ion-CSP 2.1.4__py3-none-any.whl → 2.1.8__py3-none-any.whl

ion_CSP/param/g16_sub.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+BASE_DIR="./"
+
+# 遍历所有.gjf文件
+for gjf in "$BASE_DIR"/*.gjf; do
+    # 安全校验文件存在性
+    [ -f "$gjf" ] || { echo "Skipping invalid file: $gjf"; continue; }
+    
+    # 提取带路径的文件名
+    full_name=$(basename "$gjf")
+    
+    # 安全提取基名（严格去除最后一个.gjf后缀）
+    base_name="${full_name%.*}"
+    
+    # 执行命令（示例）
+    g16 "$gjf" && formchk "${base_name}.chk"
+    if [ $? -ne 0 ] ; then 
+        touch "${base_name}.fchk"
+    fi
+done

ion_CSP/param/sub_final.sh

@@ -0,0 +1,91 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_1="INCAR_1"
+INCAR_2="INCAR_2"
+INCAR_3="INCAR_3"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_1" || ! -f "$INCAR_2" || ! -f "$INCAR_3" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第一步优化任务
+for contcar in ${BASE_DIR}/CONTCAR_*; do
+    if [[ $contcar =~ CONTCAR_(.*) ]]; then
+        sample=${BASH_REMATCH[1]}
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "$sample_dir"
+        cp "$contcar" "${sample_dir}/POSCAR"
+        cp "$INCAR_1" "${sample_dir}/INCAR"
+        create_potcar_from_poscar "${sample_dir}/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All first step tasks have been submitted."
+
+# 提交第二步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine"
+        cp "${sample_dir}/CONTCAR" "${sample_dir}/fine/POSCAR"
+        cp "$INCAR_2" "${sample_dir}/fine/INCAR"
+        cp "${sample_dir}/POTCAR" "${sample_dir}/fine/POTCAR"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All second step tasks have been submitted."
+
+# 提交第三步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/fine/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine/final"
+        cp "${sample_dir}/fine/CONTCAR" "${sample_dir}/fine/final/POSCAR"
+        cp "$INCAR_3" "${sample_dir}/fine/final/INCAR"
+        cp "${sample_dir}/fine/POTCAR" "${sample_dir}/fine/final/POTCAR"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine/final" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All third step tasks have been submitted."

ion_CSP/param/sub_ori.sh

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_1="INCAR_1"
+INCAR_2="INCAR_2"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_1" || ! -f "$INCAR_2" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第一步优化任务
+for contcar in ${BASE_DIR}/CONTCAR_*; do
+    if [[ $contcar =~ CONTCAR_(.*) ]]; then
+        sample=${BASH_REMATCH[1]}
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "$sample_dir"
+        cp "$contcar" "${sample_dir}/POSCAR"
+        cp "$INCAR_1" "${sample_dir}/INCAR"
+        create_potcar_from_poscar "${sample_dir}/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All first step tasks have been submitted."
+
+# 提交第二步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine"
+        cp "${sample_dir}/CONTCAR" "${sample_dir}/fine/POSCAR"
+        cp "$INCAR_2" "${sample_dir}/fine/INCAR"
+        cp "${sample_dir}/POTCAR" "${sample_dir}/fine/"
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All second step tasks have been submitted."

