ion-CSP 2.0.2__tar.gz → 2.0.4__tar.gz

ion_csp-2.0.4/.github/workflows/build.yml

@@ -0,0 +1,34 @@
+name: CI Build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.11]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-activate-base: false
+        channels: conda-forge,defaults
+
+    - name: Create environment
+      run: |
+        conda env create -f environment.yml --name ion-csp-env
+        conda init bash
+        conda activate ion-csp-env
+
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install setuptools-scm
+
+    - name: Build package
+      run: |
+        python -m build

ion_csp-2.0.4/.github/workflows/python-package-conda.yml

@@ -0,0 +1,43 @@
+name: Python Package using Conda
+
+on: [push]
+
+jobs:
+  build-linux:
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 5
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python 3.11
+      uses: actions/setup-python@v3
+      with:
+        python-version: '3.11'
+    - name: Add conda to system path
+      run: |
+        # $CONDA is an environment variable pointing to the root of the miniconda directory
+        echo $CONDA/bin >> $GITHUB_PATH
+    - name: Install dependencies
+      run: |
+        conda env update --file environment.yml --name ion-csp-env
+        conda init
+        conda activate ion-csp-env
+    - name: Install dependencies
+      run: |
+        pip install -r requirements.txt
+        pip install setuptools-scm
+    - name: Build package
+      run: |
+        python -m build
+    - name: Lint with flake8
+      run: |
+        conda install flake8
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        conda install pytest
+        pytest

ion_csp-2.0.4/.github/workflows/python-publish.yml

@@ -0,0 +1,70 @@
+# This workflow will upload a Python Package to PyPI when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Build release distributions
+        run: |
+          # NOTE: put your own distribution build steps here.
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
+
+    # Dedicated environments with protections for publishing are strongly recommended.
+    # For more information, see: https://docs.github.com/en/actions/deployment/targeting-different-environments/using-environments-for-deployment#deployment-protection-rules
+    environment:
+      name: pypi
+      # OPTIONAL: uncomment and update to include your PyPI project URL in the deployment status:
+      # url: https://pypi.org/p/YOURPROJECT
+      #
+      # ALTERNATIVE: if your GitHub Release name is the PyPI project version string
+      # ALTERNATIVE: exactly, uncomment the following line instead:
+      # url: https://pypi.org/project/YOURPROJECT/${{ github.event.release.name }}
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

{ion_csp-2.0.2 → ion_csp-2.0.4}/.gitignore

@@ -32,4 +32,4 @@ slurm-*.out
 server_config
 *.yaml
 model_ori.pt
-yz_opt/
+logs/*

