lammps-deepmd

Name: lammps-deepmd
Author: jinzhezenggroup

113stars23forks

How to install lammps-deepmd?

jinzhezenggroup/computational-chemistry-agent-skills/lammps-deepmd

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill lammps-deepmd

Installs into the current project.

Summary

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 e

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SKILL.md

1	# LAMMPS + DeePMD-kit
2
3	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.
4
5	## Agent responsibilities
6
7	1. Confirm the available execution mode:
8	- Online mode: if internet access is available and `uv` is installed, prefer
9	`uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp ...`
10	- Offline mode: do not guess the executable. Ask the user which LAMMPS command, module, or container should be used.
11	1. Confirm the minimum simulation inputs:
12	- structure/data file (for example `data.system`)
13	- DeePMD model file (for example `graph.pb` or compressed model)
14	- atom type to element mapping, including required per-type masses if the data file does not define them
15	- target ensemble (NVE, NVT, NPT, or another explicitly requested setup)
16	- temperature, pressure if applicable, timestep, and total number of steps
17	1. Write the LAMMPS input script yourself instead of asking the user to hand-write it.
18	1. Keep the example readable and fully explained. If you include an example input script, explain what every command does.
19	1. When possible, validate command availability against the LAMMPS docs or local `lmp -h` output before execution.
20	1. Report clearly which command was run, which files were used, and where outputs were written.
21
22	## Decide the execution mode
23
24	### Online mode (preferred when internet access is available)
25
26	Use:
27
28	```bash
29	uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps
30	```
31
32	If you need to inspect the local command-line help:
33
34	```bash
35	uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -h \| tee /dev/tty
36	```
37
38	Notes:
39
40	- This is the preferred path because it can provision LAMMPS and DeePMD-kit on demand.
41	- The `gpu,torch,lmp` extras match the requested runtime pattern from the user.
42	- If the environment is slow or the packages are large, warn the user that the first run may take time.
43
44	### Offline mode
45
46	If internet access is unavailable or the user explicitly wants a site-installed binary, ask a concrete question such as:
47
48	- "Which LAMMPS executable should I use, for example `lmp`, `lmp_mpi`, `mpirun -np 8 lmp`, or an HPC module command?"
49	- "Do you already have a DeePMD-enabled LAMMPS build on this machine or cluster?"
50
51	Do not invent a binary name or module name.
52
53	## Minimal information to collect
54
55	Ask only for what is missing:
56
57	- DeePMD model path
58	- LAMMPS data file path
59	- ensemble
60	- target temperature
61	- target pressure if using NPT
62	- timestep
63	- run length in steps
64	- whether velocities should be generated from scratch
65	- preferred execution command if offline
66
67	## Recommended workflow
68
69	1. Inspect available files in the working directory.
70	1. Draft `input.lammps`.
71	1. Explain the script to the user if they asked for an explanation or if the script is nontrivial.
72	1. Run a short smoke test first when reasonable.
73	1. Run the full simulation.
74	1. Summarize outputs such as `log.lammps`, dump trajectories, restart files, and thermodynamic data.
75
76	## Example: annotated NVT input
77
78	The following example is adapted from the user-provided tutorial pattern and slightly generalized. See also `assets/input.nvt.lammps`.
79
80	```lammps
81	variable NSTEPS equal 1000000
82	variable THERMO_FREQ equal 1000
83	variable DUMP_FREQ equal 1000
84	variable TEMP equal 300.0
85	variable TAU_T equal 0.1
86
87	units metal
88	boundary p p p
89	atom_style atomic
90
91	neighbor 1.0 bin
92
93	read_data data.system
94	mass 1 28.0855
95	mass 2 15.999
96	pair_style deepmd graph_compressed.pb
97	pair_coeff * *
98
99	thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz
100	thermo ${THERMO_FREQ}
101	dump 1 all custom ${DUMP_FREQ} traj.lammpstrj id type x y z
102
103	velocity all create ${TEMP} 743574
104	fix 1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}
105
106	timestep 0.0005
107	run ${NSTEPS}
108	```
109
110	### What every command means
111
112	- `variable NSTEPS equal 1000000`
113
114	- Defines a numeric variable called `NSTEPS` with value `1000000

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lammps-deepmd

113stars23forks

View on GitHub

How to install lammps-deepmd?

jinzhezenggroup/computational-chemistry-agent-skills/lammps-deepmd

$npx -y skills add jinzhezenggroup/computational-chemistry-agent-skills --skill lammps-deepmd

Installs into the current project.