ion_CSP/param/sub_supple.sh

@@ -0,0 +1,56 @@
+#!/bin/bash
+
+# 设置变量
+BASE_DIR="./"
+INCAR_3="INCAR_3"
+POTCAR_H="POTCAR_H"
+POTCAR_C="POTCAR_C"
+POTCAR_N="POTCAR_N"
+POTCAR_O="POTCAR_O"
+
+# 检查必要文件是否存在
+if [[ ! -f "$INCAR_3" || ! -f "$POTCAR_H" || ! -f "$POTCAR_C" || ! -f "$POTCAR_N" || ! -f "$POTCAR_O" ]]; then
+    echo "Necessary files are missing, please check the path."
+    exit 1
+fi
+
+# 创建 POTCAR 文件
+create_potcar_from_poscar() {
+    poscar_file="$1"
+    output_file="POTCAR"
+    > "$output_file"  # 清空文件
+
+    # 读取 POSCAR 文件的第六行（元素行）
+    read -r element_line < <(sed -n '6p' "$poscar_file")
+
+    # 将元素转换为数组
+    IFS=' ' read -r -a elements <<< "$element_line"
+
+    # 根据元素拼接 POTCAR
+    for element in "${elements[@]}"; do
+        case $element in
+            H) cat "$POTCAR_H" >> "$output_file" ;;
+            C) cat "$POTCAR_C" >> "$output_file" ;;
+            N) cat "$POTCAR_N" >> "$output_file" ;;
+            O) cat "$POTCAR_O" >> "$output_file" ;;
+            *) echo "Warning: POTCAR for element $element not found." ;;
+        esac
+    done
+}
+
+# 提交第三步优化任务
+for sample in $(ls ${BASE_DIR}); do
+    if [ -f "${BASE_DIR}/${sample}/fine/CONTCAR" ]; then
+        sample_dir="${BASE_DIR}/${sample}"
+        mkdir -p "${sample_dir}/fine/final"
+        cp "${sample_dir}/fine/CONTCAR" "${sample_dir}/fine/final/POSCAR"
+        cp "$INCAR_3" "${sample_dir}/fine/final/INCAR"
+        create_potcar_from_poscar "${sample_dir}/fine/final/POSCAR"  # 根据 POSCAR 创建 POTCAR
+        mv "POTCAR" "${sample_dir}/fine/final/"  # 使用自动生成的 POTCAR
+        original_dir=$(pwd)  # 保存当前目录
+        cd "${sample_dir}/fine/final" && mpirun -n ${DPDISPATCHER_CPU_PER_NODE} vasp_std > vasp.log 2>&1
+        cd $original_dir  # 返回原始工作目录
+    fi
+done
+
+echo "All third step tasks have been submitted."

ion_CSP/read_mlp_density.py

@@ -9,6 +9,13 @@ from ion_CSP.identify_molecules import identify_molecules, molecules_information
 class ReadMlpDensity:
     
     def __init__(self, work_dir:str):
+        """
+        This class is designed to read and process MLP optimized files, specifically CONTCAR files, to calculate and sort their densities.
+        The class also provides functionality to process these files using phonopy for symmetry analysis and primitive cell generation.
+
+        :params
+            work_dir: The working directory where the MLP optimized files are located.
+        """
         # 获取脚本的当前目录
         self.base_dir = work_dir
         os.chdir(self.base_dir)
@@ -39,7 +46,10 @@ class ReadMlpDensity:
         """
         Obtain the atomic mass and unit cell volume from the optimized CONTCAR file, and obtain the ion crystal density. Finally, take n CONTCAR files with the highest density and save them separately for viewing.
         
-        :param n_screen: 取前n个最大密度的文件
+        :params
+            n_screen: The number of CONTCAR files with the highest density to be saved.
+            molecules_screen: If True, only consider ionic crystals with original ions.
+            detail_log: If True, print detailed information about the molecules identified in the CONTCAR files.
         """
         os.chdir(self.base_dir)
         # 获取所有以'CONTCAR_'开头的文件，并按数字顺序处理
@@ -135,6 +145,10 @@ class ReadMlpDensity:
     def phonopy_processing_max_density(self, specific_directory :str = None):
         """
         Use phonopy to check and generate symmetric primitive cells, reducing the complexity of subsequent optimization calculations, and preventing pyxtal.from_random from generating double proportioned supercells. 
+        
+        :params
+            specific_directory: If specified, phonopy will process the files in this directory instead of the max_density directory.
+            If not specified, it will process the files in the max_density directory.
         """
         if specific_directory:
             self.phonopy_dir = os.path.join(self.base_dir, specific_directory)

ion_CSP/task_manager.py

@@ -225,7 +225,7 @@ class TaskManager:
         pid_file = work_dir / "pid.txt"
 
         # 动态加载模块
-        module_name = f"run.main_{module}"
+        module_name = f"ion_CSP.run.main_{module}"
         spec = importlib.util.find_spec(module_name)
         if not spec:
             raise ImportError(f"Module {module_name} not found")
@@ -364,7 +364,7 @@ class TaskManager:
         """主菜单循环 - Main menu loop"""
         while True:
             os.system("clear" if os.name == "posix" else "cls")
-            print("========== Task Execution Sys1tem ==========")
+            print("========== Task Execution System ==========")
             print(f"Current Version: {self.version}")
             print(f"Current Environment: {self.envs}")
             print(f"Current Directory: {self.workspace}")

ion_CSP/upload_download.py

@@ -484,4 +484,3 @@ class SSHBatchJob:
     def close_connection(self):
         self.sftp.close()
         self.client.close()
-

ion_CSP/vasp_processing.py

@@ -4,6 +4,7 @@ import json
 import yaml
 import shutil
 import logging
+import importlib.resources
 from ase.io import ParseError
 from ase.io.vasp import read_vasp_out
 from dpdispatcher import Machine, Resources, Task, Submission
@@ -13,12 +14,18 @@ from ion_CSP.identify_molecules import identify_molecules, molecules_information
 
