ion-CSP 2.2.1__tar.gz → 2.2.3__tar.gz

{ion_csp-2.2.1 → ion_csp-2.2.3}/.gitignore

@@ -5,6 +5,7 @@ venv/
 # 编译文件
 __pycache__/
 *.pyc
+*.egg-info/
 
 # IDE 配置
 .idea/

{ion_csp-2.2.1 → ion_csp-2.2.3}/CHANGELOG.md

@@ -2,6 +2,30 @@
 
 ## Latest Changes
 
+### 12e7aa8 (2025-07-10)
+
+Update version number to 2.2.3, remove redundant egg info files, and add ignore for *. egg info.
+
+### 42fad92 (2025-07-10)
+
+Stabilized version functionality, restored import of cell filters, and resumed use of UnitCellFilter to optimize atomic structure pressure constraints.
+
+## V2.2.2
+
+### 19a1b2d (2025-07-04)
+
+Adjust the sleep time in task_manager and add molecular recognition test cases.
+
+### d914d90 (2025-07-03)
+
+Update the version to 2.2.2. The redundant output content of the console is greatly reduced to control the size of the console. log file. Specifically, the redundant log records are reduced in gen_opt when exceptions occur in the structure generation process, and the redundant log records in gen_opt and read_mlp_density are reduced when calling the phonopy toolkit.
+
+## V2.2.1
+
+### 0a77f51 (2025-07-01)
+
+Due to the unsatisfactory performance of Mattersim in testing, we switched back to fine-tuning the machine learning potential of DP.  The performance of ExpCellFilter in testing is easier to identify experimental structures compared to UnitCellFilter, so it is changed to call ExpCellFilter in mlp_opt.py.
+
 ### 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.

{ion_csp-2.2.1 → ion_csp-2.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.2.1
+Version: 2.2.3
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.2.1"
-__date__ = "2025-06-30"
+__version__ = "2.2.3"
+__date__ = "2025-07-10"
 
 
 try:

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP/gen_opt.py

@@ -116,9 +116,8 @@ class CrystalGenerator:
                     pyxtal_structure.to_file(POSCAR_path, fmt="poscar")
                     total_count += 1
                     group_count += 1
+                # 捕获对于某一空间群生成结构的运行时间过长、组成兼容性错误、对称性兼容性错误等异常，使结构生成能够完全进行而不中断
                 except (RuntimeError, Comp_CompatibilityError, Symm_CompatibilityError) as e:
-                    # 捕获对于某一空间群生成结构的运行时间过长、组成兼容性错误、对称性兼容性错误等异常，使结构生成能够完全进行而不中断
-                    logging.error(f"Generating structure error: {e}")
                     # 记录异常类型并跳出当前空间群的生成循环
                     exception_message = type(e).__name__
                     break
@@ -154,7 +153,11 @@ class CrystalGenerator:
         # 按顺序处理POSCAR文件，首先复制一份无数字后缀的POSCAR文件
         shutil.copy(f"{self.POSCAR_dir}/{filename}", f"{self.POSCAR_dir}/POSCAR")
         try:
-            subprocess.run(["nohup", "phonopy", "--symmetry", "POSCAR"], check=True)
+            subprocess.run(
+                ["nohup", "phonopy", "--symmetry", "POSCAR"],
+                check=True,
+                stdout=subprocess.DEVNULL
+            )
         except subprocess.CalledProcessError as e:
             # 新增：捕获phonopy执行错误
             logging.error(f"Phonopy execution failed for {filename}: {str(e)}")
@@ -168,9 +171,6 @@ class CrystalGenerator:
         
         # 检查生成的POSCAR中的原子数，如果不匹配则删除该POSCAR并在日志中记录
         if cell_atoms != self.cell_atoms:
-            error_message = f"Atom number mismatch ({cell_atoms} vs {self.cell_atoms})"
-            print(f"{filename} - {error_message}")
-            
             # 新增：回溯空间群归属
             poscar_index = int(filename.split('_')[1])  # 提取POSCAR编号
             space_group = self._find_space_group(poscar_index)

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP/mlp_opt.py

@@ -10,17 +10,14 @@ 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.filters import ExpCellFilter
+from ase.constraints import UnitCellFilter
 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)
-# calc = MatterSimCalculator(device="cuda")
 
 
 def get_element_num(elements):
@@ -162,8 +159,7 @@ 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 = ExpCellFilter(atoms, scalar_pressure=aim_stress)
+    ucf = UnitCellFilter(atoms, scalar_pressure=aim_stress)
     # optimization
     opt = LBFGS(ucf) 
     opt.run(fmax=fmax,steps=Opt_Step) 

