### Install ReacNetGenerator with uv

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/install.md

Install ReacNetGenerator using the uv tool and check the installation.

```bash
uv tool install reacnetgenerator
reacnetgenerator -h
```

--------------------------------

### Test Pip Installation

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/build.md

Verify the pip installation by running the help command.

```bash
reacnetgenerator -h
```

--------------------------------

### Install ReacNetGenerator with Pip

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/install.md

Upgrade pip and then install ReacNetGenerator. Verify the installation with the command line.

```bash
pip install -U pip
pip install reacnetgenerator
reacnetgenerator -h
```

--------------------------------

### Install and Get Help for ReacNetGenerator

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/README.md

Install ReacNetGenerator using conda and view its help message to understand available commands and options.

```sh
conda install reacnetgenerator -c conda-forge
```

```sh
reacnetgenerator -h
```

--------------------------------

### Project and Python Setup

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/CMakeLists.txt

Initializes the CMake project and finds the required Python interpreter and development components. This is essential for projects that integrate Python code.

```cmake
cmake_minimum_required(VERSION 3.26...3.28)
project(${SKBUILD_PROJECT_NAME} LANGUAGES C CXX)

find_package(
  Python
  COMPONENTS Interpreter Development.SABIModule
  # NumPy
  REQUIRED)
```

--------------------------------

### Build ReacNetGenerator Docker Image

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/build.md

Build a Docker image for ReacNetGenerator. Docker must be installed.

```bash
docker build . -t njzjz/reacnetgenerator
docker run njzjz/reacnetgenerator reacnetgenerator -h
```

--------------------------------

### Install ReacNetGenerator via Pip

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/build.md

Install ReacNetGenerator using pip after cloning the repository. A C/C++ compiler is required.

```bash
pip install -U pip
pip install .
```

--------------------------------

### Install ReacNetGenerator with Pip

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/install.ipynb

Use this command to install the ReacNetGenerator package. Ensure you have pip installed and configured in your environment.

```bash
pip install reacnetgenerator
```

--------------------------------

### XYZ File Format Example

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/format.md

An example of a standard XYZ file format. Note that XYZ files do not contain cell information, which must be provided separately.

```xyz
3
Water frame 1
H    0.7493682    0.0000000    0.4424329
O    0.0000000    0.0000000   -0.1653507
H   -0.7493682    0.0000000    0.4424329
3
Water frame 2
H    0.7493682    0.0000000    0.4424329
O    0.0000000    0.0000000   -0.1653507
H   -0.7493682    0.0000000    0.4424329
```

--------------------------------

### ASE Mode with Custom Pair Cutoffs

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

This example demonstrates using the Atomic Simulation Environment (ASE) for bond detection with custom pair cutoff values. It's suitable for fine-tuning bond detection sensitivity.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type xyz \
    -i md.xyz \
    -a C H O \
    --use-ase \
    --ase-cutoff-mult 1.2 \
    --ase-pair-cutoffs C-O:1.8,H-O:1.2
```

--------------------------------

### Verify ReacNetGenerator Installation

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/install.ipynb

Run this command to check if ReacNetGenerator has been installed correctly and to view its usage information.

```bash
%%bash
reacnetgenerator -h
```

--------------------------------

### Reaction Overview Output - Text

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

This is an example of the output from viewing the reaction overview file. It shows a chemical reaction where a CL-20 molecule decomposes into a nitrogen dioxide molecule and another complex molecule.

```text
1 [H]C12N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O->O=NO+[H]C12NC3([H])N(N(=O)=O)C1([H])N(N(=O)=O)C1([H])N(N(=O)=O)C3([H])N(N(=O)=O)C1([H])N2N(=O)=O
```

--------------------------------

### Build ReacNetGenerator Conda Package

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/build.md

Build a conda package for ReacNetGenerator. Ensure Anaconda or Miniconda is installed.

```bash
conda config --add channels conda-forge
conda build conda/recipe
conda install reacnetgenerator --use-local
reacnetgenerator -h
```

--------------------------------

### ReacNetGenerator Command-Line Usage (Bond File)

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

Example of using ReacNetGenerator to process a LAMMPS bond file. Specify the input file, atomic elements, and file type. The --nohmm flag is used to disable HMM filtering.

```bash
$ reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm
```

--------------------------------

### ReacNetGenerator Command-Line Usage (Dump File)

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

Example of using ReacNetGenerator to process a LAMMPS dump file. Specify the input file, atomic elements, and file type. The --nohmm flag is used to disable HMM filtering.

