ion-CSP 2.2.0__tar.gz → 2.2.1__tar.gz

{ion_csp-2.2.0 → ion_csp-2.2.1}/CHANGELOG.md

@@ -2,6 +2,20 @@
 
 ## Latest Changes
 
+### 1754cc7 (2025-06-30)
+
+Update version number to 2.2.1, fix file copying logic in main_EE workflow, update mlp_opt.py to use MatterSimCalculator to develop calculation efficiency.
+
+### d6abfb5 (2025-06-28)
+
+Optimize the environment variable settings in mlp_opt.py to disable numpy's multithreading and ensure the stability of multi-threaded computation.
+
+## V2.2.0
+
+### 18b9eba (2025-06-28)
+
+Optimize the file copying logic in vasp_processing to ensure that copying operations are only performed when the file exists; Update sorting parameters to support 'NC_ratio' and modify the relevant CSV file names accordingly.
+
 ### 14ffac2 (2025-06-27)
 
 Update version number to 2.2.0, optimize file replication logic in VASP processing, add error handling to ensure errors are recorded when files do not exist, modify README and CHANGELOG to reflect the latest changes.

{ion_csp-2.2.0 → ion_csp-2.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.2.0
+Version: 2.2.1
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -14,7 +14,7 @@ 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: deepmd-kit>=3.0.1
 Requires-Dist: torch==2.5.0
 Requires-Dist: dpdispatcher==0.6.7
 Requires-Dist: numpy==1.26.4

{ion_csp-2.2.0 → ion_csp-2.2.1}/pyproject.toml

@@ -20,7 +20,7 @@ requires-python = ">=3.11"
 dependencies = [
     "ase==3.23.0",
     "scipy==1.15.2",
-    "deepmd-kit==3.0.1",
+    "deepmd-kit>=3.0.1",
     "torch==2.5.0",
     "dpdispatcher==0.6.7",
     "numpy==1.26.4",

{ion_csp-2.2.0 → ion_csp-2.2.1}/requirements.txt

@@ -1,6 +1,6 @@
 ase==3.23.0
 scipy==1.15.2
-deepmd-kit==3.0.1
+deepmd-kit>=3.0.1
 torch==2.5.0
 dpdispatcher>=0.6.7
 numpy==1.26.4

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.2.0"
-__date__ = "2025-06-27"
+__version__ = "2.2.1"
+__date__ = "2025-06-30"
 
 
 try:

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/convert_SMILES.py

@@ -131,7 +131,7 @@ class SmilesProcessing:
                 f"{self.converted_dir}/charge_{charge}"
             )
             os.makedirs(charge_dir, exist_ok=True)
-            # 通过SMILE_to函数依次处理SMILES码
+            # 通过_convert_SMILES函数依次处理SMILES码
             for _, row in group.iterrows():
                 result_code, basename = self._convert_SMILES(
                     dir=charge_dir,
@@ -238,8 +238,10 @@ class SmilesProcessing:
         for folder in folders:
             folder_dir = os.path.join(self.converted_dir, folder)
             if not os.path.exists(folder_dir):
-                logging.error(f'Provided folder {folder} is not in the directory {folder_dir}')
-                continue
+                folder_dir = os.path.join(self.base_dir, folder)
+                if not os.path.exists(folder_dir):
+                    logging.error(f'Provided folder {folder} is not either in the work directory or the converted directory.\n')
+                    continue
             # 获取文件夹中所有以 .gjf 结尾的文件
             gjf_files = [
                 f for f in os.listdir(folder_dir) if f.endswith(".gjf")

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/mlp_opt.py

@@ -1,23 +1,27 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 import os
+os.environ["MKL_NUM_THREADS"] = "1"
+os.environ["NUMEXPR_NUM_THREADS"] = "1"
+os.environ["OMP_NUM_THREADS"] = "1"
+
 import time
 import numpy as np
 import multiprocessing
 from ase.io.vasp import read_vasp
 from ase.optimize import LBFGS
-from ase.constraints import UnitCellFilter
+# from ase.constraints import UnitCellFilter
+from ase.filters import ExpCellFilter
 from deepmd.calculator import DP
+# from mattersim.forcefield import MatterSimCalculator
 