 class VaspProcessing:
     def __init__(self, work_dir: str):
+        """
+        This directory is used to store all the files related to VASP optimizations.
+
+        :params
+            work_dir: The working directory where VASP optimization files will be stored.
+        """
         redirect_dpdisp_logging(os.path.join(work_dir, "dpdispatcher.log"))
         self.base_dir = work_dir
         os.chdir(self.base_dir)
         self.for_vasp_opt_dir = f"{work_dir}/3_for_vasp_opt"
         self.vasp_optimized_dir = f"{work_dir}/4_vasp_optimized"
-        self.param_dir = os.path.join(os.path.dirname(__file__), "../../param")
+        self.param_dir = importlib.resources.files("ion_CSP.param")
 
     def dpdisp_vasp_optimization_tasks(
         self,
@@ -28,6 +35,10 @@ class VaspProcessing:
     ):
         """
         Based on the dpdispatcher module, prepare and submit files for optimization on remote server or local machine.
+        :params
+            machine: The machine configuration file, which can be in JSON or YAML format.
+            resources: The resources configuration file, which can be in JSON or YAML format.
+            nodes: The number of nodes to distribute the optimization tasks across.
         """
         # 调整工作目录，减少错误发生
         os.chdir(self.for_vasp_opt_dir)
@@ -79,7 +90,7 @@ class VaspProcessing:
             task_dir = os.path.join(self.for_vasp_opt_dir, f"{parent}pop{pop}")
             os.makedirs(task_dir, exist_ok=True)
             for file in forward_files:
-                shutil.copyfile(f"{self.param_dir}/{file}", f"{task_dir}/{file}")
+                shutil.copyfile(self.param_dir.joinpath(file), f"{task_dir}/{file}")
             for job_i in node_jobs[pop]:
                 # 将分配好的POSCAR文件添加到对应的上传文件中
                 forward_files.append(mlp_contcar_files[job_i])
@@ -146,7 +157,11 @@ class VaspProcessing:
         nodes: int = 1,
     ):
         """
-        Based on the dpdispatcher module, prepare and submit files for optimization on remote server or local machine.
+        Based on the dpdispatcher module, prepare and submit files for VASP relaxation on remote server or local machine.
+        :params
+            machine: The machine configuration file, which can be in JSON or YAML format.
+            resources: The resources configuration file, which can be in JSON or YAML format.
+            nodes: The number of nodes to distribute the optimization tasks across.
         """
         # 调整工作目录，减少错误发生
         os.chdir(self.vasp_optimized_dir)
@@ -199,7 +214,7 @@ class VaspProcessing:
             task_dir = os.path.join(self.vasp_optimized_dir, f"{parent}pop{pop}")
             os.makedirs(task_dir, exist_ok=True)
             for file in forward_files:
-                shutil.copyfile(f"{self.param_dir}/{file}", f"{task_dir}/{file}")
+                shutil.copyfile(self.param_dir.joinpath(file), f"{task_dir}/{file}")
             for job_i in node_jobs[pop]:
                 # 将分配好的POSCAR文件添加到对应的上传文件中
                 vasp_dir = vasp_optimized_folders[job_i]
@@ -311,7 +326,7 @@ class VaspProcessing:
             task_dir = os.path.join(self.for_vasp_opt_dir, f"{parent}pop{pop}")
             os.makedirs(task_dir, exist_ok=True)
             for file in forward_files:
-                shutil.copyfile(f"{self.param_dir}/{file}", f"{task_dir}/{file}")
+                shutil.copyfile(self.param_dir.joinpath(file), f"{task_dir}/{file}")
             for job_i in node_jobs[pop]:
                 # 将分配好的POSCAR文件添加到对应的上传文件中
                 forward_files.append(mlp_contcar_files[job_i])
@@ -622,6 +637,11 @@ class VaspProcessing:
             with open(csv_file_path, "r") as csvfile:
                 reader = csv.reader(csvfile)
                 # 跳过表头读取第一行结构序号，即符合结构筛选要求的最大密度结构
+                header = next(reader)
+                if header[0] != "Number":
+                    raise KeyError(
+                        "The first column of the CSV file is not 'Number', please check the file format."
+                    )
                 first_row = next(reader)
                 structure_number = str(first_row[0])
             # 根据结构序号构建要查找的文件夹路径
@@ -632,24 +652,27 @@ class VaspProcessing:
                     structure_number
                 ):
                     # 查找 CONTCAR 文件
-                    final_contcar_path = os.path.join(
-                        vasp_folder_path, "fine", "final", "CONTCAR"
-                    )
+                    # final_contcar_path = os.path.join(
+                    #     vasp_folder_path, "fine", "final", "CONTCAR"
+                    # )
+                    # print(f"Trying to get the final structure from {vasp_folder_path}")
+                    # logging.info(
+                    #     f"Trying to get the final structure from {vasp_folder_path}"
+                    # )
+                    # if os.path.exists(final_contcar_path):
+                    #     # 复制 CONTCAR 文件到 combo_n 文件夹并重命名为 POSCAR
+                    #     shutil.copy(
+                    #         final_contcar_path, os.path.join(self.base_dir, "POSCAR")
+                    #     )
+                    #     print(f"Renamed CONTCAR to POSCAR in {self.base_dir}, copied from {final_contcar_path}")
+                    #     logging.info(
+                    #         f"Renamed CONTCAR to POSCAR in {self.base_dir}, copied from {final_contcar_path}"
+                    #     )
                     fine_contcar_path = os.path.join(
                         vasp_folder_path, "fine", "CONTCAR"
                     )
-                    logging.info(
-                        f"Trying to get the final structure from {vasp_folder_path}"
-                    )
-                    if os.path.exists(final_contcar_path):
-                        # 复制 CONTCAR 文件到 combo_n 文件夹并重命名为 POSCAR
-                        shutil.copy(
-                            final_contcar_path, os.path.join(self.base_dir, "POSCAR")
-                        )
-                        logging.info(
-                            f"Renamed CONTCAR to POSCAR in {self.base_dir}, copied from {final_contcar_path}"
-                        )
-                    elif os.path.exists(fine_contcar_path):
+                    if os.path.exists(fine_contcar_path):
+                        print(f"CONTCAR not found in {os.path.join(vasp_folder_path, 'fine', 'final')}")
                         logging.info(
                             f"CONTCAR not found in {os.path.join(vasp_folder_path, 'fine', 'final')}"
                         )
@@ -657,10 +680,15 @@ class VaspProcessing:
                         shutil.copy(
                             fine_contcar_path, os.path.join(self.base_dir, "POSCAR")
                         )
+                        print(f"Renamed CONTCAR to POSCAR in {self.base_dir}, copied from {fine_contcar_path}")
                         logging.info(
                             f"Renamed CONTCAR to POSCAR in {self.base_dir}, copied from {fine_contcar_path}"
                         )
                     else:
                         print(f"Eligible CONTCAR not found in {vasp_folder_path}")
+                        logging.info(
+                            f"Eligible CONTCAR not found in {vasp_folder_path}"
+                        )
         else:
+            print(f"CSV file not found in {self.base_dir}")
             logging.info(f"CSV file not found in {self.base_dir}")

