初次提交

sci_mcp/material_mcp/pymatgen_cal/pymatgen_cal_tools.py

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+import os
+import asyncio
+from pymatgen.core import Structure
+from ...core.config import material_config
+from ...core.llm_tools import llm_tool
+from ..support.utils import read_structure_from_file_name_or_content_string
+
+@llm_tool(name="calculate_density_Pymatgen", description="Calculate the density of a crystal structure from a file or content string using Pymatgen")
+async def calculate_density_Pymatgen(structure_source: str) -> str:
+    """
+    Calculates the density of a structure from a file or content string.
+
+    Args:
+        structure_source (str): The name of the structure file (e.g., POSCAR, CIF) or the content string.
+
+    Returns:
+        str: A Markdown formatted string with the density or an error message if the calculation fails.
+    """
+    # 使用asyncio.to_thread异步执行可能阻塞的操作
+
+    try:
+            # 使用read_structure_from_file_name_or_content_string函数读取结构
+            structure_content, content_format = read_structure_from_file_name_or_content_string(structure_source)
+            # # 使用pymatgen读取结构
+            structure = Structure.from_str(structure_content,fmt=content_format)
+            density = structure.density
+
+            # 删除临时文件
+
+            return (f"## Density Calculation\n\n"
+                    f"- **Structure**: `{structure.composition.reduced_formula}`\n"
+                    f"- **Density**: `{density:.2f} g/cm³`\n")
+    except Exception as e:
+            return f"Error: error occurred while calculating density: {str(e)}\n"
+
+
+@llm_tool(name="get_element_composition_Pymatgen", description="Analyze and retrieve the elemental composition of a crystal structure from a file or content string using Pymatgen")
+async def get_element_composition_Pymatgen(structure_source: str) -> str:
+    """
+    Returns the elemental composition of a structure from a file or content string.
+
+    Args:
+        structure_source (str): The name of the structure file (e.g., POSCAR, CIF) or the content string.
+
+    Returns:
+        str: A Markdown formatted string with the elemental composition or an error message if the operation fails.
+    """
+    # 使用asyncio.to_thread异步执行可能阻塞的操作
+
+    try:
+            # 使用read_structure_from_file_name_or_content_string函数读取结构
+            structure_content, content_format = read_structure_from_file_name_or_content_string(structure_source)
+
+            # 使用pymatgen读取结构
+            structure = Structure.from_str(structure_content, fmt=content_format)
+            composition = structure.composition
+
+            return (f"## Element Composition\n\n"
+                    f"- **Structure**: `{structure.composition.reduced_formula}`\n"
+                    f"- **Composition**: `{composition}`\n")
+    except Exception as e:
+            return f"Error: error occurred while getting element composition: {str(e)}\n"
+
+
+
+@llm_tool(name="calculate_symmetry_Pymatgen", description="Determine the space group and symmetry operations of a crystal structure from a file or content string using Pymatgen")
+async def calculate_symmetry_Pymatgen(structure_source: str) -> str:
+    """
+    Calculates the symmetry of a structure from a file or content string.
+
+    Args:
+        structure_source (str): The name of the structure file (e.g., POSCAR, CIF) or the content string.
+
+    Returns:
+        str: A Markdown formatted string with the symmetry information or an error message if the operation fails.
+    """
+    # 使用asyncio.to_thread异步执行可能阻塞的操作
+
+    try:
+            # 使用read_structure_from_file_name_or_content_string函数读取结构
+            structure_content, content_format = read_structure_from_file_name_or_content_string(structure_source)
+
+
+
+            # 使用pymatgen读取结构
+            structure = Structure.from_str(structure_content, fmt=content_format)
+            symmetry = structure.get_space_group_info()
+
+            return (f"## Symmetry Information\n\n"
+                    f"- **Structure**: `{structure.composition.reduced_formula}`\n"
+                    f"- **Space Group**: `{symmetry[0]}`\n"
+                    f"- **Number**: `{symmetry[1]}`\n")
+    except Exception as e:
+            return f"Error: error occurred while calculating symmetry: {str(e)}\n"
+