Femto-Research

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Codes for femtosecond laser interaction research

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# Femto-Research

Codes for femtosecond laser interaction research, built around a modified two-temperature model (TTM) in LAMMPS.

> **LAMMPS version:** `Femto3D` is verified against the **22 Jul 2025** stable release. Other versions are not guaranteed to work.
>
> **Note:** restart files written by `fix femto3D` are not compatible across LAMMPS versions — reusing an old restart file on a different build will fail with `Fix femto3D restart file is from an incompatible version`. Always start a fresh `Preheating` run when switching LAMMPS versions rather than reusing an old restart file.

Questions: yuanweirong78@gmail.com

## Contents

| Folder | Purpose |
|---|---|
| [`Femto3D`](Femto3D) | Modified LAMMPS TTM fix (`fix_femto3D`) and build files |
| [`Preheating`](Preheating) | Preheats an MD target to a target temperature and relaxes it to equilibrium |
| [`Common Runs`](Common%20Runs) | Main production runs, started from a preheated restart file |
| [`Au Parameters`](Au%20Parameters) | Example Au material parameters used by the runs above |
| [`Analysis`](Analysis) | Post-processing of LAMMPS dump files and MATLAB figure generation |

## Installation — `Femto3D`

`Femto3D` extends LAMMPS's `fix_ttm_mod`. Reference: [LAMMPS `fix_ttm/mod` docs](https://docs.lammps.org/fix_ttm.html#fix-ttm-mod-command).

1. Copy `fix_femto3D.cpp` and `fix_femto3D.h` into your LAMMPS source tree, alongside `fix_ttm_mod.cpp` (`src/EXTRA-FIX`).
2. Copy `femto3D.cmake` into the LAMMPS `cmake/presets` folder.
3. Build LAMMPS with the preset, from the LAMMPS root folder:

```sh
   mkdir build && cd build
   cmake -C ../cmake/presets/femto3D.cmake \
         -D CMAKE_INSTALL_PREFIX=../lammps_bin \
         -D BUILD_MPI=yes \
         -D CMAKE_CXX_COMPILER=mpicxx \
         -D CMAKE_C_COMPILER=mpicc \
         -D LAMMPS_MACHINE=mpi \
         ../cmake
   cmake --build .
   make install
   ```

## Usage

### 1. Preheating

Preheats an MD-generated target to a desired temperature and relaxes it to equilibrium. Produces a LAMMPS restart file (`restart.equil` by default) for use in the next stage.

```sh
mpiexec -np 60 PATH/TO/YOUR/lmp_mpi -in Au_TTM_pre.in
```

Run with all necessary parameter files in the same folder.

### 2. Common Runs

Requires the restart file generated by `Preheating`. Rename it from `TTM_pre_restart.*` to `TTM_restart.0` before running.

```sh
mpiexec -np 60 PATH/TO/YOUR/lmp_mpi -in Au_TTM_restart.in
```

See [`run.sh`](run.sh) for a complete example, including timing output.

> **Tip:** run `Preheating` and `Common Runs` in separate folders, and use `tmux` on a remote server for long runs.

### 3. Au Parameters

Example Au parameters required by `Common Runs`, in LAMMPS metal units:

- `Ke`: eV / (ps·Å·K)
- `Ce`: eV / (Å³·K)
- `G`: eV / (Å³·ps·K)

### 4. Analysis

Run `read.cpp` then `read2.cpp`, in that order, to process LAMMPS dump files. The MATLAB scripts then generate figures from the temperature files and the `read`/`read2` outputs.

## Customization

- To support flexible atom types with different interatomic potentials, modify `void LAMMPS_NS::FixFEMTO3D::ChangeType()`.

## Reference

- [Ablation study in gold irradiated by single femtosecond laser pulse with electron temperature dependent interatomic potential and electron–phonon coupling factor](https://iopscience.iop.org/article/10.1088/1555-6611/abdcb8/meta)

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