lammps-deepmd · v1.0 · 2026-03-23 · sha256 eab4d1cc5a0f81a5
lammps-deepmd v1.0A
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---
name: lammps-deepmd
description: >
A tool and knowledge base for running molecular dynamics (MD) simulations in LAMMPS with the DeePMD-kit plugin. It handles input script preparation, ensemble selection (NVE/NVT/NPT), and job execution via `uv` or offline binaries.
USE WHEN you need to set up, write, explain, or execute a LAMMPS molecular dynamics simulation using a DeePMD machine learning potential (e.g., `graph.pb`).
compatibility: Requires LAMMPS with DeePMD-kit support. Online mode prefers `uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp`; offline mode requires a user-provided LAMMPS executable or module.
license: LGPL-3.0-or-later
metadata:
author: OpenClaw
version: '1.0'
repository: https://github.com/deepmodeling/deepmd-kit
lammps_docs: https://docs.lammps.org/
---
# LAMMPS + DeePMD-kit
Use this skill when the user wants to run molecular dynamics in LAMMPS with a DeePMD-kit potential, prepare or explain an `input.lammps` file, or switch between common ensembles such as NVE, NVT, and NPT.
## Agent responsibilities
1. Confirm the available execution mode:
- **Online mode**: if internet access is available and `uv` is installed, prefer
`uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp ...`
- **Offline mode**: do **not** guess the executable. Ask the user which LAMMPS command, module, or container should be used.
1. Confirm the minimum simulation inputs:
- structure/data file (for example `data.system`)
- DeePMD model file (for example `graph.pb` or compressed model)
- target ensemble (NVE, NVT, NPT, or another explicitly requested setup)
- temperature, pressure if applicable, timestep, and total number of steps
1. Write the LAMMPS input script yourself instead of asking the user to hand-write it.
1. Keep the example readable and fully explained. If you include an example input script, explain what **every command** does.
1. When possible, validate command availability against the LAMMPS docs or local `lmp -h` output before execution.
1. Report clearly which command was run, which files were used, and where outputs were written.
## Decide the execution mode
### Online mode (preferred when internet access is available)
Use:
```bash
uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps
```
If you need to inspect the local command-line help:
```bash
uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -h | tee /dev/tty
```
Notes:
- This is the preferred path because it can provision LAMMPS and DeePMD-kit on demand.
- The `gpu,torch,lmp` extras match the requested runtime pattern from the user.
- If the environment is slow or the packages are large, warn the user that the first run may take time.
### Offline mode
If internet access is unavailable or the user explicitly wants a site-installed binary, ask a concrete question such as:
- "Which LAMMPS executable should I use, for example `lmp`, `lmp_mpi`, `mpirun -np 8 lmp`, or an HPC module command?"
- "Do you already have a DeePMD-enabled LAMMPS build on this machine or cluster?"
Do not invent a binary name or module name.
## Minimal information to collect
Ask only for what is missing:
- DeePMD model path
- LAMMPS data file path
- ensemble
- target temperature
- target pressure if using NPT
- timestep
- run length in steps
- whether velocities should be generated from scratch
- preferred execution command if offline
## Recommended workflow
1. Inspect available files in the working directory.
1. Draft `input.lammps`.
1. Explain the script to the user if they asked for an explanation or if the script is nontrivial.
1. Run a short smoke test first when reasonable.
1. Run the full simulation.
1. Summarize outputs such as `log.lammps`, dump trajectories, restart files, and thermodynamic data.
## Example: annotated NVT input
The following example is adapted from the user-provided tutorial pattern and slightly generalized. See also `assets/input.nvt.lammps`.
```lammps
variable NSTEPS equal 1000000
variable THERMO_FREQ equal 1000
variable DUMP_FREQ equal 1000
variable TEMP equal 300.0
variable TAU_T equal 0.1
units metal
boundary p p p
atom_style atomic
neighbor 1.0 bin
read_data data.system
pair_style deepmd graph_compressed.pb
pair_coeff * *
thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz
thermo ${THERMO_FREQ}
dump 1 all custom ${DUMP_FREQ} traj.lammpstrj id type x y z
velocity all create ${TEMP} 743574
fix 1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}
timestep 0.0005
run ${NSTEPS}
```
### What every command means
- `variable NSTEPS equal 1000000`
- Defines a numeric variable called `NSTEPS` with value `1000000`.
- Used later by `run ${NSTEPS}` so the run length is easy to modify in one place.
- `variable THERMO_FREQ equal 1000`
- Defines how often LAMMPS prints thermodynamic information.
- Used by `thermo ${THERMO_FREQ}`.
- `variable DUMP_FREQ equal 1000`
- Defines how often coordinates are written to the trajectory dump.
- `variable TEMP equal 300.0`
- Sets the target temperature in the current unit system.
- Because `units metal` is used below, this temperature is interpreted in kelvin.
- `variable TAU_T equal 0.1`
- Sets the thermostat damping parameter used by the NVT fix.
- In `metal` units this is in picoseconds.
- `units metal`
- Selects the LAMMPS `metal` unit system.