```bash
$ reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm
```

--------------------------------

### ReacNetGenerator Initialization and Run

Source: https://github.com/deepmodeling/reacnetgenerator/wiki/Python-API

Demonstrates how to initialize the ReacNetGenerator class with input parameters and execute the network generation and drawing process.

```APIDOC
## ReacNetGenerator Class Usage

### Description
This section shows how to instantiate the `ReacNetGenerator` class and call its primary methods.

### Initialization
Initialize `ReacNetGenerator` with input file type, filename, and atom names.

```python
from reacnetgenerator import ReacNetGenerator

rng = ReacNetGenerator(inputfiletype='lammpsbondfile',
                       inputfilename='bonds.reaxc',
                       atomname=['C', 'H', 'O'])
```

### Running the Generator
Call the `runanddraw` method to generate the reaction network and visualize it.

```python
rng.runanddraw()
```
```

--------------------------------

### Initialize and Run ReacNetGenerator

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/python.md

Instantiate the ReacNetGenerator class with input file details and atom names, then execute the simulation and drawing process. Refer to the ReacNetGenerator class documentation for a full list of parameters.

```python
from reacnetgenerator import ReacNetGenerator
ReacNetGenerator(
  inputfiletype="dump",
  inputfilename="dump.ch4",
  atomname=['C', 'H', 'O'],
  ).runanddraw()
```

--------------------------------

### Launch ReacNetGenerator GUI

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/gui.md

To open the graphical user interface, execute this command in your terminal.

```bash
reacnetgeneratorgui
```

--------------------------------

### Launch Local Browser UI

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Launch the ReacNetGenerator web application locally for interactive visualization and analysis. Specify the host and port.

```bash
uvx --refresh --from reacnet-md-tools rng-webapp \
    --reac out/run/run.reactionabcd \
    --host 127.0.0.1 \
    --port 8000
```

--------------------------------

### Reacnetgenerator CLI Help

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/cli.md

Displays the help message for the Reacnetgenerator command line tool, outlining all available arguments and options.

```bash
reacnetgenerator --help
```

--------------------------------

### View Reaction Overview - Bash

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

Use the 'cat' command in bash to view the overview of reactions in the trajectory file. This is useful for quickly inspecting the decomposition products.

```bash
cat cl20.lammpstrj.reactionabcd
```

--------------------------------

### Initialize and Run ReacNetGenerator

Source: https://github.com/deepmodeling/reacnetgenerator/wiki/Python-API

Initializes the ReacNetGenerator with specified input file type and atom names, then runs the generation and drawing process. Ensure the input file exists and is correctly formatted.

```python
from reacnetgenerator import ReacNetGenerator

rng = ReacNetGenerator(inputfiletype='lammpsbondfile',
                       inputfilename='bonds.reaxc',
                       atomname=['C', 'H', 'O'],
                       )
rng.runanddraw()
```

--------------------------------

### Native CLI for XYZ with Explicit Cell

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Process XYZ files using the native CLI, specifying an explicit cell for periodic boundary conditions.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type xyz \
    -i /path/to/md.xyz \
    -a C H O \
    --nohmm \
    --cell 10 0 0 0 10 0 0 0 10
```

--------------------------------

### Download Trajectory Data

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

Use wget to download the CL-20 trajectory data file. This is a prerequisite for the analysis.

```bash
%%bash
wget https://raw.githubusercontent.com/tongzhugroup/TRAJREAX/f10a5c2cab77d3f3b659d9dd08256ae7b27c2820/cl20/cl20.lammpstrj -O cl20.lammpstrj
```

--------------------------------

### Run ReacNetGenerator with Singularity

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/install.md

Use Singularity to run the ReacNetGenerator Docker image. Mount local directories when analyzing trajectories.

```bash
singularity run docker://ghcr.io/deepmodeling/reacnetgenerator reacnetgenerator -h
```

--------------------------------

### Native CLI for Non-Periodic XYZ

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Process non-periodic XYZ files using the native CLI. The `--nopbc` flag disables periodic boundary conditions.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type xyz \
    -i /path/to/md.xyz \
    -a C H O \
    --nohmm \
    --nopbc
```

--------------------------------

### Run ReacNetGenerator with Docker

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/install.md

Execute ReacNetGenerator using an official Docker image. Mount local directories when analyzing trajectories.

