初次提交

sci_mcp/material_mcp/mp_query/get_mp_id.py

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+import os
+from typing import List
+from mp_api.client import MPRester
+from ...core.config import material_config
+
+async def get_mpid_from_formula(formula: str) -> List[str]:
+    """
+    Get material IDs (mpid) from Materials Project database by chemical formula.
+    Returns mpids for the lowest energy structures.
+
+    Args:
+        formula: Chemical formula (e.g., "Fe2O3")
+
+    Returns:
+        List of material IDs
+    """
+    os.environ['HTTP_PROXY'] = material_config.HTTP_PROXY or ''
+    os.environ['HTTPS_PROXY'] =material_config.HTTPS_PROXY or ''
+
+
+    try:
+        id_list = []
+
+        cleaned_formula = formula.replace(" ", "").replace("\n", "").replace("\'", "").replace("\"", "")
+        if "=" in cleaned_formula:
+            name, id = cleaned_formula.split("=")
+        else:
+            id = cleaned_formula
+
+        formula_list = [id]
+
+        with MPRester(material_config.MP_API_KEY) as mpr:
+            docs = mpr.materials.summary.search(formula=formula_list)
+            if not docs:
+                return "No materials found"
+            else:
+                for doc in docs:
+                    id_list.append(doc.material_id)
+                return id_list
+    except Exception as e:
+
+        return f"Error: get_mpid_from_formula: {str(e)}"

