sync(skills): Add a description about mass (#73)

Imported from jinzhezenggroup/computational-chemistry-agent-skills.
Upstream-Commit: jinzhezenggroup/computational-chemistry-agent-skills@37ed5a2
Upstream-Paths:
- machine-learning-potentials/deepmd-finetune-dpa3
- machine-learning-potentials/deepmd-python-inference
- machine-learning-potentials/deepmd-train-dpa3
- machine-learning-potentials/deepmd-train-se-e2-a
- molecular-dynamics/lammps-deepmd

Author: light-cyan

skills/lammps-deepmd/SKILL.md

@@ -25,6 +25,7 @@ Use this skill when the user wants to run molecular dynamics in LAMMPS with a De
 1. Confirm the minimum simulation inputs:
    - structure/data file (for example `data.system`)
    - DeePMD model file (for example `graph.pb` or compressed model)
+   - atom type to element mapping, including required per-type masses if the data file does not define them
    - 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.
@@ -104,6 +105,8 @@ atom_style      atomic
 neighbor        1.0 bin
 
 read_data       data.system
+mass            1 28.0855
+mass            2 15.999
 pair_style      deepmd graph_compressed.pb
 pair_coeff      * *
 
@@ -171,6 +174,11 @@ run             ${NSTEPS}
   - 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.
 
+- `mass 1 28.0855`, `mass 2 15.999`
+
+  - Defines per-type atomic masses when the data file does not contain a `Masses` section.
+  - These example values correspond to a two-type Si/O mapping; adjust them to the actual atom type to element mapping. LAMMPS velocity creation and thermostats require masses; without them, runs can fail with `Not all per-type masses are set`.
+
 - `pair_style deepmd graph_compressed.pb`
 
   - Selects the DeePMD pair style.

skills/lammps-deepmd/assets/input.nvt.lammps

@@ -11,6 +11,8 @@ atom_style      atomic
 neighbor        1.0 bin
 
 read_data       data.system
+mass            1 28.0855
+mass            2 15.999
 pair_style      deepmd graph_compressed.pb
 pair_coeff      * *
 

skills/lammps-deepmd/references/commands-and-workflow.md

@@ -2,17 +2,6 @@
 
 This reference expands the main skill with practical operating guidance.
 
-## When to use this skill
-
-Use this skill when a user needs to:
-
-- run LAMMPS with a DeePMD-kit model
-- write or modify `input.lammps`
-- explain what a LAMMPS command does
-- switch between NVE, NVT, and NPT
-- run through `uvx` in an internet-connected environment
-- run through a site-installed `lmp` command in an offline or HPC environment
-
 ## Practical rules for agents
 
 1. Prefer small, explicit input scripts over clever but opaque templates.
@@ -34,6 +23,7 @@ This helps catch obvious issues such as:
 - missing model file
 - unsupported pair style in the local LAMMPS build
 - malformed data file
+- missing per-type masses in the data file or input script
 - immediate numerical instability
 
 Then replace the short run with the intended production length.
@@ -49,6 +39,7 @@ Then replace the short run with the intended production length.
 ## Caution points
 
 - The correct timestep depends on the physical system and the DeePMD model quality.
+- Ensure every atom type has a mass, either in the LAMMPS data file `Masses` section or via explicit `mass` commands after `read_data`.
 - `velocity ... create ...` should usually not be repeated when continuing from a restart.
 - NPT settings need physically sensible damping constants; avoid copying values blindly.
 - Some local LAMMPS builds may support DeePMD under slightly different package configurations. Check `lmp -h` if unsure.