extract/compute (e.g., Gibbs free energy)
    dpti_CLI->>OutputFiles: Write processed results

Estimated code review effort

🎯 4 (Complex) | ⏱️ ~40 minutes

Possibly related PRs

• deepmodeling/dpti#90: Modifies gen_equi_ensemble_settings with conditional logic for if_dump_avg_posi and updates related function calls, directly relating to the function signature change in this PR.

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