# mdanowarulshafinkhan/h-aln-thermal-transport-nemd architecture

> Architecture diagram of the GitHub repository mdanowarulshafinkhan/h-aln-thermal-transport-nemd, generated by GitDiagram from its file tree, README and a sample of source files (last updated 2026-11-13). It is an AI-made overview: check details against the source.

- Interactive diagram: https://gitdiagram.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd
- Repository: https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd

## Overview

This is a curated h-AlN molecular-dynamics research package: representative LAMMPS inputs and structures accompany analyzed thermal-transport data and Python post-processing tools. Users can analyze transport workbooks for conductivity and finite-size estimates, or process a velocity-dump trajectory into species-projected spectra; a separate script adds Cartesian directional VDOS. The README also documents validation outputs and study coverage across temperature, geometry, strain, pores, and dopants. Edges reflect only README statements and sampled script behavior; exact production-simulation wiring is not established by the excerpts.

Main entry points: [`scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py`](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py) (Workbook analyzer), [`inputs/representative_nemd/new.langevin.lmp`](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/inputs/representative_nemd/new.langevin.lmp) (NEMD input), [`scripts/vdos/pdos_publication.py`](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication.py) (Species PDOS), [`scripts/vdos/pdos_publication_directional.py`](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication_directional.py) (Directional VDOS)

## Diagram (Mermaid)

```mermaid
flowchart TD

subgraph group_simulation["Simulation inputs"]
  node_input["NEMD input<br/>[new.langevin.lmp]"]
  node_structures["Structures"]
  node_potential["Tersoff potential<br/>[XN.tersoff]"]
end

subgraph group_transport["Transport analysis"]
  node_transport_tool["Workbook analyzer"]
  node_analysis_results["Analyzed workbook"]
end

subgraph group_spectra["Spectral analysis"]
  node_pdos["Species PDOS"]
  node_directional["Directional VDOS"]
end

subgraph group_research["Research data"]
  node_workbooks["Transport workbooks"]
  node_bias["Bias workbooks"]
  node_validation["Validation outputs"]
  node_velocity_dump["Velocity dump"]
  node_spectra_results["VDOS/PDOS outputs"]
end

node_researcher(("Researcher"))
node_lammps["LAMMPS"]

node_researcher -->|"runs"| node_transport_tool
node_workbooks -->|"analyzed by"| node_transport_tool
node_bias -.->|"analyzed by"| node_transport_tool
node_transport_tool -->|"writes"| node_analysis_results
node_researcher -->|"runs"| node_pdos
node_velocity_dump -->|"reads"| node_pdos
node_pdos -->|"writes"| node_spectra_results
node_researcher -->|"runs"| node_directional
node_velocity_dump -->|"reads"| node_directional
node_directional -->|"writes"| node_spectra_results
node_lammps -.->|"executes"| node_input
node_input -.->|"uses"| node_structures
node_input -.->|"uses"| node_potential

click node_input "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/inputs/representative_nemd/new.langevin.lmp"
click node_structures "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/structures"
click node_potential "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/potentials/XN.tersoff"
click node_workbooks "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/thermal_transport"
click node_bias "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/temperature_bias"
click node_validation "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/validation"
click node_transport_tool "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py"
click node_analysis_results "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/thermal_transport"
click node_pdos "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication.py"
click node_directional "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication_directional.py"
click node_spectra_results "https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/vdos"

classDef toneNeutral fill:#f8fafc,stroke:#334155,stroke-width:1.5px,color:#0f172a
classDef toneBlue fill:#dbeafe,stroke:#2563eb,stroke-width:1.5px,color:#172554
classDef toneAmber fill:#fef3c7,stroke:#d97706,stroke-width:1.5px,color:#78350f
classDef toneMint fill:#dcfce7,stroke:#16a34a,stroke-width:1.5px,color:#14532d
classDef toneRose fill:#ffe4e6,stroke:#e11d48,stroke-width:1.5px,color:#881337
classDef toneIndigo fill:#e0e7ff,stroke:#4f46e5,stroke-width:1.5px,color:#312e81
classDef toneTeal fill:#ccfbf1,stroke:#0f766e,stroke-width:1.5px,color:#134e4a
class node_input,node_structures,node_potential toneBlue
class node_transport_tool,node_analysis_results toneAmber
class node_pdos,node_directional toneMint
class node_workbooks,node_bias,node_validation,node_velocity_dump,node_spectra_results toneRose
class node_researcher,node_lammps toneIndigo
```

## Components

### Simulation inputs

- [NEMD input](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/inputs/representative_nemd/new.langevin.lmp): `inputs/representative_nemd/new.langevin.lmp`
- [Structures](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/structures): `structures`
- [Tersoff potential](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/potentials/XN.tersoff): `potentials/XN.tersoff`

### Transport analysis

- [Workbook analyzer](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py): `scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py`
- [Analyzed workbook](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/thermal_transport): `results/thermal_transport`

### Spectral analysis

- [Species PDOS](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication.py): `scripts/vdos/pdos_publication.py`
- [Directional VDOS](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/blob/main/scripts/vdos/pdos_publication_directional.py): `scripts/vdos/pdos_publication_directional.py`

### Research data

- [Transport workbooks](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/thermal_transport): `results/thermal_transport`
- [Bias workbooks](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/temperature_bias): `results/temperature_bias`
- [Validation outputs](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/validation): `validation`
- **Velocity dump**
- [VDOS/PDOS outputs](https://github.com/mdanowarulshafinkhan/h-aln-thermal-transport-nemd/tree/main/results/vdos): `results/vdos`

### Other components

- **Researcher**
- **LAMMPS**

## Connections

- Researcher → Workbook analyzer: runs (evidence: `README.md`)
- Transport workbooks → Workbook analyzer: analyzed by (evidence: `README.md`)
- Bias workbooks → Workbook analyzer: analyzed by
- Workbook analyzer → Analyzed workbook: writes (evidence: `scripts/thermal_transport/thermal_transport_analysis_ALL_CASES_FINAL.py`)
- Researcher → Species PDOS: runs (evidence: `README.md`)
- Velocity dump → Species PDOS: reads (evidence: `scripts/vdos/pdos_publication.py`)
- Species PDOS → VDOS/PDOS outputs: writes (evidence: `scripts/vdos/pdos_publication.py`)
- Researcher → Directional VDOS: runs (evidence: `README.md`)
- Velocity dump → Directional VDOS: reads (evidence: `scripts/vdos/pdos_publication_directional.py`)
- Directional VDOS → VDOS/PDOS outputs: writes (evidence: `scripts/vdos/pdos_publication_directional.py`)
- LAMMPS → NEMD input: executes
- NEMD input → Structures: uses
- NEMD input → Tersoff potential: uses