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Add new MCP server manifests for web-fetch, materials-project, ssh-exec, txyz-search, python-code-execution (#29)
adding 5 open sourced mcp servers from [mcp.science](https://github.com/pathintegral-institute/mcp.science) Co-authored-by: Jonathan Wang <[email protected]>
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{
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"name": "materials-project",
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"description": "A MCP (Model Context Protocol) server that interacts with the Materials Project database, allowing for material search, structure visualization, and manipulation.",
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"display_name": "Materials Project",
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"repository": {
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"type": "git",
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"url": "https://github.com/pathintegral-institute/mcp.science"
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},
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"homepage": "https://github.com/pathintegral-institute/mcp.science/tree/main/servers/materials-project",
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"author": {
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"name": "pathintegral-institute"
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},
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"license": "MIT",
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"tags": [
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"materials",
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"science"
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],
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"arguments": {
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"MP_API_KEY": {
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"description": "API key from the Materials Project",
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"required": true,
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"example": "your_materials_project_api_key_here"
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}
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},
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"tools": [
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{
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"name": "search_materials_by_formula",
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"description": "Search for materials in the Materials Project database by chemical formula. Returns a list of text descriptions for structures matching the given formula.",
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"prompt": "Find materials with the chemical formula Fe2O3",
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"inputSchema": {
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"type": "object",
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"properties": {
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"chemical_formula": {
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"type": "string",
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"description": "The chemical formula of the material"
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}
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}
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},
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"required": ["chemical_formula"]
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},
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{
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"name": "select_material_by_id",
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"description": "Select a specific material by its material ID. Returns a list of TextContent objects containing the structure description and URI.",
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"prompt": "Get details for material mp-149",
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"inputSchema": {
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"type": "object",
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"properties": {
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"material_id": {
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"type": "string",
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"description": "The ID of the material"
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}
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}
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},
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"required": ["material_id"]
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},
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{
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"name": "get_structure_data",
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"description": "Retrieve structure data in specified format (CIF or POSCAR). Returns the structure file content as a string.",
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"prompt": "Get the CIF file for silicon",
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"inputSchema": {
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"type": "object",
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"properties": {
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"structure_uri": {
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"type": "string",
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"description": "The URI of the structure"
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},
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"format": {
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"type": "string",
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"description": "Output format, either 'cif' or 'poscar'",
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"enum": ["cif", "poscar"],
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"default": "poscar"
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}
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}
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},
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"required": ["structure_uri"]
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},
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{
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"name": "create_structure_from_poscar",
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"description": "Create a new structure from a POSCAR string. Returns information about the newly created structure, including its URI.",
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"prompt": "Create a structure from this POSCAR data",
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"inputSchema": {
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"type": "object",
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"properties": {
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"poscar_str": {
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"type": "string",
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"description": "The POSCAR string of the structure"
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}
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}
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},
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"required": ["poscar_str"]
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},
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{
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"name": "plot_structure",
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"description": "Visualize the crystal structure. Returns a PNG image of the structure and a Plotly JSON representation.",
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"prompt": "Show me the crystal structure of silicon",
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"inputSchema": {
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"type": "object",
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"properties": {
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"structure_uri": {
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"type": "string",
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"description": "The URI of the structure"
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},
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"duplication": {
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"type": "array",
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"description": "The duplication of the structure along a, b, c axes",
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"items": {
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"type": "integer"
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},
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"default": [1, 1, 1]
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}
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}
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},
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"required": ["structure_uri"]
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},
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{
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"name": "build_supercell",
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"description": "Create a supercell from a bulk structure. Returns information about the newly created supercell structure.",
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"prompt": "Create a 2x2x2 supercell of graphite",
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"inputSchema": {
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"type": "object",
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"properties": {
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"bulk_structure_uri": {
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"type": "string",
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"description": "The URI of the bulk structure"
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},
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"supercell_parameters": {
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"type": "object",
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"description": "Parameters defining the supercell",
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"properties": {
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"scaling_matrix": {
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"type": "array",
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"description": "3x3 matrix or list of 3 integers for scaling",
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"items": {
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"type": "integer"
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}
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}
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}
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}
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}
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},
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"required": ["bulk_structure_uri", "supercell_parameters"]
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},
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{
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"name": "moire_homobilayer",