 # 根据脚本位置确定model.pt文件的位置, 减少错误发生
 base_dir = os.path.dirname(__file__)
 relative_path = './model.pt'
 file_path = os.path.join(base_dir, relative_path)
 calc = DP(file_path)
-"""
-structure optimization with DP model and ASE
-PSTRESS and fmax should exist in input.dat
-"""
+# calc = MatterSimCalculator(device="cuda")
+
 
 def get_element_num(elements):
     """
@@ -51,7 +55,7 @@ def write_CONTCAR(element, ele, lat, pos, index):
         pos: atomic positions in direct coordinates
         index: index for the output file""" 
     f = open(f'{base_dir}/CONTCAR_'+str(index),'w')
-    f.write('ASE-DPKit-Optimization\n')
+    f.write('ASE-MLP-Optimization\n')
     f.write('1.0\n') 
     for i in range(3):
         f.write('%15.10f %15.10f %15.10f\n' % tuple(lat[i]))
@@ -139,7 +143,7 @@ def get_indexes():
 
 def run_opt(index: int): 
     """
-    Using the ASE&DP to Optimize Configures
+    Using the ASE & MLP to Optimize Configures
     :params
         index: index of the POSCAR file to be optimized
     """
@@ -147,7 +151,7 @@ def run_opt(index: int):
         os.system(f'mv {base_dir}/OUTCAR {base_dir}/OUTCAR-last')
     fmax, pstress = 0.03, 0
 
-    print('Start to Optimize Structures by DP----------')
+    print('Start to Optimize Structures by MLP----------')
         
     Opt_Step = 2000
     start = time.time() 
@@ -158,7 +162,8 @@ def run_opt(index: int):
     aim_stress = 1.0 * pstress * 0.01 * 0.6242 / 10.0 
     atoms = read_vasp('POSCAR_'+str(index)) 
     atoms.calc = calc 
-    ucf = UnitCellFilter(atoms, scalar_pressure=aim_stress)
+    # ucf = UnitCellFilter(atoms, scalar_pressure=aim_stress)
+    ucf = ExpCellFilter(atoms, scalar_pressure=aim_stress)
     # optimization
     opt = LBFGS(ucf) 
     opt.run(fmax=fmax,steps=Opt_Step) 

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/read_mlp_density.py

@@ -8,7 +8,7 @@ from ion_CSP.identify_molecules import identify_molecules, molecules_information
 
 class ReadMlpDensity:
     
-    def __init__(self, work_dir:str):
+    def __init__(self, work_dir:str, folder:str = '2_mlp_optimized'):
         """
         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.
@@ -20,7 +20,7 @@ class ReadMlpDensity:
         self.base_dir = work_dir
         os.chdir(self.base_dir)
         # 寻找同一目录下的2_mlp_optimized文件夹
-        self.folder_dir = os.path.join(self.base_dir, '2_mlp_optimized')
+        self.folder_dir = os.path.join(self.base_dir, folder)
         self.max_density_dir = os.path.join(self.folder_dir, 'max_density')
         self.primitive_cell_dir = os.path.join(self.folder_dir, 'primitive_cell')
         print(f"Processing MLP CONTCARs in {self.folder_dir}")

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/run/main_EE.py

@@ -109,6 +109,8 @@ def combination_task(work_dir, config):
     elif config["empirical_estimate"]["sort_by"] == "nitrogen":
         # 最终将预测的离子晶体氮含量以及对应的组分输出到 .csv 文件并根据氮含量从大到小排序
         combination.nitrogen_content_estimate()
+    elif config["empirical_estimate"]["sort_by"] == "NC_ratio":
+        combination.carbon_nitrogen_ratio_estimate()
     # 基于排序依据 sort_by 对应的 .csv 文件创建 combo_n 文件夹，并复制相应的 .gjf 结构文件。
     if config["empirical_estimate"]["make_combo_dir"]:
         combination.make_combo_dir(

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP/task_manager.py

@@ -219,7 +219,9 @@ class TaskManager:
     def task_runner(self, module: str, work_dir: str):
         """任务执行器 - Task execution handler"""
         work_dir = Path(work_dir)
-        work_dir.mkdir(exist_ok=True)
+        if not os.path.exists(work_dir):
+            print(f"Work directory {work_dir} does not exist")
+            return
 
         console_log = work_dir / f"main_{module}_console.log"
         pid_file = work_dir / "pid.txt"

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.2.0
+Version: 2.2.1
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang
@@ -14,7 +14,7 @@ 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: deepmd-kit>=3.0.1
 Requires-Dist: torch==2.5.0
 Requires-Dist: dpdispatcher==0.6.7
 Requires-Dist: numpy==1.26.4

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP.egg-info/SOURCES.txt

@@ -100,6 +100,5 @@ src/ion_CSP/run/run_read_mlp_density.py
 src/ion_CSP/run/run_upload_download.py
 src/ion_CSP/run/run_vasp_processing.py
 tests/__init__.py
-tests/test1_task_manager1.py
 tests/test_log_and_time.py
 tests/test_task_manager.py