ion_csp-2.0.4/MANIFEST.in

@@ -0,0 +1,2 @@
+include README.md
+include LICENSE

ion_csp-2.0.4/PKG-INFO

@@ -0,0 +1,236 @@
+Metadata-Version: 2.4
+Name: ion_CSP
+Version: 2.0.4
+Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
+Home-page: https://github.com/bagabaga007/ion_CSP
+Author: Ze Yang
+Author-email: Ze Yang <yangze1995007@163.com>
+License-Expression: MIT
+Keywords: ion_crystal, crystal_structure_prediction
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: ase==3.23.0
+Requires-Dist: deepmd-kit==3.0.1
+Requires-Dist: torch==2.5.0
+Requires-Dist: dpdispatcher==0.6.7
+Requires-Dist: numpy==1.26.4
+Requires-Dist: paramiko==3.5.1
+Requires-Dist: pyxtal==1.0.4
+Requires-Dist: phonopy==2.28.0
+Requires-Dist: rdkit==2024.3.3
+Requires-Dist: pytest==8.3.4
+Dynamic: author
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-python
+
+# Crystal Structure Design Software V2.0
+
+## 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筛选。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  
+- **智能任务管理**  
+  - 实时进程监控（PID跟踪）
+  - 日志文件自动符号链接
+  - 进程安全终止与资源清理
+- **高级日志系统**  
+  - 分页浏览（10条/页）
+  - 模块过滤（CSP/EE）
+  - 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     |
+| psutil      | 5.9      |
+| Docker      | 20.10    |
+| ase         | 3.23.0   |
+| deepmd-kit  | 3.0.1    |
+| torch       | 2.5.0    |
+| dpdispatcher| 0.6.7    |
+| numpy       | 1.26.4   |
+| paramiko    | 3.5.1    |
+| pyxtal      | 1.0.4    |
+| phonopy     | 2.28.0   |
+| rdkit       | 2023.03.3|
+
+### 安装步骤
+```bash
+# 创建虚拟环境
+python -m venv venv
+source venv/bin/activate  # Linux/Mac
+
+# 安装依赖
+pip install ion-csp
+```
+
+## 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]
+    B --> C[EE模块]
+    B --> D[CSP模块]
+    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]
+    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5月
+- **最新版本**：v2.0.4
+- **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
+
+---
+
+# Crystal Structure Design Software V2.0
+
+## Project Overview
+This software enables efficient crystal structure screening 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
+- **Intelligent Task Management**
+  - Real-time process monitoring (PID tracking)
+  - Automatic log file symlink creation
+  - Safe process termination with resource cleanup
+- **Advanced Logging System**
+  - Paginated log viewing (10 entries/page)
+  - Module-based filtering (CSP/EE)
+  - 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     |
+| psutil      | 5.9      |
+| Docker      | 20.10    |
+| ase         | 3.23.0   |
+| deepmd-kit  | 3.0.1    |
+| torch       | 2.5.0    |
+| dpdispatcher| 0.6.7    |
+| numpy       | 1.26.4   |
+| paramiko    | 3.5.1    |
+| pyxtal      | 1.0.4    |
+| phonopy     | 2.28.0   |
+| rdkit       | 2023.03.3|
+
+### Installation Steps
+```bash
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # Linux/Mac
+
+# Install dependencies
+pip install ion-csp
+```
+
+## 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]
+    B --> C[EE Module]
+    B --> D[CSP Module]
+    B --> E[Log System]
+    B --> F[Task Scheduler]
+    C --> G[Empirical Evaluation Engine]
+    D --> H[Crystal 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: May 2025
+- Latest version: v2.0.4
+- Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

ion_csp-2.0.4/README.md

@@ -0,0 +1,207 @@
+# Crystal Structure Design Software V2.0
+
+## 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筛选。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  
+- **智能任务管理**  
+  - 实时进程监控（PID跟踪）
+  - 日志文件自动符号链接
+  - 进程安全终止与资源清理
+- **高级日志系统**  
+  - 分页浏览（10条/页）
+  - 模块过滤（CSP/EE）
+  - 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     |
+| psutil      | 5.9      |
+| Docker      | 20.10    |
+| ase         | 3.23.0   |
+| deepmd-kit  | 3.0.1    |
+| torch       | 2.5.0    |
+| dpdispatcher| 0.6.7    |
+| numpy       | 1.26.4   |
+| paramiko    | 3.5.1    |
+| pyxtal      | 1.0.4    |
+| phonopy     | 2.28.0   |
+| rdkit       | 2023.03.3|
+
+### 安装步骤
+```bash
+# 创建虚拟环境
+python -m venv venv
+source venv/bin/activate  # Linux/Mac
+
+# 安装依赖
+pip install ion-csp
+```
+
+## 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]
+    B --> C[EE模块]
+    B --> D[CSP模块]
+    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]
+    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5月
+- **最新版本**：v2.0.4
+- **问题追踪**：https://github.com/bagabaga007/ion_CSP/issues
+
+---
+
+# Crystal Structure Design Software V2.0
+
+## Project Overview
+This software enables efficient crystal structure screening 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
+- **Intelligent Task Management**
+  - Real-time process monitoring (PID tracking)
+  - Automatic log file symlink creation
+  - Safe process termination with resource cleanup
+- **Advanced Logging System**
+  - Paginated log viewing (10 entries/page)
+  - Module-based filtering (CSP/EE)
+  - 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     |
+| psutil      | 5.9      |
+| Docker      | 20.10    |
+| ase         | 3.23.0   |
+| deepmd-kit  | 3.0.1    |
+| torch       | 2.5.0    |
+| dpdispatcher| 0.6.7    |
+| numpy       | 1.26.4   |
+| paramiko    | 3.5.1    |
+| pyxtal      | 1.0.4    |
+| phonopy     | 2.28.0   |
+| rdkit       | 2023.03.3|
+
+### Installation Steps
+```bash
+# Create virtual environment
+python -m venv venv
+source venv/bin/activate  # Linux/Mac
+
+# Install dependencies
+pip install ion-csp
+```
+
+## 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]
+    B --> C[EE Module]
+    B --> D[CSP Module]
+    B --> E[Log System]
+    B --> F[Task Scheduler]
+    C --> G[Empirical Evaluation Engine]
+    D --> H[Crystal 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: May 2025
+- Latest version: v2.0.4
+- Issue tracker: https://github.com/bagabaga007/ion_CSP/issues