```bash
docker run ghcr.io/deepmodeling/reacnetgenerator reacnetgenerator -h
```

--------------------------------

### Native CLI with Isomer Merging

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Process dump files using the native CLI and enable isomer merging with the `--miso` flag. This groups similar isomers together.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type dump \
    -i /path/to/dump.reaxc \
    -a C H O \
    --miso 1
```

--------------------------------

### Inspect Reaction Formula with rng-query

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Query for reaction formulas using reactant and product information. This is useful for verifying reaction pathways.

```bash
uvx --refresh --from reacnet-md-tools rng-query rxn-formula \
    --reac out/run/run.reactionabcd \
    --reactants C6H6 \
    --products C6H5+H
```

--------------------------------

### Native CLI for Bond Trajectory

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Use the native ReacNetGenerator CLI to process bond trajectory files. Specify the atoms to analyze.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type bond \
    -i /path/to/bonds.reaxc \
    -a C H O \
    --nohmm
```

--------------------------------

### Native CLI with Selective Graph Elements

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Process dump files using the native CLI, selecting specific atoms for graph element analysis. This is useful for focusing on particular species.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type dump \
    -i /path/to/dump.reaxc \
    -a C H O Cl \
    --nohmm \
    --selectatoms C O
```

--------------------------------

### HMM Tuning with Matrix Parameters

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

Tune the Hidden Markov Model (HMM) parameters by providing custom transition and emission matrices. This allows for precise control over the reaction network's species identification.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type dump \
    -i dump.reaxc \
    -a C H O \
    --matrixa 0.999 0.001 0.001 0.999 \
    --matrixb 0.6 0.4 0.4 0.6
```

--------------------------------

### Inspect Next Reaction with rng-query

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Query for the next reaction in the output using SMILES notation. This helps in identifying sequential reaction steps.

```bash
uvx --refresh --from reacnet-md-tools rng-query next \
    --reac out/run/run.reactionabcd \
    --smiles '[CH3][CH3]'
```

--------------------------------

### Inspect Species with rng-query

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Use `rng-query` to inspect existing outputs, specifically querying for species information. Provide the reaction output path and the desired chemical formula.

```bash
uvx --refresh --from reacnet-md-tools rng-query species \
    --reac out/run/run.reactionabcd \
    --formula C6H6
```

--------------------------------

### XYZ Trajectory Analysis with Explicit Cell

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

Analyze XYZ trajectory files with explicit cell parameters. This command is useful when the input file lacks cell information but periodic boundary conditions are enabled.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type xyz \
    -i md.xyz \
    -a C H O \
    --nohmm \
    --cell 10 0 0 0 10 0 0 0 10
```

--------------------------------

### Freeze Deep Potential Model

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Extract the trained neural network model into a protobuf file. The output file name is specified with the `-o` flag.

```sh
$deepmd_root/bin/dp freeze -o graph.pb
```

--------------------------------

### Clone ReacNetGenerator Repository

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/build.md

Clone the ReacNetGenerator source code from GitHub to build it locally.

```bash
git clone https://github.com/deepmodeling/reacnetgenerator
cd reacnetgenerator
```

--------------------------------

### Run Native ReacNetGenerator with Official Flags

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/SKILL.md

Execute the native ReacNetGenerator CLI, allowing access to all official low-level flags. This is useful when the high-level wrapper does not expose specific options.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator --help
```

--------------------------------

### Webpack Build Configuration

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/CMakeLists.txt

Configures the build process for webpack assets. It finds the Node.js executable, determines the Yarn path using a Python script, and defines a custom command to build the bundle.html.

```cmake
# webpack
set(WEBPACK_DIR ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/static/webpack)
# find node
find_program(
  NODE_EXECUTABLE
  NAMES node
  DOC "Node.js executable"
  REQUIRED)
message(STATUS "Found Node.js: ${NODE_EXECUTABLE}")
# use python to get yarn path from .yarnrc.yml
execute_process(
  COMMAND ${Python_EXECUTABLE} -c
          "import yaml; print(yaml.safe_load(open('.yarnrc.yml'))['yarnPath'])"
  WORKING_DIRECTORY ${WEBPACK_DIR}
  OUTPUT_VARIABLE YARN_EXECUTABLE
  OUTPUT_STRIP_TRAILING_WHITESPACE)
if(NOT YARN_EXECUTABLE)
  message(FATAL_ERROR "Yarn executable not found")
endif()
message(STATUS "Found Yarn: ${YARN_EXECUTABLE}")

add_custom_command(
  OUTPUT bundle.html
  COMMAND ${NODE_EXECUTABLE} ${YARN_EXECUTABLE}
  COMMAND ${NODE_EXECUTABLE} ${YARN_EXECUTABLE} start
  COMMENT "Building bundle.html using webpack"
  WORKING_DIRECTORY ${WEBPACK_DIR}
  VERBATIM)
add_custom_target(run ALL DEPENDS bundle.html)
# install generated bundle.html
install(
  FILES ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/static/webpack/bundle.html
  DESTINATION reacnetgenerator/static/webpack/)
```

--------------------------------

### Train Deep Potential Model

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Execute the DeepMD training command with the specified JSON parameter file. Ensure the `deepmd_root` environment variable is set.

