Chatmosp File Organizer

Language routing / 语言路由 Detect the user's language from the latest message.

• If the user writes in English, continue with this English file and respond in English.
• If the user writes in Chinese, read SKILL.md in this same directory and respond in Chinese. Always match the response language to the user's input language.

chatmosp-file-organizer

1. Core Responsibilities

1. Intelligent task naming — generate task names per MSR / KMC format
2. Standard directory creation — MSR and KMC standard structures
3. Path logic management — direct KMC vs sequential KMC
4. Secure file operations — path-traversal protection + whitelist

2. Security-First Principles

• ✅ Path-traversal protection: auto-clean ../, //, ~ and other dangerous chars
• ✅ Whitelist paths: all operations restricted to mosp-for-chatMOSP/OUTPUT/
• ✅ TaskNameValidator: validates task name legality, supports new naming format
• ✅ Permission check: ensure appropriate read/write permissions

Forbidden patterns: .., //, ~, /root, /etc, *.exe, *.sh

Allowed characters: a-zA-Z0-9_-.Å

Max path length: 512

3. Task Naming Rules

3.1 MSR tasks

Format: {metal}_{gas-pp}_{T}K_{P}Pa_R{size}

Example: Pd_CO9_O18_473K_101325Pa_R50

3.2 KMC tasks

⚠️ IMPORTANT: KMC task directory MUST be created as a subdirectory under the corresponding MSR task directory.

Recommended format: KMC_{steps}steps (concise; T/P already encoded in MSR dir name)

Alternative format: KMC_{T}K_{P}Pa_{steps}steps

Examples:

• Concise: KMC_5000000steps
• Verbose: KMC_473K_101325Pa_5000000steps

4. Directory Structures

4.1 MSR task directory

mosp-for-chatMOSP/OUTPUT/{msr_task_name}/
├── faceinfo.txt            # Facet information
├── ini.xyz                 # Real cluster (KMC input)
├── {task_name}_cluster.xyz # Structure for plotting
├── rotation.gif            # Rotation animation
├── structure.png           # Structure image
├── parameter_analysis.md   # Parameter analysis
├── paint.py                # Plotting script
├── input.json              # MSR parameter file
└── metadata.json           # Task metadata

4.2 KMC task directory (under MSR directory)

mosp-for-chatMOSP/OUTPUT/{msr_task_name}/
└── KMC_{steps}steps/
    ├── input.json          # KMC params (required)
    ├── ini.xyz             # Copied from MSR
    ├── coverage.csv        # Coverage data
    ├── coverage.png        # Coverage vs Time
    ├── coverage_steps.png  # Coverage vs Steps
    ├── run.log             # Run log
    ├── site_tof.csv        # Site TOF
    ├── tof.csv             # TOF data
    ├── tof.png             # TOF vs Time
    ├── tof_time.png        # TOF vs Steps
    ├── INPUT/              # KMC auto-fills
    │   ├── events.txt
    │   ├── input.txt
    │   ├── LI.txt
    │   ├── products.txt
    │   └── species.txt
    └── OUTPUT/             # KMC auto-output
        ├── rec_cov.data
        ├── rec_event.data
        └── rec_site_spc.data

5. Path Logic

5.1 MSR task path

• Location: mosp-for-chatMOSP/OUTPUT/{msr_task_name}/
• MSR generates ini.xyz and {task_name}_cluster.xyz
• DO NOT prepare ini.xyz for MSR (MSR generates it)

5.2 KMC task path (two modes)

Mode 1: Direct KMC (no corresponding MSR, copy from MOSP_database)

• Location: mosp-for-chatMOSP/OUTPUT/{kmc_task_name}/
• Use when: no MSR result available

Mode 2: Sequential KMC (use MSR-generated ini.xyz, recommended)

• Location: mosp-for-chatMOSP/OUTPUT/{msr_task_name}/{kmc_task_name}/
• Use when: MSR result available

Prefer Mode 2 for cluster consistency.

6. Visualization Commands (for MSR)

# Static structure image
python3 utils/paint.py OUTPUT/{task_name}/{task_name}_cluster.xyz \
  --output OUTPUT/{task_name}/structure.png

# Rotation animation
python3 utils/paint.py OUTPUT/{task_name}/{task_name}_cluster.xyz \
  --gif OUTPUT/{task_name}/rotation.gif

See msr-generator §5.3 for details.

7. API Examples

Create MSR directory

Input:

{
  "action": "create_msr_directory",
  "parameters": {
    "metal": "Pd",
    "temperature": "473",
    "gases": ["CO", "O2"],
    "partial_pressures": {"CO": 9, "O2": 18},
    "pressure": "101325",
    "radius": "50"
  }
}

Output:

{
  "success": true,
  "task_type": "MSR",
  "task_name": "Pd_CO9_O18_473K_101325Pa_R50",
  "directory_path": "mosp-for-chatMOSP/OUTPUT/Pd_CO9_O18_473K_101325Pa_R50",
  "standard_files": [
    "faceinfo.txt", "ini.xyz", "{task_name}_cluster.xyz",
    "rotation.gif", "structure.png", "parameter_analysis.md",
    "paint.py", "input.json", "metadata.json"
  ]
}

Create KMC directory

Input:

{
  "action": "create_kmc_directory",
  "parameters": {
    "metal": "Pd",
    "temperature": "473",
    "gases": ["CO", "O2"],
    "partial_pressures": {"CO": 9, "O2": 18},
    "pressure": "101325",
    "steps": "200000000",
    "parent_msr_task": null
  }
}

Output:

{
  "success": true,
  "task_type": "KMC",
  "task_name": "Pd_CO9_O18_473K_101325Pa_200000000steps",
  "directory_path": "mosp-for-chatMOSP/OUTPUT/Pd_CO9_O18_473K_101325Pa_200000000steps",
  "required_files": ["input.json", "ini.xyz"],
  "empty_directories": ["INPUT", "OUTPUT"],
  "output_files": ["coverage.csv", "coverage.png", "coverage_steps.png", "run.log", "site_tof.csv", "tof.csv", "tof.png", "tof_time.png"]
}

8. Error Handling

9. Cross-Skill Handoff

• parameter-builder → this skill: called after parameter confirmation
• this skill → msr-generator: after MSR directory creation
• this skill → kmc-simulator: after KMC directory creation
• msr-generator → this skill: for KMC subdirectory creation after MSR

10. Dependencies

• chatmosp-parameter-builder — get task parameters
• chatmosp-input-coordinator — get task type
• chatmosp-msr-generator — MSR calculation receiver
• chatmosp-kmc-simulator — KMC simulation receiver

11. File Structure

chatmosp-file-organizer/
├── SKILL.md       # Chinese reference
└── SKILL_cn.md    # This file (English)

ChatMOSP Companion Skills

This skill is part of the ChatMOSP skill set. For complete functionality, install the companion ChatMOSP skills from ClawHub when they are missing:

• chatmosp-input-coordinator
• chatmosp-parameter-builder
• chatmosp-msr-generator
• chatmosp-kmc-simulator
• chatmosp-literature-search
• chatmosp-file-organizer

If a required companion skill is unavailable, ask the user to install the missing ChatMOSP skill from ClawHub before continuing. Use the GitHub repository only as a fallback.