ion-CSP 2.0.4__tar.gz → 2.0.8__tar.gz

{ion_csp-2.0.4 → ion_csp-2.0.8}/.github/workflows/build.yml

@@ -21,14 +21,13 @@ jobs:
     - 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
+        conda run --name ion-csp-env pip install -r requirements.txt
+        conda run --name ion-csp-env pip install setuptools-scm
+        conda run --name ion-csp-env pip install build
 
     - name: Build package
       run: |
-        python -m build
+        conda run --name ion-csp-env python -m build

ion_csp-2.0.8/.github/workflows/python-package-conda.yml

@@ -0,0 +1,47 @@
+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: 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
+
+    - name: Install dependencies
+      run: |
+        conda run --name ion-csp-env pip install -r requirements.txt
+        conda run --name ion-csp-env pip install setuptools-scm
+        conda run --name ion-csp-env pip install build
+
+    - name: Build package
+      run: |
+        conda run --name ion-csp-env python -m build
+
+    - name: Lint with flake8
+      run: |
+        conda run --name ion-csp-env conda install -y flake8
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        
+    - name: Test with pytest
+      run: |
+        conda run --name ion-csp-env conda install -y pytest
+        pytest

{ion_csp-2.0.4 → ion_csp-2.0.8}/.github/workflows/python-publish.yml

@@ -27,6 +27,9 @@ jobs:
           python-version: "3.11"
 
       - name: Build release distributions
+        env:
+          TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+          TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           # NOTE: put your own distribution build steps here.
           python -m pip install build

{ion_csp-2.0.4 → ion_csp-2.0.8}/.gitignore

@@ -33,3 +33,6 @@ server_config
 *.yaml
 model_ori.pt
 logs/*
+dist/*
+*.tar.gz
+*.whl

{ion_csp-2.0.4 → ion_csp-2.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.0.4
+Version: 2.0.8
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -67,7 +67,7 @@ Dynamic: requires-python
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### 安装步骤
 ```bash
@@ -172,7 +172,7 @@ This software enables efficient crystal structure screening from molecular/ion c
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### Installation Steps
 ```bash

{ion_csp-2.0.4 → ion_csp-2.0.8}/README.md

@@ -38,7 +38,7 @@
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### 安装步骤
 ```bash
@@ -143,7 +143,7 @@ This software enables efficient crystal structure screening from molecular/ion c
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### Installation Steps
 ```bash

{ion_csp-2.0.4 → ion_csp-2.0.8}/src/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.0.4"
-__date__ = "2025-04-24"
+__version__ = "2.0.8"
+__date__ = "2025-05-14"
 
 
 try:

{ion_csp-2.0.4 → ion_csp-2.0.8}/src/ion_CSP/read_mlp_density.py

@@ -1,4 +1,5 @@
 import os
+import csv
 import shutil
 import logging
 import subprocess
@@ -76,15 +77,30 @@ class ReadMlpDensity:
             os.makedirs(backup_dir, exist_ok=True)
             for item in os.listdir(self.max_density_dir):
                 shutil.move(os.path.join(self.max_density_dir, item), os.path.join(backup_dir, item))
-        
+        numbers, mlp_densities, mlp_energies = [], [], []
         os.makedirs(self.max_density_dir, exist_ok=True)
         for density, CONTCAR_filename in sorted_filename[:n_screen]:
             # 生成新的包含密度值的文件名，并重命名文件
             # 密度转换为字符串，保留4位小数
             density_str = f'{density:.4f}'
+            mlp_densities.append(density_str)
             # 保留 CONTCAR 的序数信息，方便回推检查
             number = CONTCAR_filename.split("_")[1]
+            numbers.append(number)
             OUTCAR_filename = f'OUTCAR_{number}'
+            try:
+                with open(f"{self.folder_dir}/OUTCAR_{number}") as mlp_out:
+                    lines = mlp_out.readlines()
+                    for line in lines:
+                        if "TOTEN" in line:
+                            values = line.split()
+                            mlp_energy = round(float(values[-2]), 2)
+            except FileNotFoundError:
+                logging.error(
+                    f"  No avalible MLP OUTCAR_{number} found"
+                )
+                mlp_energy = False
+            mlp_energies.append(mlp_energy)
             new_CONTCAR_filename = f'CONTCAR_{density_str}_{number}'
             new_OUTCAR_filename = f'OUTCAR_{density_str}_{number}'
             shutil.copy(f'{self.folder_dir}/{CONTCAR_filename}', f'{self.max_density_dir}/{new_CONTCAR_filename}')
@@ -92,6 +108,30 @@ class ReadMlpDensity:
             print(f'New CONTCAR and OUTCAR of {density_str}_{number} are renamed and saved')
             logging.info(f'New CONTCAR and OUTCAR of {density_str}_{number} are renamed and saved')
 