{ion_csp-2.1.4.dist-info → ion_csp-2.1.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.4
+Version: 2.1.8
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -13,6 +13,7 @@ Requires-Python: >=3.11
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase==3.23.0
+Requires-Dist: scipy==1.15.2
 Requires-Dist: deepmd-kit==3.0.1
 Requires-Dist: torch==2.5.0
 Requires-Dist: dpdispatcher==0.6.7
@@ -27,13 +28,16 @@ Dynamic: home-page
 Dynamic: license-file
 Dynamic: requires-python
 
-# Crystal Structure Design Software V2.1
+# 基于分子/离子构型的晶体结构设计软件 V2.1
 
 ## 项目概述
+
 基于分子/离子构型的晶体结构设计软件通过结合经验公式、机器学习势函数微调、第一性原理分步优化和分子/离子识别技术，实现了从分子/离子构型出发的高效晶体结构设计。该软件采用模块化设计，支持全流程自动化材料筛选，在保证预测精度的同时显著提升计算效率。
 
 ## 功能特性
+
 ### 核心功能
+
 - **双模块工作流**  
   - **EE模块**：基于经验评估的离子组合生成  
   - **CSP模块**：基于离子晶体结构预测的优化筛选  
@@ -47,13 +51,16 @@ Dynamic: requires-python
   - 软链接解析显示实际路径
 
 ### 技术特性
+
 - 跨平台支持（Linux/Docker）
 - 基于Python 3.11+的面向对象架构
 - 集成psutil进程管理
 - 结构化日志记录系统
 
 ## 安装指南
+
 ### 环境要求
+
 | 组件        | 最低版本 |
 |-------------|----------|
 | Python      | 3.11     |
@@ -70,10 +77,13 @@ Dynamic: requires-python
 | rdkit       | 2024.03.3|
 
