Computational-chemistry-agent-skills lammps-deepmd

install

source · Clone the upstream repo

git clone https://github.com/jinzhezenggroup/computational-chemistry-agent-skills

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/jinzhezenggroup/computational-chemistry-agent-skills "$T" && mkdir -p ~/.claude/skills && cp -r "$T/molecular-dynamics/lammps-deepmd" ~/.claude/skills/jinzhezenggroup-computational-chemistry-agent-skills-lammps-deepmd && rm -rf "$T"

manifest: molecular-dynamics/lammps-deepmd/SKILL.md

source content

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

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.
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
Write the LAMMPS input script yourself instead of asking the user to hand-write it.
Keep the example readable and fully explained. If you include an example input script, explain what every command does.
When possible, validate command availability against the LAMMPS docs or local
```
lmp -h
```
output before execution.
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:

uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps

If you need to inspect the local command-line help:

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

Inspect available files in the working directory.
Draft
```
input.lammps
```
.
Explain the script to the user if they asked for an explanation or if the script is nontrivial.
Run a short smoke test first when reasonable.
Run the full simulation.
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

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:

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:

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

uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps

Online help

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:

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
```