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"description": "Generate a moiré superstructure of a 2D homobilayer. Returns information about the newly created moiré structure.",
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"prompt": "Create a moiré structure of graphene with 5 degree twist",
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"inputSchema": {
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"type": "object",
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"properties": {
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"bulk_structure_uri": {
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"type": "string",
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"description": "The URI of the bulk structure"
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},
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"interlayer_spacing": {
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"type": "number",
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"description": "The interlayer spacing between the two layers in Ångström"
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},
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"max_num_atoms": {
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"type": "integer",
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"description": "Maximum number of atoms in the moiré superstructure",
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"default": 10
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},
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"twist_angle": {
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"type": "number",
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"description": "Twist angle in degrees",
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"default": 0.0
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},
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"vacuum_thickness": {
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"type": "number",
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"description": "Vacuum thickness in z-direction in Ångström",
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"default": 15.0
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}
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}
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},
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"required": ["bulk_structure_uri", "interlayer_spacing"]
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}
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],
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"installations": {
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"uvx": {
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"type": "uvx",
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"command": "uv",
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"args": [
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"--from",
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"git+https://github.com/pathintegral-institute/mcp.science#subdirectory=servers/materials-project",
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"mcp-materials-project"
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],
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"env": {
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"MP_API_KEY": "your_materials_project_api_key_here"
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}
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}
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},
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"examples": [
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{
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"title": "Search for materials",
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"description": "Search for materials by chemical formula",
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"prompt": "Find materials with the chemical formula Fe2O3"
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},
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{
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"title": "Get material by ID",
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"description": "Select a specific material by its ID",
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"prompt": "Get details for material mp-149"
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},
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{
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"title": "Download structure file",
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"description": "Get structure data in CIF format",
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"prompt": "Download the CIF file for mp-149"
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},
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{
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"title": "Visualize crystal structure",
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"description": "Plot the crystal structure of a material",
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"prompt": "Show me the crystal structure of silicon"
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},
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{
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"title": "Create a supercell",
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"description": "Build a supercell from a bulk structure",
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"prompt": "Create a 2x2x2 supercell of graphite"
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},
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{
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"title": "Create moiré structure",
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"description": "Generate a moiré superstructure",
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"prompt": "Create a moiré structure of graphene with 3.4Å interlayer spacing and 5° twist angle"
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}
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],
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"categories": [
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"MCP Tools"
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],
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"is_official": true
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}
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{
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"name": "python-code-execution",
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"display_name": "Python Code Execution",
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"description": "A secure sandboxed Python code execution environment for MCP (Model-Client-Program) architecture.",
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"repository": {
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"type": "git",
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"url": "https://github.com/pathintegral-institute/mcp.science"
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},
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"homepage": "https://github.com/pathintegral-institute/mcp.science/tree/main/servers/python-code-execution",
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"author": {
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"name": "pathintegral-institute"
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},
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"license": "MIT",
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"tags": [
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"python",
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"code-execution"
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],
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"arguments": {},
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"installations": {
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"uvx": {
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"type": "uvx",
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"command": "uvx",
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"args": [
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"--from",
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"git+https://github.com/pathintegral-institute/mcp.science@main#subdirectory=servers/python-code-execution",
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"mcp-python-code-execution"
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],
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"description": "Run using uv (recommended)"
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}
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},
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"examples": [
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{
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"title": "Execute simple Python code",
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"description": "Run a simple Python calculation",
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"prompt": "Execute this Python code: `print(\"Hello World\")`"
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}
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],
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"categories": [
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"Dev Tools"
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],
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"tools": [
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{
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"name": "python_code_execution",
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"description": "Execute Python code in a secure sandbox with restricted imports and resource limits. Supports visualization with matplotlib and numerical computation with numpy.",
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"prompt": "Execute this Python code: print('Hello, world!')",
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"inputSchema": {
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"type": "object",
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"properties": {
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"code": {
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"type": "string",
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"description": "Python code to execute",
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"minLength": 1
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},
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"show_output": {
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"type": "boolean",
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"description": "Whether to show the output of the code execution",
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"default": true
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}
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}
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},
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"required": ["code"]
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}
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],
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"is_official": true
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}

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