 ### 安装步骤
+
 ```bash
 pip install ion-csp
 ```
+
 或
+
 ```bash
 # 创建虚拟环境
 python -m venv venv
@@ -86,29 +96,39 @@ pip install -e .
 ```
 
 ## 快速入门
+
 ### 交互模式
+
 ```bash
 ion-csp
 ```
+
 启动交互式命令行界面，支持以下操作：
+
 - 模块选择
 - 日志查看
 - 进程管理
 
 ### 脚本调用
+
 #### EE模块示例
+
 ```bash
 ./scripts/main_EE.sh examples/example_1
 ```
+
 从SMILES表格生成离子组合
 
 #### CSP模块示例
+
 ```bash
 ./scripts/main_CSP.sh examples/example_2
 ```
+
 从离子组合生成并优化晶体结构
 
 ## 技术架构
+
 ```mermaid
 graph TD
     A[用户界面] --> B[任务管理器]
@@ -117,34 +137,32 @@ graph TD
     B --> E[日志系统]
     B --> F[任务调度]
     C --> G[经验评估引擎]
-    D --> H[晶体预测引擎]
+    D --> H[离子晶体结构预测引擎]
     E --> I[结构化日志]
     F --> J[进程终止]
 ```
 
 ## 贡献指南
+
 1. Fork仓库并创建特性分支
 2. 编写单元测试覆盖新功能
 3. 提交Pull Request时注明关联Issue
 4. 遵循PEP8代码规范
 
 ## 许可证
-本项目采用MIT许可证，详见LICENSE文件。
 
-## 技术支持
-- **文档更新**：2025年6月
-- **最新版本**：v2.1.4
-- **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
+本项目采用MIT许可证，详见LICENSE文件。
 
 ---
 
-# Crystal Structure Design Software V2.1
-
 ## Project Overview
+
 This software enables efficient crystal structure design from molecular/ion configurations by integrating empirical formulas, tuned machine learning potentials, stepwise first-principles optimization, and molecular/ion recognition techniques. The modular architecture ensures extensibility and maintainability while maintaining prediction accuracy.
 
 ## Key Features
+
 ### Core Functionalities
+
 - **Dual-Module Workflow**
   - **EE Module**: Empirical evaluation-based ion combination generation
   - **CSP Module**: Ion crystal structure prediction and optimization
@@ -158,13 +176,16 @@ This software enables efficient crystal structure design from molecular/ion conf
   - Symlink resolution for actual log paths
 
 ### Technical Specifications
+
 - Cross-platform support (Linux/Docker)
 - Object-oriented architecture with Python 3.11+
 - Integrated process management via psutil
 - Structured logging system
 
 ## Installation
+
 ### Prerequisites
+
 | Component   | Min Version |
 |-------------|-------------|
 | Python      | 3.11     |
@@ -181,6 +202,7 @@ This software enables efficient crystal structure design from molecular/ion conf
 | rdkit       | 2024.03.3|
 
 ### Installation Steps
+
 ```bash
 # Create virtual environment
 python -m venv venv
@@ -193,29 +215,39 @@ pip install -e .
 ```
 
 ## Quick Start
+
 ### Interactive Mode
+
 ```bash
 ion-csp
 ```
+
 Launches CLI interface with:
+
 - Module selection
 - Log management
 - Process control
 
 ### Script Execution
+
 #### EE Module Example
+
 ```bash
 ./scripts/main_EE.sh examples/example_1
 ```
+
 Generates ion combinations from SMILES tables
 
 #### CSP Module Example
+
 ```bash
 ./scripts/main_CSP.sh examples/example_2
 ```
+
 Optimizes crystal structures from ion combinations
 
 ## Technical Architecture
+
 ```mermaid
 graph TD
     A[User Interface] --> B[Task Manager]
@@ -224,21 +256,18 @@ graph TD
     B --> E[Log System]
     B --> F[Task Scheduler]
     C --> G[Empirical Evaluation Engine]
-    D --> H[Crystal Prediction Engine]
+    D --> H[Ionic Crystal Structure Prediction Engine]
     E --> I[Structured Logs]
     F --> J[Process Termination]
 ```
 
 ## Contribution Guide
+
 1. Fork repository and create feature branch
 2. Write unit tests for new features
 3. Submit PR with issue reference
 4. Follow PEP8 coding standards
 
 ## License
-MIT License, see LICENSE file.
 
-## Support
-- Documentation last updated: June 2025
-- Latest version: v2.1.4
-- Issue tracker: https://github.com/bagabaga007/ion_CSP/issues
+MIT License, see LICENSE file.