lammpskit package

Subpackages

• lammpskit.ecellmodel package
  • Package Overview
  • Key Capabilities
  • Architecture
  • Usage Workflow
  • Integration with LAMMPSKit Ecosystem
  • Performance Considerations
  • Submodules
    • lammpskit.ecellmodel.data_processing module
      • Key Functions
      • Data Processing Workflow
      • Statistical Analysis Examples
      • Data Quality and Validation
      • Performance Optimization
      • Integration Examples
      • Common Use Cases
      • Error Handling and Diagnostics
      • Related Functions
      • Module Documentation
    • lammpskit.ecellmodel.filament_layer_analysis module
      • Key Functions
      • Filament Analysis Workflow
      • Connectivity Analysis Examples
      • Temporal Evolution Analysis
      • Device State Classification
      • Gap Analysis and Critical Path Finding
      • Visualization and Reporting
      • Performance Optimization
      • Research Applications
      • Integration Examples
      • Related Functions
      • Module Documentation
  • Common Analysis Tasks
  • Research Applications
  • Related Documentation
  • Module contents
• lammpskit.io package
  • Key Features
  • Core Functions
  • Performance Considerations
  • Submodules
    • lammpskit.io.lammps_readers module
      • Functions Overview
      • File Format Support
      • Usage Examples
      • Error Handling
      • Related Functions
      • Module Documentation
  • Module contents
• lammpskit.plotting package
  • Key Features
  • Package Architecture
  • Core Functions
  • Styling Standards
  • Usage Examples
  • Performance Notes
  • Related Modules
  • Submodules
    • lammpskit.plotting.timeseries_plots module
      • Key Functions
      • Configuration System
      • Usage Examples
      • Font Control Examples
      • Performance Considerations
      • Common Applications
      • Related Functions
      • Module Documentation
    • lammpskit.plotting.utils module
      • Design Philosophy
      • Core Function
      • Array Dimension Support
      • Customization Options
      • Usage Examples
      • Output Format
      • Performance Considerations
      • Common Applications
      • Related Functions
      • Module Documentation
  • Module contents

Submodules

• lammpskit.config module
  • Key Functions
  • Plot Configuration System
  • Font Configuration Examples
  • Analysis Configuration Usage
  • System Configuration Examples
  • Configuration Inheritance
  • Runtime Configuration Override
  • Validation and Type Safety
  • Best Practices
  • Related Components
  • Module Documentation
    • LAMMPSKit Configuration Module
      • Architecture Design
      • Key Components
      • Validation Philosophy
      • Performance Considerations
    • validate_filepath()
    • validate_dataindex()
    • validate_file_list()
    • validate_loop_parameters()
    • validate_chunks_parameter()
    • validate_cluster_parameters()

Module contents

LAMMPSKit: A modular toolkit for LAMMPS molecular dynamics simulation analysis.

LAMMPSKit provides a streamlined framework for analyzing raw data from molecular dynamics simulations, with particular emphasis on electrochemical systems. The package follows a hierarchical design allowing both general-purpose trajectory analysis and specialized domain-specific workflows.

Modules

iomodule

LAMMPS trajectory file readers and data parsers. Handles standard LAMMPS dump formats with automatic column detection and efficient memory management for large datasets.

plottingmodule

Scientific visualization utilities with standardized styling and publication-ready output. Includes time series analysis, dual-axis plots, and statistical overlays.

configmodule

Centralized configuration management for file paths, analysis parameters, and computational settings. Supports both programmatic and file-based configuration.

ecellmodelmodule

Specialized analysis for electrochemical cell simulations. Provides filament tracking, charge distribution and displacement analyses, and clustering algorithms optimized for HfTaO systems.

Target Applications

• Electrochemical memory device simulations (ReRAM, memristors).

• Ion transport and defect migration studies.

• Phase transition analysis in oxide materials.

• General LAMMPS trajectory post-processing.

Performance Notes

Memory usage scales linearly with trajectory size. For datasets >1GB, use chunked reading via io.lammps_readers with appropriate buffer sizes.

Community Extensions

To extend for other MD simulation types: 1. Add new analysis modules following ecellmodel structure 2. Implement domain-specific atom type mappings in config. 3. Create specialized plotting functions for new data types. 4. Add validation functions for new simulation parameters.

Examples

Basic workflow for electrochemical analysis:

>>> import lammpskit as lk
>>> from lammpskit.config import DEFAULT_COLUMNS_TO_READ
>>> file_list = ['trajectory1.lammpstrj', 'trajectory2.lammpstrj']
>>> coords, timesteps, total_atoms, xlo, xhi, ylo, yhi, zlo, zhi = lk.io.read_coordinates(
...     file_list, skip_rows=9, columns_to_read=DEFAULT_COLUMNS_TO_READ)
>>> from lammpskit.ecellmodel.filament_layer_analysis import analyze_clusters
>>> analyze_clusters('trajectory1.lammpstrj')

General trajectory parsing and plotting:

>>> timestep, total_atoms, xlo, xhi, ylo, yhi, zlo, zhi = lk.io.read_structure_info('dump.lammpstrj')
>>> import numpy as np
>>> x_data, y_data = np.array([1, 2, 3]), np.array([[4, 5, 6]])
>>> lk.plotting.plot_multiple_cases(x_data, y_data, ['Case1'], 'X', 'Y', 'output', 8, 6)