CSM及TET，CS

.idea/Screen.iml

@@ -2,7 +2,7 @@
 <module type="PYTHON_MODULE" version="4">
   <component name="NewModuleRootManager">
     <content url="file://$MODULE_DIR$" />
-    <orderEntry type="jdk" jdkName="C:\Users\PC20230606\Miniconda3" jdkType="Python SDK" />
+    <orderEntry type="jdk" jdkName="Python 3.11" jdkType="Python SDK" />
     <orderEntry type="sourceFolder" forTests="false" />
   </component>
 </module>

py/CSM_reconstruct.py

@@ -0,0 +1,224 @@
+import os
+import sys
+import numpy as np
+import argparse
+from tqdm import tqdm
+from scipy.spatial import ConvexHull
+from pymatgen.core import Structure
+from pymatgen.core.periodic_table import Element
+from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
+
+# ================= 配置区域 =================
+# 建议使用绝对路径，避免找不到文件夹
+INPUT_DIR = "../../solidstate-tools/corner-sharing/data/1209/input"  # 请确保这里有你的 .cif 文件
+OUTPUT_DIR = "../output/CSM"
+TARGET_ELEMENT = 'Li'
+ENV_TYPE = 'both'
+
+
+# ===========================================
+
+class HiddenPrints:
+    '''用于隐藏 pymatgen 繁杂的输出'''
+
+    def __enter__(self):
+        self._original_stdout = sys.stdout
+        sys.stdout = open(os.devnull, 'w')
+
+    def __exit__(self, exc_type, exc_val, exc_tb):
+        sys.stdout.close()
+        sys.stdout = self._original_stdout
+
+
+def non_elements(struct):
+    """
+    【关键修复】保留卤素(F, Cl, Br, I) 和其他阴离子，防止氯化物结构被清空。
+    """
+    # 这里加入了 F, Cl, Br, I, P, Se, Te 等
+    anions_to_keep = {"O", "S", "N", "F", "Cl", "Br", "I", "P", "Se", "Te", "As", "Sb", "C"}
+    stripped = struct.copy()
+    species_to_remove = [el.symbol for el in stripped.composition.elements
+                         if el.symbol not in anions_to_keep]
+    if species_to_remove:
+        stripped.remove_species(species_to_remove)
+    return stripped
+
+
+def site_env(coord, struct, sp="Li", envtype='both'):
+    stripped = non_elements(struct)
+
+    # 如果剥离后结构为空（例如纯金属锂），直接返回
+    if len(stripped) == 0:
+        return {'csm': np.nan, 'vol': np.nan, 'type': 'Error_NoAnions'}
+
+    with_li = stripped.copy()
+    # 插入一个探测用的 Li 原子
+    with_li.append(sp, coord, coords_are_cartesian=False, validate_proximity=False)
+
+    # 尝试排序，如果因为部分占据导致排序失败，则使用原始顺序
+    try:
+        with_li = with_li.get_sorted_structure()
+    except:
+        pass
+
+    tet_oct_competition = []
+
+    # ---------------- 四面体 (Tet) 检测 ----------------
+    if envtype == 'both' or envtype == 'tet':
+        for dist in np.linspace(1, 4, 601):  # 扫描距离 1A 到 4A
+            neigh = with_li.get_neighbors(with_li.sites[0], dist)
+            if len(neigh) < 4:
+                continue
+            elif len(neigh) > 4:
+                break
+
+            neigh_coords = [i.coords for i in neigh]
+            try:
+                with HiddenPrints():
+                    lgf = LocalGeometryFinder(only_symbols=["T:4"])
+                    lgf.setup_structure(structure=with_li)
+                    lgf.setup_local_geometry(isite=0, coords=neigh_coords)
+
+                site_volume = ConvexHull(neigh_coords).volume
+                # 获取 CSM
+                csm_val = lgf.get_coordination_symmetry_measures()['T:4']['csm']
+
+                tet_env = {'csm': csm_val, 'vol': site_volume, 'type': 'tet'}
+                tet_oct_competition.append(tet_env)
+            except Exception:
+                pass
+            if len(neigh) == 4: break
+
+    # ---------------- 八面体 (Oct) 检测 ----------------
+    if envtype == 'both' or envtype == 'oct':
+        for dist in np.linspace(1, 4, 601):
+            neigh = with_li.get_neighbors(with_li.sites[0], dist)
+            if len(neigh) < 6:
+                continue
+            elif len(neigh) > 6:
+                break
+
+            neigh_coords = [i.coords for i in neigh]
+            try:
+                with HiddenPrints():
+                    lgf = LocalGeometryFinder(only_symbols=["O:6"], permutations_safe_override=False)
+                    lgf.setup_structure(structure=with_li)
+                    lgf.setup_local_geometry(isite=0, coords=neigh_coords)
+
+                site_volume = ConvexHull(neigh_coords).volume
+                csm_val = lgf.get_coordination_symmetry_measures()['O:6']['csm']
+
+                oct_env = {'csm': csm_val, 'vol': site_volume, 'type': 'oct'}
+                tet_oct_competition.append(oct_env)
+            except Exception:
+                pass
+            if len(neigh) == 6: break
+
+    # ---------------- 结果判定 ----------------
+    if len(tet_oct_competition) == 0:
+        return {'csm': np.nan, 'vol': np.nan, 'type': 'Non_' + envtype}
+    elif len(tet_oct_competition) == 1:
+        return tet_oct_competition[0]
+    elif len(tet_oct_competition) >= 2:
+        return min(tet_oct_competition, key=lambda x: x['csm'])
+
+
+def extract_sites(struct, sp="Li", envtype='both'):
+    envlist = []
+    # 遍历所有位点寻找 Li
+    for i, site in enumerate(struct):
+        site_elements = [el.symbol for el in site.species.elements]
+        if sp in site_elements:
+            try:
+                # 传入结构副本以防修改原结构
+                singleenv = site_env(site.frac_coords, struct.copy(), sp, envtype)
+                envlist.append({
+                    'site_index': i,
+                    'frac_coords': site.frac_coords,
+                    'type': singleenv.get('type', 'unknown'),
+                    'csm': singleenv.get('csm', np.nan),
+                    'volume': singleenv.get('vol', np.nan)
+                })
+            except Exception as e:
+                # 捕捉单个位点计算错误，不中断程序
+                # print(f"  [Warn] Site {i} calculation failed: {e}")
+                pass
+    return envlist
+
+
+def export_envs(envlist, sp, envtype, fname):
+    with open(fname, 'w') as f:
+        f.write('List of environment information\n')
+        f.write(f'Species : {sp}\n')
+        f.write(f'Envtype : {envtype}\n')
+        for item in envlist:
+            # 格式化输出，确保没有数据也能看懂
+            f.write(f"Site index {item['site_index']}: {item}\n")
+
+
+# ================= 主程序 =================
+def run_csm_analysis():
+    # 1. 检查目录
+    if not os.path.exists(INPUT_DIR):
+        print(f"错误: 输入目录不存在 -> {os.path.abspath(INPUT_DIR)}")
+        return
+
+    cif_files = []
+    for root, dirs, files in os.walk(INPUT_DIR):
+        for file in files:
+            if file.endswith(".cif"):
+                cif_files.append(os.path.join(root, file))
+
+    if not cif_files:
+        print(f"在 {INPUT_DIR} 中未找到 .cif 文件。")
+        return
+
+    print(f"开始分析 {len(cif_files)} 个文件 (目标元素: {TARGET_ELEMENT}, 包含阴离子: F,Cl,Br,I,O,S,N...)")
+
+    success_count = 0
+
+    for cif_path in tqdm(cif_files, desc="Calculating CSM"):
+        try:
+            # 准备路径
+            rel_path = os.path.relpath(cif_path, INPUT_DIR)
+            rel_dir = os.path.dirname(rel_path)
+            file_base = os.path.splitext(os.path.basename(cif_path))[0]
+
+            target_dir = os.path.join(OUTPUT_DIR, rel_dir)
+            if not os.path.exists(target_dir):
+                os.makedirs(target_dir)
+
+            target_dat_path = os.path.join(target_dir, f"{file_base}.dat")
+
+            # 如果文件已存在且不为空，可选择跳过
+            # if os.path.exists(target_dat_path) and os.path.getsize(target_dat_path) > 0:
+            #     continue
+
+            # 读取结构
+            struct = Structure.from_file(cif_path)
+
+            # 检查是否含 Li
+            if Element(TARGET_ELEMENT) not in struct.composition.elements:
+                continue
+
+            # 计算环境
+            env_list = extract_sites(struct, sp=TARGET_ELEMENT, envtype=ENV_TYPE)
+
+            # 写入结果 (即使 env_list 为空也写入一个标记文件，方便debug)
+            if env_list:
+                export_envs(env_list, sp=TARGET_ELEMENT, envtype=ENV_TYPE, fname=target_dat_path)
+                success_count += 1
+            else:
+                with open(target_dat_path, 'w') as f:
+                    f.write(f"No {TARGET_ELEMENT} environments found (Check connectivity or anion types).")
+
+        except Exception as e:
+            print(f"\n[Error] File: {os.path.basename(cif_path)} -> {e}")
+            continue
+
+    print(f"\n分析完成！成功生成 {success_count} 个文件。")
+    print(f"输出目录: {os.path.abspath(OUTPUT_DIR)}")
+
+
+if __name__ == "__main__":
+    run_csm_analysis()

