ion-CSP 2.2.1__py3-none-any.whl → 2.2.3__py3-none-any.whl

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/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/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/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/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.dist-info → ion_csp-2.2.3.dist-info}/METADATA

@@ -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.dist-info → ion_csp-2.2.3.dist-info}/RECORD

@@ -1,14 +1,14 @@
-ion_CSP/__init__.py,sha256=r22zEoL_7sKE557XIpVNUnM5WcNc7i0k58ySIqd24_s,356
+ion_CSP/__init__.py,sha256=jMZJMwgE30wGC-Ej_2ghlbE9UnLRCcLb0W-3kQ4mVnM,356
 ion_CSP/__main__.py,sha256=XlNCx5eMSrL7yld9ddSYXhjXvg2ZYGD_uk9LdqNabvs,74
 ion_CSP/convert_SMILES.py,sha256=i_f9cbCAr6SpZUvClZRAPGjK-_v9U9lFGA-06i041Tk,15755
 ion_CSP/empirical_estimate.py,sha256=aSidH3jyoG39ky-kDNUY0ix8hPefeVVWmPABVjTmy0g,37866
-ion_CSP/gen_opt.py,sha256=F_gEopuOO-b-tHfS0V4OMeThktY2QvPGWCVRXOCemfk,21605
+ion_CSP/gen_opt.py,sha256=EEMIPZ7oEOR9iGLRL-eJleHaWBiOK90o4a8_go9f-9o,21468
 ion_CSP/identify_molecules.py,sha256=GxDWq815Bk_Fq_SR8fe-dbrbEi1YgATVa7UINw3hAu4,5535
 ion_CSP/log_and_time.py,sha256=Db53LAM2KH_ty6M9_5FF8xDGiULgExh7pcKOvFtS7DQ,11697
-ion_CSP/mlp_opt.py,sha256=NoUSYoGVNVbijsB37xkOy7hwSFIhFTFD6gCB7UVloj0,7249
-ion_CSP/read_mlp_density.py,sha256=JkgfkI7qHme1e8IxeYMTYum_vRXea7RzYfmmiAmO7KA,12125
+ion_CSP/mlp_opt.py,sha256=DP8gldX07O2jXDhopUOodh8nqa5JeusLJjChTtt_DSE,7049
+ion_CSP/read_mlp_density.py,sha256=0fymqrpqoAmWosnyoNwH3GAvml42skZp_6SLvrXN0SI,12232
 ion_CSP/steps_opt_monitor.sh,sha256=1klPjnK0gqkDbvI9PtjdK5qidJ5G0Mo8q1SfrlLW5xM,3330
-ion_CSP/task_manager.py,sha256=_mYlHpDVmSdIZR4SS5iglswY6NQoFJWzA2VLkt5JraE,16654
+ion_CSP/task_manager.py,sha256=62E5s2bkVkRJiKroSGWVfTNYBRbzVcMPqTfZ1FPN61A,16654
 ion_CSP/upload_download.py,sha256=HXxVQMUydEoHe2vV89wR7De4Ut1lEte6pmp8Q82decI,23800
 ion_CSP/vasp_processing.py,sha256=Q4OotC5eK4RN4R3GZu5DnLk7wnkYSh-yC1oeGvrtT5U,28436
 ion_CSP/model/model.pt,sha256=5D9HTP5b7jUOv3kHltT71ORzhgt5p96awjbqC4oZVjQ,24649402
@@ -35,9 +35,9 @@ ion_CSP/run/run_gen_opt.py,sha256=_Zcsu0FkuZTfiGKSWNaK17LiyQ3qrP30F66UN5QemCo,27
 ion_CSP/run/run_read_mlp_density.py,sha256=aSJjWS1jH-D7qzx7RnpMPSTH7KEZp2b35dg1b2OQSCM,1864
 ion_CSP/run/run_upload_download.py,sha256=wuTAdy4bgdduD7TJtgHwo_fTpHKlkAwmgRknClDLYDo,2436
 ion_CSP/run/run_vasp_processing.py,sha256=hziE4cZwmIWvVaZtwHn9Dl35apYSLlMvSVIbCyd5mFg,1612
-ion_csp-2.2.1.dist-info/licenses/LICENSE,sha256=yeL9PshY_rGAt3GKqn8U7NafHifpmZipb-Owu0DDrHo,1070
-ion_csp-2.2.1.dist-info/METADATA,sha256=nA_4DWmRdeBSCdfS5GwOURvO_UomOcOvjPRrkGCvCMw,6314
-ion_csp-2.2.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ion_csp-2.2.1.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
-ion_csp-2.2.1.dist-info/top_level.txt,sha256=aYZa43dDebjLpWPN6bDIlBb6BVwA8gk4ajEjDDK9b9I,8
-ion_csp-2.2.1.dist-info/RECORD,,
+ion_csp-2.2.3.dist-info/licenses/LICENSE,sha256=yeL9PshY_rGAt3GKqn8U7NafHifpmZipb-Owu0DDrHo,1070
+ion_csp-2.2.3.dist-info/METADATA,sha256=hCXl6gqOMqsmHyptied9QekguXqh-YctkAX5Y9QR124,6314
+ion_csp-2.2.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+ion_csp-2.2.3.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
+ion_csp-2.2.3.dist-info/top_level.txt,sha256=aYZa43dDebjLpWPN6bDIlBb6BVwA8gk4ajEjDDK9b9I,8
+ion_csp-2.2.3.dist-info/RECORD,,