{ion_csp-2.2.0 → ion_csp-2.2.1}/src/ion_CSP.egg-info/requires.txt

@@ -1,6 +1,6 @@
 ase==3.23.0
 scipy==1.15.2
-deepmd-kit==3.0.1
+deepmd-kit>=3.0.1
 torch==2.5.0
 dpdispatcher==0.6.7
 numpy==1.26.4

ion_csp-2.2.0/tests/test1_task_manager1.py

@@ -1,121 +0,0 @@
-import os
-import time
-import pytest
-from pathlib import Path
-from unittest.mock import patch, MagicMock, Mock
-from ion_CSP.task_manager import TaskManager
-
-
-@pytest.fixture(scope="session", autouse=True)
-def set_working_directory():
-    """设置工作目录为项目根目录"""
-    project_root = Path(__file__).resolve().parent  # 假设测试文件在 tests 目录下
-    os.chdir(project_root)
-    yield
-
-@pytest.fixture
-def task_manager(tmp_path):
-    # 使用临时目录替代工作目录，避免污染真实文件系统
-    tm = TaskManager()
-    tm.workspace = tmp_path
-    tm.log_dir = tmp_path / tm.log_base
-    tm.log_dir.mkdir(parents=True, exist_ok=True)
-    return tm
-
-
-def test_task_runner_creates_log_and_pid(monkeypatch, tmp_path, task_manager):
-    # 模拟 subprocess.Popen，避免真正启动子进程
-    mock_process = MagicMock()
-    mock_process.pid = 9999
-
-    def fake_popen(*args, **kwargs):
-        return mock_process
-
-    monkeypatch.setattr("subprocess.Popen", fake_popen)
-
-    # 调用 task_runner
-    work_dir = tmp_path / "work"
-    task_manager.task_runner("CSP", str(work_dir))
-
-    # 检查日志目录下是否生成了符号链接（symlink）
-    symlink_path = task_manager.log_dir / f"CSP_{mock_process.pid}.log"
-    assert symlink_path.exists()
-    assert symlink_path.is_symlink()
-
-
-def test_get_related_tasks_basic(task_manager, monkeypatch):
-    """测试标准日志文件处理"""
-    # 验证 log_dir 是 Path 对象
-    assert isinstance(task_manager.log_dir, Path), "log_dir 必须是 pathlib.Path 对象"
-    log_dir = task_manager.log_dir
-    log_dir.mkdir(parents=True, exist_ok=True)
-    print(log_dir)
-    # 模拟的时间戳
-    now = time.time()
-
-    # 创建模拟的 stat 对象
-    mock_stats = {
-        8: Mock(st_mtime=now - 8000),
-        5: Mock(st_mtime=now - 5000),
-        3: Mock(st_mtime=now - 3000),
-        1: Mock(st_mtime=now - 1000),
-    }
-
-    # 模拟 os.stat 行为
-    def mock_os_stat(path, **kwargs):
-        try:
-            base_name = path.name.split(".")[0]
-            pid = int(base_name.split("_")[-1])
-            return mock_stats.get(pid, Mock(st_mtime=0))
-        except (IndexError, ValueError):
-            return Mock(st_mtime=0)
-
-    monkeypatch.setattr("os.stat", mock_os_stat)
-    monkeypatch.setattr(task_manager, "_is_pid_running", lambda _: True)
-
-    # 创建日志文件
-    for pid in [8, 5, 3, 1]:
-        log_file = log_dir / f"CSP_{pid:04d}.log"
-        log_file.touch()
-
-    # 调用方法
-    tasks = task_manager.get_related_tasks()
-    print(tasks)
-    # 断言
-    assert len(tasks) == 4
-    for task in tasks:
-        assert task["pid"] in [8, 5, 3, 1]
-        assert task["status"] == "Running"
-
-
-def test_main_menu_navigation(monkeypatch, task_manager):
-    """测试主菜单导航"""
-    monkeypatch.setattr("builtins.input", MagicMock(side_effect=["3", "q"]))
-    with patch("sys.stdout") as mock_stdout:
-        task_manager.main_menu()
-        output = mock_stdout.getvalue()
-        assert "View Logs" in output
-        assert "Terminate Tasks" in output
-
-
-# def test_get_related_tasks_process_status(task_manager, monkeypatch):
-#     """测试进程状态判断"""
-#     test_file = task_manager.log_dir / "CSP_0001.log"
-#     test_file.touch()
-
-#     # 模拟 os.stat
-#     mock_stat = Mock(st_mtime=time.time())
-#     monkeypatch.setattr("os.stat", lambda _: mock_stat)
-
-#     # 模拟进程状态
-#     monkeypatch.setattr(task_manager, "_is_pid_running", lambda pid: pid % 2 == 0)
-
-#     # 执行测试
-#     tasks = task_manager.get_related_tasks()
-
-#     # 验证结果
-#     assert len(tasks) == 1
-#     assert tasks[0]["status"] == "Terminated"  # PID=1 为奇数，应标记为终止
-
-
-# 你可以继续添加针对 _safe_kill、_is_pid_running 等方法的单元测试