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP/read_mlp_density.py

@@ -174,7 +174,11 @@ class ReadMlpDensity:
                     # 使用phonopy模块处理POSCAR结构文件，获取对称化的原胞和常规胞。
                     # 应用晶体的对称操作优化后的原胞可以最好地符合晶体的对称性，减少后续优化计算的复杂性。
                     log.write(f'\nProcessing file: {new_CONTCAR_filename}\n')
-                    result = subprocess.run(['nohup', 'phonopy', '--symmetry', 'POSCAR'], stderr=subprocess.STDOUT)
+                    result = subprocess.run(
+                        ["nohup", "phonopy", "--symmetry", "POSCAR"],
+                        check=True,
+                        stdout=subprocess.DEVNULL
+                    )
                     log.write(f'Finished processing file: {new_CONTCAR_filename} with return code: {result.returncode}\n')
                 # 将phonopy生成的PPOSCAR（对称化原胞）和BPOSCAR（对称化常规胞）放到对应的文件夹中，并将文件名改回POSCAR_index
                 shutil.move(f'{self.phonopy_dir}/PPOSCAR', f'{self.primitive_cell_dir}/{new_CONTCAR_filename}')

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP/task_manager.py

@@ -264,7 +264,7 @@ class TaskManager:
             std_log.symlink_to(output_log)
 
         print('Starting task ......')
-        time.sleep(6)
+        time.sleep(3)
         logging.info(f"Started {module} module (PID: {process.pid})")
         print(f"Task started (PID: {process.pid})")
         print(f"Normalized log file: {std_log}")

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.2.1
+Version: 2.2.3
 Summary: Crystal Structure Design Software Based on Molecular/Ionic Configuration.
 Home-page: https://github.com/bagabaga007/ion_CSP
 Author: Ze Yang

{ion_csp-2.2.1 → ion_csp-2.2.3}/src/ion_CSP.egg-info/SOURCES.txt

@@ -100,5 +100,6 @@ 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/test_identify_molecules.py
 tests/test_log_and_time.py
 tests/test_task_manager.py

