[WIP]rewrite workflow implementation. Add prefect framework. prepare for paper.

[felix5572]

rewrite workflow implementation. Add prefect framework. prepare for paper.

Summary by CodeRabbit

• New Features

  • Introduced a comprehensive simulation framework that supports diverse thermodynamic integration and free energy calculations, including molecular dynamics workflows for liquids, water, and ice.
  • Enhanced command-line interfaces and configuration options for generating, executing, and analyzing simulation tasks.
  • Added advanced visualization tools to plot Gibbs free energy surfaces and compare simulation results.
  • Improved infrastructure for dependency management, job execution, and file operations.

• Tests & Examples

  • Provided sample workflows and testing routines to demonstrate and validate the new features.

[coderabbitai[bot]]

📝 Walkthrough

Walkthrough

This pull request introduces a comprehensive set of new modules and functionalities for molecular dynamics free energy calculations and thermodynamic integration. New simulation modules and workflows have been added to generate LAMMPS input files, manage simulation tasks, process results, and provide analysis and visualization tools. Additional infrastructure includes CLI interfaces, dependency‑injection services, report generators, file handlers, and utility scripts. The changes also update package inclusion patterns and add example configurations, LAMMPS data files, and testing workflows to support various simulation setups (e.g., high-pressure liquids and water–ice phase diagrams).

Changes

File(s)	Change Summary
dpti/hti_liq.py, dpti/ti.py, dpti/ti_water.py	New simulation modules implementing Hamiltonian thermodynamic integration, LAMMPS input generation, task management, CLI handling, and water-specific integration workflows.
dpti/workflows/{__init__.py, flows/base_flow.py, flows/flow_settings.py, flows/free_energy_ti_line.py}, dpti/workflows/prefect/prefect_task_hash.py, dpti/workflows/service/{di.py, dpdispatcher_configs.py, file_handler.py, job_executor.py, report_generator.py, workflow_decorator.py, workflow_service_module.py}	New workflow infrastructure including base flow classes, dynamic module imports, dependency injection, file handling, job execution, report generation, task decoration, and service module definitions.
dpti/workflows/simulations/{base.py, equi_sim.py, hti_sim.py, result_base.py, ti_sim.py}	New simulation framework components for NPT/NVT, HTI, and TI simulations with base classes, settings, input generators, result extractors, and utility functions for thermodynamic calculations.
dpti/workflows/analyze/{build_gibbs_surface.py, compare_ti_plot.py}	New analysis tools for constructing Gibbs free energy surfaces and comparing thermodynamic integration results through visualization and statistical functions.
dpti/workflows/examples/{prefect_example_cmd.sh, Sn_SCAN_high_pressure/*, Water_Ice_Phase_Diagram/*}	New example files including YAML configuration files, LAMMPS data files, shell scripts for deployment and file downloads, illustrating simulation setups for high-pressure systems and water–ice phase diagrams.
pyproject.toml	Updated package inclusion patterns to add "examples/*" and "jsons/*" alongside the existing "dpti*" pattern.
.cursor/rules/dpti-default-ai-rules.mdc	New guidelines and rule definitions for developing molecular dynamics free energy calculation applications.
dpti/aitools/codebase/collect_py_files_context.py	New utility script to collect, group, and save Python file contents from a specified directory into JSON format.
tests/workflows/flows/test_flow_instance_method.py	New test file defining a greeting workflow with instance methods and helper functions for Prefect flow integration.
dpti/gdi.py	Modified file path references for LAMMPS input files from "out.lmp" to "final.lmp", added debug print statements for task submission metadata, broadened backward file matching patterns, and enforced float casting for pressure and temperature parameters in GibbsDuhemFunc.
.gitignore	Added rule to ignore all directories matching *_*/ under dpti/workflows/examples/Sn_beta_quicktest/.

Sequence Diagram(s)

sequenceDiagram
    participant U as User
    participant CLI as CLI Handler
    participant WS as Workflow Service
    participant SIM as Simulation Engine
    participant REP as Report Generator

    U->>CLI: Invoke simulation command
    CLI->>WS: Initialize workflow (job generation, task creation)
    WS->>SIM: Prepare simulation (LAMMPS input, configuration)
    SIM->>SIM: Execute simulation tasks (NPT/NVT/HTI/TI)
    SIM->>WS: Return simulation results
    WS->>REP: Process results and generate reports
    REP-->>U: Return report and artifacts

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