Summary

Files · 1

View on GitHub

SKILL.md

1	# LAMMPS + DeePMD-kit
2
3	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.
4
5	## Agent responsibilities
6
7	1. Confirm the available execution mode:
8	- Online mode: if internet access is available and `uv` is installed, prefer
9	`uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp ...`
10	- Offline mode: do not guess the executable. Ask the user which LAMMPS command, module, or container should be used.
11	1. Confirm the minimum simulation inputs:
12	- structure/data file (for example `data.system`)
13	- DeePMD model file (for example `graph.pb` or compressed model)
14	- atom type to element mapping, including required per-type masses if the data file does not define them
15	- target ensemble (NVE, NVT, NPT, or another explicitly requested setup)
16	- temperature, pressure if applicable, timestep, and total number of steps
17	1. Write the LAMMPS input script yourself instead of asking the user to hand-write it.
18	1. Keep the example readable and fully explained. If you include an example input script, explain what every command does.
19	1. When possible, validate command availability against the LAMMPS docs or local `lmp -h` output before execution.
20	1. Report clearly which command was run, which files were used, and where outputs were written.
21
22	## Decide the execution mode
23
24	### Online mode (preferred when internet access is available)
25
26	Use:
27
28	```bash
29	uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -in input.lammps
30	```
31
32	If you need to inspect the local command-line help:
33
34	```bash
35	uvx --from lammps --with deepmd-kit[gpu,torch,lmp] lmp -h \| tee /dev/tty
36	```
37
38	Notes:
39
40	- This is the preferred path because it can provision LAMMPS and DeePMD-kit on demand.
41	- The `gpu,torch,lmp` extras match the requested runtime pattern from the user.
42	- If the environment is slow or the packages are large, warn the user that the first run may take time.
43
44	### Offline mode
45
46	If internet access is unavailable or the user explicitly wants a site-installed binary, ask a concrete question such as:
47
48	- "Which LAMMPS executable should I use, for example `lmp`, `lmp_mpi`, `mpirun -np 8 lmp`, or an HPC module command?"
49	- "Do you already have a DeePMD-enabled LAMMPS build on this machine or cluster?"
50
51	Do not invent a binary name or module name.
52
53	## Minimal information to collect
54
55	Ask only for what is missing:
56
57	- DeePMD model path
58	- LAMMPS data file path
59	- ensemble
60	- target temperature
61	- target pressure if using NPT
62	- timestep
63	- run length in steps
64	- whether velocities should be generated from scratch
65	- preferred execution command if offline
66
67	## Recommended workflow
68
69	1. Inspect available files in the working directory.
70	1. Draft `input.lammps`.
71	1. Explain the script to the user if they asked for an explanation or if the script is nontrivial.
72	1. Run a short smoke test first when reasonable.
73	1. Run the full simulation.
74	1. Summarize outputs such as `log.lammps`, dump trajectories, restart files, and thermodynamic data.
75
76	## Example: annotated NVT input
77
78	The following example is adapted from the user-provided tutorial pattern and slightly generalized. See also `assets/input.nvt.lammps`.
79
80	```lammps
81	variable NSTEPS equal 1000000
82	variable THERMO_FREQ equal 1000
83	variable DUMP_FREQ equal 1000
84	variable TEMP equal 300.0
85	variable TAU_T equal 0.1
86
87	units metal
88	boundary p p p
89	atom_style atomic
90
91	neighbor 1.0 bin
92
93	read_data data.system
94	mass 1 28.0855
95	mass 2 15.999
96	pair_style deepmd graph_compressed.pb
97	pair_coeff * *
98
99	thermo_style custom step temp pe ke etotal press vol lx ly lz xy xz yz
100	thermo ${THERMO_FREQ}
101	dump 1 all custom ${DUMP_FREQ} traj.lammpstrj id type x y z
102
103	velocity all create ${TEMP} 743574
104	fix 1 all nvt temp ${TEMP} ${TEMP} ${TAU_T}
105
106	timestep 0.0005
107	run ${NSTEPS}
108	```
109
110	### What every command means
111
112	- `variable NSTEPS equal 1000000`
113
114	- Defines a numeric variable called `NSTEPS` with value `1000000

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