Agent skill

add-vasp

Configure VASP integration. Connect your HPC cluster or local VASP installation so the agent can run VASP calculations via the 213 built-in computation skills.

View SKILL.md on GitHub Repository
Stars 163
Forks 31

Install this agent skill to your Project

npx add-skill https://github.com/majiayu000/claude-skill-registry/tree/main/skills/other/other/add-vasp

SKILL.md

Add VASP Integration

This skill configures VASP access for MatClaw. VASP is proprietary and cannot be bundled in the container, so we connect to your existing VASP installation — either on a remote HPC cluster (via SSH) or on the local host (via volume mount).

Phase 1: Pre-flight

Check if already configured

bash
ls ~/.vasp-remote/config.json 2>/dev/null

If config exists, show it with vasp-remote config and ask the user if they want to reconfigure.

Ask the user

Use AskUserQuestion to determine the setup mode:

How is VASP available to you?

  1. Remote HPC cluster — I have SSH access to a cluster with VASP installed (most common)
  2. Local installation — VASP is installed on this machine
  3. I don't have VASP — Skip this, use QE and MACE instead

If option 3, tell the user that all 213 computation skills already work without VASP (Method A: MACE for fast screening, Method B: QE for DFT accuracy). Exit.

Phase 2: SSH Cluster Setup

Collect cluster details

Ask the user for:

Field Example Required
SSH host login.hpc.example.edu Yes
SSH user jdoe Yes
SSH key path (on host) ~/.ssh/id_rsa Yes (or use default)
VASP binary path on cluster /opt/vasp/6.4.3/bin/vasp_std Yes
POTCAR directory on cluster /opt/vasp/potpaw_PBE No (agent generates POTCAR)
Scratch/work directory /scratch/jdoe/vasp-jobs Yes
Scheduler type slurm or pbs Yes
Default queue/partition normal No
Default number of cores 16 No (default: 16)
Default walltime 24:00:00 No (default: 24:00:00)
Modules to load vasp/6.4.3 intel/2024 No

Write configuration

bash
mkdir -p ~/.vasp-remote
cat > ~/.vasp-remote/config.json << 'JSONEOF'
{
  "mode": "ssh",
  "ssh": {
    "host": "<HOST>",
    "user": "<USER>",
    "key": "<KEY_PATH>",
    "vasp_bin": "<VASP_BIN>",
    "potcar_dir": "<POTCAR_DIR>",
    "work_dir": "<WORK_DIR>",
    "scheduler": "<slurm|pbs>",
    "queue": "<QUEUE>",
    "nprocs": <NPROCS>,
    "walltime": "<WALLTIME>",
    "modules": "<MODULES>"
  }
}
JSONEOF

Replace all <PLACEHOLDERS> with the user's actual values.

Set up SSH key for container access

The container agent needs to reach the cluster. The user's SSH key must be mounted into the container.

Check if there's a VASP-specific SSH key already, or use the default:

bash
# Verify the key exists
ls -la <KEY_PATH>

Add the SSH key mount to container-runner by setting the environment variable:

bash
# Add to .env file
echo "VASP_SSH_KEY_PATH=<KEY_PATH>" >> .env

Then update src/container-runner.ts to mount SSH keys. In the buildVolumeMounts function, after the Gmail credentials section, add:

typescript
// VASP remote SSH key (for cluster access from container)
const vaspSshKey = process.env.VASP_SSH_KEY_PATH;
if (vaspSshKey && fs.existsSync(vaspSshKey)) {
  // Mount the specific key file
  mounts.push({
    hostPath: path.dirname(vaspSshKey),
    containerPath: '/home/node/.ssh',
    readonly: true,
  });
}

// VASP remote configuration
const vaspConfigDir = path.join(homeDir, '.vasp-remote');
if (fs.existsSync(vaspConfigDir)) {
  mounts.push({
    hostPath: vaspConfigDir,
    containerPath: '/home/node/.vasp-remote',
    readonly: true,
  });
}

Test SSH connection

bash
# Test from host first
ssh -i <KEY_PATH> -o BatchMode=yes -o ConnectTimeout=10 <USER>@<HOST> "echo OK && which vasp_std || ls <VASP_BIN>"

If this fails, troubleshoot:

  • Key permissions: chmod 600 <KEY_PATH>
  • Host key: ssh-keyscan <HOST> >> ~/.ssh/known_hosts
  • Firewall/VPN: user may need to be on campus network

Test from container

Rebuild and test:

bash
npm run build
echo '{"prompt":"Run: vasp-remote config","groupFolder":"test","chatJid":"[email protected]","isMain":false,"secrets":{"ANTHROPIC_API_KEY":"...","ANTHROPIC_BASE_URL":"https://api.anthropic.com"}}' | docker run -i \
  -v ./workspace:/workspace/group \
  -v ~/.vasp-remote:/home/node/.vasp-remote:ro \
  -v ~/.ssh:/home/node/.ssh:ro \
  matclaw-agent:latest