ion_csp-2.2.3/tests/test_identify_molecules.py

@@ -0,0 +1,171 @@
+import os
+import logging
+import pytest
+from ase import Atoms
+from ion_CSP.identify_molecules import identify_molecules, molecules_information
+
+# 配置日志
+logging.basicConfig(level=logging.INFO, format="%(levelname)s: %(message)s")
+
+
+def create_gjf_file(path: str, filename: str, atoms: Atoms):
+    """手动创建临时的GJF文件"""
+    filepath = os.path.join(path, filename)
+    with open(filepath, "w") as f:
+        f.write("#N\n\n")  # Gaussian 文件头
+        f.write("Generated by ASE test\n\n")
+        f.write("0 1\n")
+        for atom in atoms:
+            f.write(f"{atom.symbol} {atom.x} {atom.y} {atom.z}\n")
+        f.write("\n\n")  # 文件结束
+    return filepath
+
+
+@pytest.fixture
+def setup_test_environment(tmp_path):
+    """设置测试环境，创建临时目录并切换工作目录"""
+    os.chdir(tmp_path)
+    return tmp_path
+
+
+def test_single_water_molecule(setup_test_environment):
+    """测试单个水分子"""
+    # 创建初始GJF文件
+    water = Atoms("OH2", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+    create_gjf_file(setup_test_environment, "water.gjf", water)
+
+    # 运行识别函数
+    merged_molecules, molecules_flag, initial_info = identify_molecules(water)
+
+    # 验证结果
+    expected_molecule = frozenset([("O", 1), ("H", 2)])
+    assert len(merged_molecules) == 1
+    assert expected_molecule in merged_molecules
+    assert merged_molecules[expected_molecule] == 1
+    assert molecules_flag is True
+    assert initial_info == [{"O": 1, "H": 2}]
+
+
+def test_two_isolated_water_molecules(setup_test_environment):
+    """测试两个独立的水分子"""
+    # 创建两个初始GJF文件
+    water1 = Atoms("OH2", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+    water2 = Atoms("OH2", positions=[[10, 0, 0], [11, 0, 0], [10, 1, 0]])
+    create_gjf_file(setup_test_environment, "water1.gjf", water1)
+    create_gjf_file(setup_test_environment, "water2.gjf", water2)
+
+    # 合并两个分子
+    combined = water1 + water2
+
+    # 运行识别函数
+    merged_molecules, molecules_flag, initial_info = identify_molecules(combined)
+
+    # 验证结果
+    expected_molecule = frozenset([("O", 1), ("H", 2)])
+    assert len(merged_molecules) == 1
+    assert expected_molecule in merged_molecules
+    assert merged_molecules[expected_molecule] == 2
+    assert molecules_flag is True
+
+
+def test_water_and_methane_molecules(setup_test_environment):
+    """测试水分子和甲烷分子"""
+    # 创建初始GJF文件
+    water = Atoms("OH2", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+    methane = Atoms(
+        "CH4", positions=[[10, 0, 0], [11, 0, 0], [10, 1, 0], [10, 0, 1], [9, 0, 0]]
+    )
+    create_gjf_file(setup_test_environment, "water.gjf", water)
+    create_gjf_file(setup_test_environment, "methane.gjf", methane)
+
+    # 合并两个分子
+    combined = water + methane
+
+    # 运行识别函数
+    merged_molecules, molecules_flag, initial_info = identify_molecules(combined)
+
+    # 验证结果
+    water_mol = frozenset([("O", 1), ("H", 2)])
+    methane_mol = frozenset([("C", 1), ("H", 4)])
+
+    assert len(merged_molecules) == 2
+    assert water_mol in merged_molecules
+    assert methane_mol in merged_molecules
+    assert merged_molecules[water_mol] == 1
+    assert merged_molecules[methane_mol] == 1
+    assert molecules_flag is True
+    assert sorted(initial_info, key=lambda x: sorted(x.items())) == sorted(
+        [{"O": 1, "H": 2}, {"C": 1, "H": 4}], key=lambda x: sorted(x.items())
+    )
+
+
+def test_mismatched_molecules(setup_test_environment):
+    """测试分子不匹配的情况"""
+    # 只创建一个初始GJF文件
+    water = Atoms("OH2", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+    create_gjf_file(setup_test_environment, "water.gjf", water)
+
+    # 创建两个独立的水分子
+    water1 = Atoms("OH", positions=[[0, 0, 0], [1, 0, 0]])
+    water2 = Atoms("OH3", positions=[[10, 0, 0], [11, 0, 0], [10, 1, 0], [10, 1, 1]])
+    combined = water1 + water2
+
+    # 运行识别函数
+    merged_molecules, molecules_flag, initial_info = identify_molecules(combined)
+
+    # 验证结果
+    expected_molecule = frozenset([("O", 1), ("H", 2)])
+    assert len(merged_molecules) == 2
+    assert expected_molecule not in merged_molecules
+    assert merged_molecules[expected_molecule] == 0
+    assert molecules_flag is False
+    assert initial_info == [{"O": 1, "H": 2}]
+
+
+def test_no_gjf_files(setup_test_environment):
+    """测试没有GJF文件的情况"""
+    water = Atoms("OH2", positions=[[0, 0, 0], [1, 0, 0], [0, 1, 0]])
+
+    # 运行识别函数
+    merged_molecules, molecules_flag, initial_info = identify_molecules(water)
+
+    # 验证结果
+    expected_molecule = frozenset([("O", 1), ("H", 2)])
+    assert len(merged_molecules) == 1
+    assert expected_molecule in merged_molecules
+    assert merged_molecules[expected_molecule] == 1
+    assert molecules_flag is False  # 没有初始GJF文件
+    assert initial_info == []
+
+
+def test_molecules_information_logging(caplog):
+    """测试分子信息日志输出"""
+    # 准备测试数据
+    molecules = {frozenset([("C", 1), ("H", 4)]): 1, frozenset([("O", 1), ("H", 2)]): 2}
+    molecules_flag = True
+    initial_info = [{"C": 1, "H": 4}, {"O": 1, "H": 2}]
+
+    # 运行信息输出函数
+    with caplog.at_level(logging.INFO):
+        molecules_information(molecules, molecules_flag, initial_info)
+
+    # 验证日志输出
+    assert "Initial molecules: [{'C': 1, 'H': 4}, {'O': 1, 'H': 2}]" in caplog.text
+    assert "Molecule 1 (Total Atoms: 5, Count: 1): C1H4" in caplog.text
+    assert "Molecule 2 (Total Atoms: 3, Count: 2): O1H2" in caplog.text
+    assert "Molecular Comparison Successful" in caplog.text
+
+
+def test_molecules_information_failed_logging(caplog):
+    """测试分子比较失败的日志输出"""
+    # 准备测试数据
+    molecules = {frozenset([("C", 1), ("H", 4)]): 1, frozenset([("O", 1), ("H", 2)]): 2}
+    molecules_flag = False
+    initial_info = [{"C": 1, "H": 4}, {"O": 1, "H": 2}]
+
+    # 运行信息输出函数
+    with caplog.at_level(logging.INFO):
+        molecules_information(molecules, molecules_flag, initial_info)
+
+    # 验证日志输出
+    assert "Molecular Comparison Failed" in caplog.text