- This determines the physical meaning of timestep, temperature, pressure, energy, distance, and time.
- In this unit system, distances are in angstrom, time is in picoseconds, and the timestep should be chosen accordingly.
- `boundary p p p`
- Applies periodic boundary conditions in x, y, and z.
- Suitable for bulk condensed-phase simulations.
- `atom_style atomic`
- Uses the `atomic` atom style, appropriate when atoms have no explicit bonds, angles, or molecular topology in the force field description.
- Common for DeePMD simulations of condensed phases when the structure is provided as atoms in a box.
- `neighbor 1.0 bin`
- Sets the neighbor-list skin distance to `1.0` in the current distance unit.
- Uses the `bin` neighbor-building method.
- Neighbor lists help LAMMPS efficiently find nearby atoms for force evaluation.
- `read_data data.system`
- Reads the initial atomic structure, atom types, simulation box, and related information from the LAMMPS data file `data.system`.
- Replace this filename with the actual user file.
- `pair_style deepmd graph_compressed.pb`
- Selects the DeePMD pair style.
- Loads the DeePMD model from `graph_compressed.pb`.
- Replace the model filename with the actual model path, for example `graph.pb`, `graph-compress.pb`, or another supported exported model.
- `pair_coeff * *`
- Activates the previously selected pair style for all atom types.
- For DeePMD this often takes the simple form `* *` because the mapping is embedded in the model workflow rather than through conventional pairwise parameters.
- `thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz`
- Chooses exactly which thermodynamic quantities to print.
- `step`: timestep index.
- `temp`: instantaneous temperature.
- `pe`: potential energy.
- `ke`: kinetic energy.
- `etotal`: total energy.
- `press`: pressure.
- `vol`: box volume.
- `lx ly lz`: box lengths.
- `xy xz yz`: triclinic tilt factors, which are harmless to print even for an orthogonal box.
- `thermo ${THERMO_FREQ}`
- Prints the thermo block every `THERMO_FREQ` timesteps.
- `dump 1 all custom ${DUMP_FREQ} traj.lammpstrj id type x y z`
- Creates dump ID `1`.
- Dumps atoms from group `all`.
- Uses the `custom` dump format.
- Writes every `DUMP_FREQ` steps.
- Saves to `traj.lammpstrj`.
- Outputs per-atom columns `id type x y z`.
- `velocity all create ${TEMP} 743574`
- Assigns random initial velocities to all atoms.
- The target temperature is `TEMP`.
- `743574` is the random seed.
- Use this when starting a fresh MD trajectory. If restarting from a previous equilibrated state, this command may be unnecessary.
- `fix 1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}`
- Creates fix ID `1` on group `all`.
- Applies the Nose-Hoover NVT thermostat.
- The target temperature is ramped from `${TEMP}` to `${TEMP}`, meaning constant temperature here.
- `${TAU_T}` is the thermostat damping constant.
- `timestep 0.0005`
- Sets the MD timestep.
- In `metal` units, `0.0005` means `0.0005 ps = 0.5 fs`.
- The safe choice depends on the system and model quality.
- `run ${NSTEPS}`
- Runs molecular dynamics for `NSTEPS` timesteps.
## Common ensemble modifications
### NVE
Replace the NVT thermostat line with:
```lammps
fix 1 all nve
```
Meaning:
- integrates Newton's equations in the microcanonical ensemble
- no thermostat or barostat is applied
- useful for short stability checks or production runs after equilibration
### NPT
A typical isotropic NPT alternative is:
```lammps
variable PRESS equal 1.0
variable TAU_P equal 1.0
fix 1 all npt temp ${TEMP} ${TEMP} ${TAU_T} iso ${PRESS} ${PRESS} ${TAU_P}
```
Meaning:
- `PRESS` is the target pressure
- `TAU_P` is the barostat damping constant
- `iso` applies isotropic pressure control to the simulation box
- this simultaneously thermostats and barostats the system
When using NPT, it is often useful to keep `vol`, `lx`, `ly`, and `lz` in the thermo output.
## Execution templates
### Online run
```bash
uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps
```
### Online help
```bash
uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -h | tee /dev/tty
```
### Offline run
Only after the user specifies the executable, use a command such as one of these exact patterns:
```bash
lmp -in input.lammps
mpirun -np 8 lmp_mpi -in input.lammps
srun lmp -in input.lammps
```
The agent must not choose one of these on its own without user guidance in offline mode.
## Output checklist
After a run, report at least:
- executed command
- input script path
- data file path
- model path
- main log path
- trajectory path if any
- whether the run completed successfully
- any obvious warnings or errors from the log
## References
- LAMMPS command categories: https://docs.lammps.org/Commands_category.html
- LAMMPS command index: https://docs.lammps.org/Commands_all.html
- DeePMD-kit: https://github.com/deepmodeling/deepmd-kit
- User-provided tutorial reference: https://github.com/tongzhugroup/Chapter13-tutorial/blob/master/input.lammps
- Detailed notes: `references/commands-and-workflow.md`