Phase 3: Local VASP Setup

Collect local details

Field Example Required
VASP binary path /opt/vasp/bin/vasp_std Yes
POTCAR directory /opt/vasp/potpaw_PBE No
Number of cores 4 No (default: 4)

Write configuration

bash
mkdir -p ~/.vasp-remote
cat > ~/.vasp-remote/config.json << 'JSONEOF'
{
  "mode": "local",
  "local": {
    "vasp_bin": "<VASP_BIN>",
    "potcar_dir": "<POTCAR_DIR>",
    "nprocs": <NPROCS>
  }
}
JSONEOF

Set up volume mounts

Add to src/container-runner.ts in buildVolumeMounts:

typescript
// Local VASP binary mount
const vaspBinPath = process.env.VASP_BIN_PATH;
if (vaspBinPath && fs.existsSync(vaspBinPath)) {
  mounts.push({
    hostPath: path.dirname(vaspBinPath),
    containerPath: '/opt/vasp/bin',
    readonly: true,
  });
}

// Local VASP POTCAR library mount
const vaspPpPath = process.env.VASP_PP_PATH;
if (vaspPpPath && fs.existsSync(vaspPpPath)) {
  mounts.push({
    hostPath: vaspPpPath,
    containerPath: '/opt/vasp/pp',
    readonly: true,
  });
}

Add to .env:

bash
VASP_BIN_PATH=/opt/vasp/bin/vasp_std
VASP_PP_PATH=/opt/vasp/potpaw_PBE

Test

bash
vasp_std --version  # or just check it exists

Phase 4: Rebuild Container

The container needs openssh-client for SSH mode and the vasp-remote script:

bash
./container/build.sh

Phase 5: Verify

Ask the user to test with a simple calculation:

VASP is now configured! Try asking me to calculate something, for example: "Relax the structure of Si using VASP"

The agent will:

  1. Generate INCAR, POSCAR, KPOINTS, POTCAR
  2. Run vasp-remote run to execute on your cluster
  3. Parse vasprun.xml and return the results

How It Works

Agent (in container)
  ├─ Reads skill → generates VASP input files
  ├─ Runs: vasp-remote run
  │   ├─ SSH mode: scp files → sbatch → poll → fetch results
  │   └─ Local mode: mpirun vasp_std
  └─ Parses vasprun.xml with pymatgen → returns results

The vasp-remote script is at /usr/local/bin/vasp-remote inside the container. It reads config from ~/.vasp-remote/config.json (mounted from host).

All 213 computation skills with VASP methods work automatically — they generate input files and the agent calls vasp-remote run instead of vasp_std directly.

Troubleshooting

Problem Cause Fix
Config not found Not configured Run /add-vasp
SSH connection refused Network/firewall Check VPN, try ssh -v from host
Permission denied (publickey) Wrong key or permissions chmod 600 ~/.ssh/id_rsa
vasp_std: not found Wrong binary path Check ssh user@host "which vasp_std"
sbatch: command not found Wrong scheduler type Try pbs instead of slurm
Job stuck in PENDING Queue full Try different queue: vasp-remote run --queue express
Dynamic library errors (local) Container lib mismatch Use SSH mode instead

Removal

bash
rm -rf ~/.vasp-remote
# Remove VASP_* lines from .env
# Remove VASP mount sections from src/container-runner.ts

Recommended Agent Skills

Expand your agent's capabilities with these related and highly-rated skills.

majiayu000/claude-skill-registry

agent-ops-spec

Manage specification documents in .agent/specs/. Use when user provides requirements, acceptance criteria, or feature descriptions that need to be tracked and validated against implementation.

163 31
Explore
majiayu000/claude-skill-registry

agent-ops-state

Maintain .agent state files. Use at session start, after meaningful steps, and before concluding: read/update constitution/memory/focus/issues/baseline consistently.

163 31
Explore
majiayu000/claude-skill-registry

agent-ops-spec

Manage specification documents in .agent/specs/. Use when user provides requirements, acceptance criteria, or feature descriptions that need to be tracked and validated against implementation.

163 31
Explore
majiayu000/claude-skill-registry

agent-ops-testing

Test strategy, execution, and coverage analysis. Use when designing tests, running test suites, or analyzing test results beyond baseline checks.

163 31
Explore
majiayu000/claude-skill-registry

agent-ops-testing

Test strategy, execution, and coverage analysis. Use when designing tests, running test suites, or analyzing test results beyond baseline checks.

163 31
Explore
majiayu000/claude-skill-registry

agent-ops-state

Maintain .agent state files. Use at session start, after meaningful steps, and before concluding: read/update constitution/memory/focus/issues/baseline consistently.

163 31
Explore

Didn't find tool you were looking for?

Be as detailed as possible for better results