```sh
$deepmd_root/bin/dp train methane_param.json
```

--------------------------------

### Standard LAMMPS Dump Workflow

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

Use this for normal LAMMPS dump workflows. It processes a trajectory file and generates output.

```bash
uvx --refresh --from reacnet-md-tools rng-pipeline \
    --input /path/to/trajectory.lammpstrj \
    --type dump \
    --outroot out \
    --data /path/to/system.data \
    --nohmm \
    --stepinterval 10 \
    --maxspecies 50
```

--------------------------------

### Compress Frozen Model

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Compress the frozen model for efficient use in simulations. Requires the input frozen model, output file name, and the parameter JSON file.

```sh
$deepmd_root/bin/dp compress -i graph.pb -o graph_compressed.pb -t methane_param.json
```

--------------------------------

### Cython Module Compilation (dps)

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/CMakeLists.txt

Defines a custom command to compile a Cython file (dps.pyx) into a C++ source file and then adds it as a Python library module. This is used for performance-critical Python extensions.

```cmake
# dps
add_custom_command(
  OUTPUT dps.cpp
  COMMENT
    "Making ${CMAKE_CURRENT_BINARY_DIR}/dps.cpp from ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/dps.pyx"
  COMMAND
    Python::Interpreter -m cython
    "${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/dps.pyx" --output-file dps.cpp
  DEPENDS reacnetgenerator/dps.pyx
  VERBATIM)

python_add_library(
  dps
  MODULE
  USE_SABI
  3.7
  ${CMAKE_CURRENT_BINARY_DIR}/dps.cpp
  ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/c_stack.cpp
  WITH_SOABI)
target_include_directories(dps
                           PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator)
target_compile_definitions(dps PRIVATE CYTHON_LIMITED_API=1)
if(CMAKE_BUILD_TYPE STREQUAL "Debug")
  target_compile_definitions(dps PRIVATE CYTHON_TRACE=1 CYTHON_TRACE_NOGIL=1)
endif()

install(TARGETS dps DESTINATION reacnetgenerator/)
```

--------------------------------

### ReacNetGenerator CLI Basic Structure

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

This is the fundamental structure of the ReacNetGenerator CLI command. It requires input files and atom names, with several optional flags for customization.

```bash
reacnetgenerator -i INPUT... -a ATOMNAME... [options]
```

--------------------------------

### Interactive Data File Selection Workflow

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/examples.md

This command allows interactive selection of the data file during a LAMMPS dump workflow. It is TTY only.

```bash
uvx --refresh --from reacnet-md-tools rng-pipeline \
    --input /path/to/trajectory.lammpstrj \
    --type dump \
    --outroot out \
    --pick-data
```

--------------------------------

### Display Reaction Network - Python

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

This code snippet is part of the analysis process and is likely used internally by the ReacNetGenerator tool to draw the reaction network. It is not directly executable by the user but indicates a step in the analysis.

```python
2022-11-05 08:51:48,855 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 6: Done! Time consumed (s): 0.204 (Draw reaction network)
```

--------------------------------

### Run LAMMPS Simulation with DP

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Invoke LAMMPS to perform reactive MD simulations using the trained Deep Potential model. The simulation is controlled by the `input.lammps` file.

```sh
$deepmd_root/bin/lmp -i input.lammps
```

--------------------------------

### Generate Analysis Report - Python

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

This log entry indicates the completion of the analysis report generation step. The report is typically saved as an HTML file for detailed viewing.

```python
2022-11-05 08:51:48,942 - ReacNetGenerator 1.6.6.dev24+g068dac4 - INFO: Step 7: Done! Time consumed (s): 0.087 (Generate analysis report)
```

--------------------------------

### Analyze Trajectory with ReacNetGenerator

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/analysis.ipynb

Run ReacNetGenerator to analyze the downloaded trajectory. Ensure the element order matches the trajectory's atom types. The --nohmm flag disables Hidden Markov Model filtering.

```bash
%%bash
reacnetgenerator -i cl20.lammpstrj -a H C N O --type dump --nohmm
```

--------------------------------

### Run Standard LAMMPS Dump Workflow

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/SKILL.md

Execute a typical LAMMPS dump trajectory analysis using the reacnet-md-tools wrapper. This command ensures the latest version is used and displays help information for the rng-pipeline subcommand.

```bash
uvx --refresh --from reacnet-md-tools rng-pipeline --help
```

--------------------------------

### Configure LAMMPS for DeepMD

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Specify the DeepMD pair style and coefficients in the LAMMPS input script. Ensure the `graph_compressed.pb` file is accessible.