+        with open(
+            f"{self.max_density_dir}/mlp_density_energy.csv",
+            "w",
+            newline="",
+            encoding="utf-8",
+        ) as csv_file:
+            writer = csv.writer(csv_file)
+            header = [
+                "Number",
+                "MLP_E",
+                "MLP_Density",
+            ]
+            datas = list(
+                zip(
+                    numbers,
+                    mlp_energies,
+                    mlp_densities,
+                )
+            )
+            datas.sort(key=lambda x: -float(x[-1]))
+            writer.writerow(header)
+            for data in datas:
+                writer.writerow(data)
+
     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. 
@@ -127,14 +167,18 @@ class ReadMlpDensity:
                 # 复制对应的OUTCAR文件到primitive_cell目录下
                 density_number = new_CONTCAR_filename.split("CONTCAR_")[1]
                 new_OUTCAR_filename = f'OUTCAR_{density_number}'
-                shutil.copy(f'{self.max_density_dir}/{new_OUTCAR_filename}', f'{self.primitive_cell_dir}/{new_OUTCAR_filename}')
+                shutil.copy(f'{self.phonopy_dir}/{new_OUTCAR_filename}', f'{self.primitive_cell_dir}/{new_OUTCAR_filename}')
+            shutil.copy(
+                f"{self.phonopy_dir}/mlp_density_energy.csv",
+                f"{self.primitive_cell_dir}/mlp_density_energy.csv",
+            )
             for_vasp_opt_dir = os.path.join(self.base_dir, '3_for_vasp_opt')
             if os.path.exists(for_vasp_opt_dir):
                 shutil.rmtree(for_vasp_opt_dir)
             shutil.copytree(self.primitive_cell_dir, for_vasp_opt_dir)
             logging.info('The phonopy processing has been completed!!\nThe symmetrized primitive cells have been saved in POSCAR format to the primitive_cell folder.\nThe output content of phonopy has been saved to the phonopy.log file in the same directory.')
             # 在 phonopy 成功进行对称化处理后，删除 2_mlp_optimized/max_density 文件夹以节省空间
-            shutil.rmtree(self.max_density_dir)
+            shutil.rmtree(self.phonopy_dir)
         except FileNotFoundError:
             logging.error(
                 "There are no CONTCAR structure files after screening.\nPlease check if the ions correspond to the crystals and adjust the screening criteria"

{ion_csp-2.0.4 → ion_csp-2.0.8}/src/ion_CSP/task_manager.py

@@ -125,7 +125,7 @@ class TaskManager:
     def _display_tasks(self, tasks, total, current_page, total_pages, function):
         """标准化任务显示 - Standardized tasks display"""
         display = "logs" if function == "view" else "tasks" 
-        print(f"\033cPage {current_page}/{total_pages} ({total} {display})")
+        print(f"\033cPage {current_page}/{total_pages} ({total} {display})\n")
         if function == "kill":
             for i, task in enumerate(tasks, 1):
                 print(
@@ -138,11 +138,11 @@ class TaskManager:
                 )
         else:
             raise ValueError(f"Not supported function {function}. Available function: 'view' and 'kill' ")
-        print("\nPage {} of {}".format(current_page, total_pages))
         # 分页控制
         print("\nOptions:")
         if function == "view":
             print("n) Next page | p) Previous page | f) Filter | q) Quit")
+            print("Enter number to view log in detail")
         elif function == "kill":
             print("n) Next page | p) Previous page | f) Filter | k) Kill | q) Quit")
         else:
@@ -171,10 +171,11 @@ class TaskManager:
             elif function == "kill" and choice == "K":
                 try:
                     task_num = input("Enter task number to kill: ").strip()
-                    if not task_num.isdigit():
+                    if task_num.isdigit() and 1 <= int(task_num) <= 10:
+                        # 计算全局任务索引
+                        global_index = current_page * 10 + (int(task_num) - 1)
+                    else: 
                         raise ValueError
-                    # 计算全局任务索引
-                    global_index = current_page * 10 + (int(task_num) - 1)
                     if 0 <= global_index < len(tasks):
                         selected_index = global_index
                         confirm = input(
@@ -189,10 +190,10 @@ class TaskManager:
                     else:
                         print("Invalid task number")
                         input("\nPress Enter to continue...")
-                except ValueError:
+                except (ValueError, TypeError):
                     print("Please enter a valid number")
                     input("\nPress Enter to continue...")
-            elif function == "view" and choice.isdigit():
+            elif function == "view" and choice.isdigit() and 1<= int(choice) <=10:
                 # 计算全局任务索引
                 global_index = current_page * 10 + (int(choice) - 1)
                 if 0 <= global_index < len(tasks):
@@ -255,6 +256,8 @@ class TaskManager:
             os.remove(std_log)
             std_log.symlink_to(output_log)
 
+        print('Starting task ......')
+        time.sleep(6)
         logging.info(f"Started {module} module (PID: {process.pid})")
         print(f"Task started (PID: {process.pid})")
         print(f"Normalized log file: {std_log}")
@@ -366,7 +369,7 @@ class TaskManager:
             print("q) Exit")
             print("=" * 50)
 
-            choice = input("Please enter operation: ").strip().lower()
+            choice = input("Please select an operation: ").strip().lower()
             if choice == "1":
                 work_dir = input("Enter EE working directory: ").strip()
                 self.task_runner("EE", work_dir)

{ion_csp-2.0.4 → ion_csp-2.0.8}/src/ion_CSP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.0.4
+Version: 2.0.8
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -67,7 +67,7 @@ Dynamic: requires-python
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### 安装步骤
 ```bash
@@ -172,7 +172,7 @@ This software enables efficient crystal structure screening from molecular/ion c
 | paramiko    | 3.5.1    |
 | pyxtal      | 1.0.4    |
 | phonopy     | 2.28.0   |
-| rdkit       | 2023.03.3|
+| rdkit       | 2024.03.3|
 
 ### Installation Steps
 ```bash

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

@@ -1,43 +0,0 @@
-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