sci_mcp/material_mcp/mp_query/mp_query_tools.py

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+
+import glob
+import json
+from typing import Dict, Any, Union
+from ...core.llm_tools import llm_tool
+from .get_mp_id import get_mpid_from_formula
+from ..support.utils import extract_cif_info, remove_symmetry_equiv_xyz
+from ...core.config import material_config
+
+from pymatgen.core import Structure
+from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
+from pymatgen.io.cif import CifWriter
+
+@llm_tool(name="search_crystal_structures_from_materials_project",
+          description="Retrieve and optimize crystal structures from Materials Project database using a chemical formula")
+async def search_crystal_structures_from_materials_project(
+    formula: str,
+    conventional_unit_cell: bool = True,
+    symprec: float = 0.1
+) -> str:
+    """
+    Retrieves crystal structures for a given chemical formula from Materials Project database and applies symmetry optimization.
+
+    Args:
+        formula: Chemical formula to search for (e.g., "Fe2O3")
+        conventional_unit_cell: If True, returns conventional unit cell; if False, returns primitive cell
+        symprec: Symmetry precision parameter for structure refinement (default: 0.1)
+
+    Returns:
+        Formatted CIF data for the retrieved crystal structures with symmetry analysis
+    """
+    try:
+        structures = {}
+        mp_id_list = await get_mpid_from_formula(formula=formula)
+        if isinstance(mp_id_list, str):
+            return mp_id_list  # 直接返回错误信息
+
+        for i, mp_id in enumerate(mp_id_list):
+            try:
+                # 文件操作可能引发异常
+                cif_files = glob.glob(material_config.LOCAL_MP_CIF_ROOT + f"/{mp_id}.cif")
+                if not cif_files:
+                    continue  # 如果没有找到文件，跳过这个mp_id
+
+                cif_file = cif_files[0]
+                structure = Structure.from_file(cif_file)
+
+                # 结构处理可能引发异常
+                if conventional_unit_cell:
+                    structure = SpacegroupAnalyzer(structure).get_conventional_standard_structure()
+
+                # 对结构进行对称化处理
+                sga = SpacegroupAnalyzer(structure, symprec=symprec)
+                symmetrized_structure = sga.get_refined_structure()
+
+                # 使用CifWriter生成CIF数据
+                cif_writer = CifWriter(symmetrized_structure, symprec=symprec, refine_struct=True)
+                cif_data = str(cif_writer)
+
+                # 删除CIF文件中的对称性操作部分
+                cif_data = remove_symmetry_equiv_xyz(cif_data)
+                cif_data = cif_data.replace('# generated using pymatgen', "")
+
+                # 生成一个唯一的键
+                formula_key = structure.composition.reduced_formula
+                key = f"{formula_key}_{i}"
+
+                structures[key] = cif_data
+
+                # 只保留前config.MP_TOPK个结果
+                if len(structures) >= material_config.MP_TOPK:
+                    break
+
+            except (FileNotFoundError, IndexError) as file_error:
+                # 处理文件相关错误
+                continue  # 跳过这个mp_id，继续处理下一个
+            except ValueError as value_error:
+                # 处理结构处理中的值错误
+                continue  # 跳过这个mp_id，继续处理下一个
+            except Exception as process_error:
+                # 记录处理特定结构时的错误，但继续处理其他结构
+                print(f"Error： processing structure {mp_id}: {str(process_error)}")
+                continue
+
+        # 如果没有成功处理任何结构
+        if not structures:
+            return f"No valid crystal structures found for formula: {formula}"
+
+        # 格式化结果为可读字符串
+        prompt = f"""
+# Materials Project Symmetrized Crystal Structure Data
+
+Below are symmetrized crystal structure data for {len(structures)} materials from the Materials Project database, in CIF (Crystallographic Information File) format.
+These structures have been analyzed and optimized for symmetry using SpacegroupAnalyzer with precision parameter symprec={symprec}.\n
+"""
+
+        for i, (key, cif_data) in enumerate(structures.items(), 1):
+            prompt += f"[cif {i} begin]\n"
+            prompt += cif_data
+            prompt += f"\n[cif {i} end]\n\n"
+
+        return prompt
+
+    except Exception as e:
+        # 捕获整个函数执行过程中的任何未处理异常
+        return f"Error: An unexpected error occurred while processing crystal structures: {str(e)}"
+
+@llm_tool(name="search_material_property_from_material_project",
+          description="Query material properties from Materials Project database using chemical formula")
+async def search_material_property_from_materials_project(
+        formula: str,
+    ) -> str:
+    """
+    Retrieve detailed property data for materials matching a chemical formula from Materials Project database.
+
+    Args:
+        formula: Chemical formula of the material(s) to search for (e.g. 'Fe2O3', 'LiFePO4')
+
+    Returns:
+        Formatted string containing material properties including structure, electronic, thermodynamic and mechanical data
+    """
+    # 获取MP ID列表
+    mp_id_list = await get_mpid_from_formula(formula=formula)
+
+    # 检查get_mpid_from_formula的返回值类型
+    # 如果返回的是字符串，说明发生了错误或没有找到材料
+    if isinstance(mp_id_list, str):
+        return mp_id_list  # 直接返回错误信息
+
+    # 如果代码执行到这里，说明mp_id_list是一个有效的ID列表
+    try:
+        # 获取材料属性
+        properties = []
+        for mp_id in mp_id_list:
+            try:
+                file_path = material_config.LOCAL_MP_PROPS_ROOT + f"/{mp_id}.json"
+                crystal_props = extract_cif_info(file_path, ['all_fields'])
+                properties.append(crystal_props)
+            except Exception as file_error:
+                # 记录单个文件处理错误但继续处理其他ID
+                continue
+
+        # 检查是否有结果
+        if len(properties) == 0:
+            return "No material properties found for the given formula, please try again."
+
+        # 只保留前MP_TOPK个结果
+        properties = properties[:material_config.MP_TOPK]
+
+        # 格式化结果
+        formatted_results = []
+        for i, item in enumerate(properties, 1):
+            formatted_result = f"[property {i} begin]\n"
+            formatted_result += json.dumps(item, indent=2)
+            formatted_result += f"\n[property {i} end]\n\n"
+            formatted_results.append(formatted_result)
+
+        # 将所有结果合并为一个字符串
+        res_chunk = "\n\n".join(formatted_results)
+        res_template = f"""
+Here are the search material property from the Materials Project database:
+Due to length limitations, only the top {len(properties)} results are shown below:\n
+{res_chunk}
+"""
+        return res_template
+
+    except Exception as e:
+        return f"Error: processing material properties: {str(e)}"