```lammps
pair_style deepmd graph_compressed.pb
pair_coeff * *

```

--------------------------------

### Analyze Existing ReacNetGenerator Outputs

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/SKILL.md

Query and analyze pre-existing ReacNetGenerator outputs without rerunning the main analysis. This command uses the reacnet-md-tools wrapper to access query functionalities.

```bash
uvx --refresh --from reacnet-md-tools rng-query --help
```

--------------------------------

### Analyze Dump Trajectory File

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/run.md

Use this command to process a dump trajectory file. Specify the input file, atomic elements, and disable HMM filtering.

```bash
reacnetgenerator --type dump -i dump.reaxc -a C H O --nohmm
```

--------------------------------

### Bond Trajectory Analysis

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

Use this command to analyze bond information from a ReacNetGenerator bond trajectory file. It disables the Hidden Markov Model (HMM) for analysis.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type bond \
    -i bonds.reaxc \
    -a C H O \
    --nohmm
```

--------------------------------

### Analyze CL-20 Trajectory with ReacNetGenerator

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/cl20.md

Use ReacNetGenerator to analyze reactive simulation trajectories. Specify the input trajectory file, elements, trajectory type, and disable HMM analysis.

```bash
reacnetgenerator -i cl20.lammpstrj -a H C N O --type dump --nohmm
```

--------------------------------

### Analyze LAMMPS Bond File

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/run.md

Use this command to process a LAMMPS bond trajectory file. Specify the input file, atomic elements, and disable HMM filtering.

```bash
reacnetgenerator --type bond -i bonds.reaxc -a C H O --nohmm
```

--------------------------------

### Dump Trajectory Analysis

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/skills/reacnetgenerator/references/cli.md

This command is used for analyzing dump trajectories. It specifies the output type as 'dump' and disables the HMM.

```bash
uvx --refresh --from reacnetgenerator reacnetgenerator \
    --type dump \
    -i dump.reaxc \
    -a C H O \
    --nohmm
```

--------------------------------

### Generate LAMMPS ReaxFF Bonds File

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/format.md

This command generates a LAMMPS ReaxFF bonds file when ReaxFF is used as the pair style. The atomic names must map to types in the bond file.

```lammps
fix 1 all reaxff/bonds 100 bonds.reaxff
```

--------------------------------

### Run ReacNetGenerator on Methane Trajectory

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/tutorial/methane.md

Execute ReacNetGenerator to analyze a LAMMPS trajectory file for methane combustion. This command extracts reaction networks and species, dumping them for further analysis.

```sh
reacnetgenerator -i methane.lammpstrj -a C H O --dump
```

--------------------------------

### Conditional Cython Module Compilation (utils_np)

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/CMakeLists.txt

Conditionally compiles another Cython module (utils_np.pyx) if the build type is not Debug. It links against NumPy and sets specific compile definitions for Cython. This section is currently disabled by 'if(FALSE)'.

```cmake
# utils_np temporary disable until limited api is supported
if(FALSE)
  add_custom_command(
    OUTPUT utils_np.c
    COMMENT
      "Making ${CMAKE_CURRENT_BINARY_DIR}/utils_np.cpp from ${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/utils_np.pyx"
    COMMAND
      Python::Interpreter -m cython
      "${CMAKE_CURRENT_SOURCE_DIR}/reacnetgenerator/utils_np.pyx" --output-file
      utils_np.c
    DEPENDS reacnetgenerator/utils_np.pyx
    VERBATIM)

  python_add_library(utils_np MODULE USE_SABI 3.11
                     ${CMAKE_CURRENT_BINARY_DIR}/utils_np.c WITH_SOABI)
  target_link_libraries(utils_np PRIVATE Python::NumPy)
  target_compile_definitions(utils_np PRIVATE CYTHON_LIMITED_API=1)
  if(CMAKE_BUILD_TYPE STREQUAL "Debug")
    target_compile_definitions(utils_np PRIVATE CYTHON_TRACE=1
                                                CYTHON_TRACE_NOGIL=1)
  endif()
  install(TARGETS utils_np DESTINATION reacnetgenerator/)
endif()
```

--------------------------------

### Generate LAMMPS Dump File

Source: https://github.com/deepmodeling/reacnetgenerator/blob/master/docs/guide/format.md

This command generates a LAMMPS dump file for ReacNetGenerator. Ensure the file contains 'id', 'type', 'x', 'y', and 'z' keys.

```lammps
dump 1 all custom 100 dump.reaxc id type x y z
```

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