ion_csp-2.0.4/SECURITY.md

@@ -0,0 +1,21 @@
+# Security Policy
+
+## Supported Versions
+
+Use this section to tell people about which versions of your project are
+currently being supported with security updates.
+
+| Version | Supported          |
+| ------- | ------------------ |
+| 5.1.x   | :white_check_mark: |
+| 5.0.x   | :x:                |
+| 4.0.x   | :white_check_mark: |
+| < 4.0   | :x:                |
+
+## Reporting a Vulnerability
+
+Use this section to tell people how to report a vulnerability.
+
+Tell them where to go, how often they can expect to get an update on a
+reported vulnerability, what to expect if the vulnerability is accepted or
+declined, etc.

ion_csp-2.0.4/environment.yml

@@ -0,0 +1,20 @@
+name: ion-csp-env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.11
+  - pip
+  - setuptools
+  - wheel
+  - setuptools-scm
+  - ase=3.23.0
+  - numpy=1.26.4
+  - paramiko=3.5.1
+  - pyxtal=1.0.4
+  - phonopy=2.28.0
+  - rdkit=2023.03.3
+  - pip:
+    - torch==2.5.0
+    - deepmd-kit==3.0.1
+    - dpdispatcher==0.6.7

ion_csp-2.0.4/examples/example_usage.py

@@ -0,0 +1,4 @@
+from ion_CSP.task_manager import main
+
+if __name__ == "__main__":
+    main()

{ion_csp-2.0.2 → ion_csp-2.0.4}/param/INCAR_1

@@ -4,7 +4,7 @@ PREC = Accurate
 ENCUT = 600  # 800
 EDIFF = 1e-4  # 1e-6
 IBRION = 2 
-ISIF = 3 
+ISIF = 8 
 NSW = 300  # 200
 ISMEAR = 0 ; SIGMA = 0.05 
 POTIM = 0.05 
@@ -16,4 +16,4 @@ LWAVE = FALSE
 #Finer optimization 
 EDIFFG = -0.05  # 1e-4
 KSPACING = 0.7  # 0.25 
-IVDW = 11
+IVDW = 12

{ion_csp-2.0.2 → ion_csp-2.0.4}/param/INCAR_2

@@ -4,7 +4,7 @@ PREC = Accurate
 ENCUT = 800
 EDIFF = 1e-6
 IBRION = 2 
-ISIF = 3 
+ISIF = 8 
 NSW = 300  # 200
 ISMEAR = 0 ; SIGMA = 0.05 
 POTIM = 0.05 
@@ -16,4 +16,4 @@ LWAVE = FALSE
 #Finer optimization 
 EDIFFG = -0.02
 KSPACING = 0.5
-IVDW = 11
+IVDW = 12