py/csm.py

@@ -12,11 +12,11 @@ from tqdm import tqdm
 
 # ================= 配置区域 =================
 # 输入目录：使用筛选后的目录，只计算符合要求的材料
-INPUT_DIR = "../data/after_screening"
+INPUT_DIR = "../../solidstate-tools/corner-sharing/data/1209/input"
 # 输出目录
 OUTPUT_DIR = "../output/CSM"
 # 分析参数
-TARGET_ELEMENT = 'Li'
+TARGET_ELEMENT = 'Na'
 ENV_TYPE = 'both'  # 可选 'tet', 'oct', 'both'
 # ===========================================
 

py/step1.py

@@ -110,4 +110,4 @@ def read_files_check_basic(folder_path):
 if __name__ == "__main__":
     # 根据你的 readme，MP数据在 input_pre，ICSD在 input
     # 这里默认读取 input，你可以根据实际情况修改
-    read_files_check_basic("../data/input")
+    read_files_check_basic("../../solidstate-tools/corner-sharing/data/1209/input")

py/step1_direct.py

@@ -96,7 +96,7 @@ def organize_files_direct(input_folder, output_base):
 
 if __name__ == "__main__":
     # 输入路径
-    input_dir = "../data/input"  # 如果是MP数据请改为 ../data/input_pre
+    input_dir = "../../solidstate-tools/corner-sharing/data/1209/input"  # 如果是MP数据请改为 ../data/input_pre
     # 输出路径
     output_dir = "../data/after_step1"
 

py/utils/analyze_env_st.py

@@ -52,7 +52,7 @@ def non_elements(struct, sp='Li'):
     sp : the mobile specie
     returns a new structure containing only the framework anions (O, S, N).
     """
-    anions_to_keep = {"O", "S", "N"}
+    anions_to_keep = {"O", "S", "N","Br","Cl"}
     stripped = struct.copy()
     species_to_remove = [el.symbol for el in stripped.composition.elements
                          if el.symbol not in anions_to_keep]