How lavishlohiya/avaranx-h2s works
This repository is a LAMMPS-based H₂S dosimeter-material comparison workflow. Its main path generates atomic systems for four metal oxides, runs molecular-dynamics inputs, then compares adsorption behavior and visualizes results. The runner coordinates these stages; analysis also offers demonstration plots and OVITO modes. Generator and runner behavior is visible in sampled source, while some LAMMPS input details are unsampled, so the graph omits uncertain simulation internals.
Main entry points: run_all.py Pipeline runner · ovito_analysis.py Analysis and visualization · generate_cuo_h2s_system.py CuO generator · generate_zno_h2s_system.py ZnO generator
Components 20
System generation
- CuO generator
generate_cuo_h2s_system.py - ZnO generator
generate_zno_h2s_system.py - PbO generator
generate_pbo_h2s_system.py - Bi₂O₃ generator
generate_bi2o3_h2s_system.py - CuO system data
h2s_cuo_system.data - ZnO system data
h2s_zno_system.data - PbO system data
h2s_pbo_system.data - Bi₂O₃ system data
h2s_bi2o3_system.data
LAMMPS simulations
- LAMMPS engine
- CuO simulation input
h2s_cuo_reaxff.in - ZnO simulation input
h2s_zno.in - PbO simulation input
h2s_pbo.in - Bi₂O₃ simulation input
h2s_bi2o3.in - Simulation outputs
- LAMMPS log
log.lammps
Workflow control
- Pipeline runner
run_all.py
Analysis and visualization
- Analysis and visualization
ovito_analysis.py - Comparison plots
- OVITO tools
Other components
- Engineer
Connections 25
- Engineer → Pipeline runner: starts workflow
- Engineer → Analysis and visualization: runs analysis
- Pipeline runner → CuO generator: runs generator
- Pipeline runner → ZnO generator: runs generator
- Pipeline runner → PbO generator: runs generator
- Pipeline runner → Bi₂O₃ generator: runs generator
- CuO generator → CuO system data: writes data
- ZnO generator → ZnO system data: writes data
- PbO generator → PbO system data: writes data
- Bi₂O₃ generator → Bi₂O₃ system data: writes data
- Pipeline runner → LAMMPS engine: launches simulations
- LAMMPS engine → CuO simulation input: runs input
- LAMMPS engine → ZnO simulation input: runs input
- LAMMPS engine → PbO simulation input: runs input
- LAMMPS engine → Bi₂O₃ simulation input: runs input
- CuO simulation input → CuO system data: uses system data
- ZnO simulation input → ZnO system data: uses system data
- PbO simulation input → PbO system data: uses system data
- Bi₂O₃ simulation input → Bi₂O₃ system data: uses system data
- LAMMPS engine → Simulation outputs: writes results
- LAMMPS engine → LAMMPS log: writes log
- Pipeline runner → Analysis and visualization: runs matplotlib mode
- Analysis and visualization → Simulation outputs: reads simulation results
- Analysis and visualization → Comparison plots: generates plots
- Analysis and visualization → OVITO tools: offers API mode