ion-CSP 2.2.0__py3-none-any.whl → 2.2.2__py3-none-any.whl

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__ = "2.2.2"
+__date__ = "2025-07-02"
 
 
 try:

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/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

@@ -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/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}")
@@ -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/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/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"
@@ -262,7 +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-2.2.0.dist-info → ion_csp-2.2.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.2.0
+Version: 2.2.2
 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.dist-info → ion_csp-2.2.2.dist-info}/RECORD

@@ -1,14 +1,14 @@
-ion_CSP/__init__.py,sha256=1WGzlZrB669L2oFjKynPwf89qMUaSmlCttuR4864M_Y,356
+ion_CSP/__init__.py,sha256=X870lzd7xUyDvBsUfjnDBqMJbCXtUlGh1hbxqI7coX0,356
 ion_CSP/__main__.py,sha256=XlNCx5eMSrL7yld9ddSYXhjXvg2ZYGD_uk9LdqNabvs,74
-ion_CSP/convert_SMILES.py,sha256=HAexqf6HXZAqRuMww5BKmU68MIO3d7XIaUtPKv_QwMs,15595
+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=uJaqjNYLzc4dRogNcGIP_Ukta_fMd5YdYVf9cNweOA4,7029
-ion_CSP/read_mlp_density.py,sha256=KwVgniroT46uFQ7_HROd5Fk9YxJCMip1jnufWvHHEiw,12104
+ion_CSP/mlp_opt.py,sha256=NoUSYoGVNVbijsB37xkOy7hwSFIhFTFD6gCB7UVloj0,7249
+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=JglPNDKpsv-bjbCm42D4k6GegDkSylX4oDWAdFa-oSU,16569
+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
@@ -28,16 +28,16 @@ ion_CSP/param/sub_ori.sh,sha256=JBERlc-VOVCNaKGwiJR8oq7Nyf0KV4JpHEVT5sE5s8E,2497
 ion_CSP/param/sub_supple.sh,sha256=23cam7WyW7-80J8O-Bs45qYkabk3mxZDgiHZvf48KBM,1887
 ion_CSP/run/__init__.py,sha256=_9EAXp4cv41ARbxahCkihwqY4F00Y18tBeTauWeD9mw,186
 ion_CSP/run/main_CSP.py,sha256=UaYHlh7BSxar4uGppPi-V0cFDpB14212Oy6gta59LfA,5898
-ion_CSP/run/main_EE.py,sha256=8TFlJx7QhJKGc4qZ2O0ESRYrlySp3r1WjeGLkUBeL5k,6217
+ion_CSP/run/main_EE.py,sha256=rX02_752odK16VTLK2qSHcxPCooPviy27DOlAtOYgpc,6334
 ion_CSP/run/run_convert_SMILES.py,sha256=85a8-UXPxPo3Yw_iYED_QF47yNTvYRnJHm3PC1d-d_Q,2056
 ion_CSP/run/run_empirical_estimate.py,sha256=U_yvQ5gMiBkDEabHXLJSAEm0EzGHhSKs6xmWoEC_gjc,2831
 ion_CSP/run/run_gen_opt.py,sha256=_Zcsu0FkuZTfiGKSWNaK17LiyQ3qrP30F66UN5QemCo,2727
 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-2.2.0.dist-info/licenses/LICENSE,sha256=yeL9PshY_rGAt3GKqn8U7NafHifpmZipb-Owu0DDrHo,1070
-ion_csp-2.2.0.dist-info/METADATA,sha256=7vO9oy9g9NEA_XQWdWBZSXda1VxTcE8NzuyCvr06VQ8,6314
-ion_csp-2.2.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-ion_csp-2.2.0.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
-ion_csp-2.2.0.dist-info/top_level.txt,sha256=aYZa43dDebjLpWPN6bDIlBb6BVwA8gk4ajEjDDK9b9I,8
-ion_csp-2.2.0.dist-info/RECORD,,
+ion_csp-2.2.2.dist-info/licenses/LICENSE,sha256=yeL9PshY_rGAt3GKqn8U7NafHifpmZipb-Owu0DDrHo,1070
+ion_csp-2.2.2.dist-info/METADATA,sha256=C35tKmC9pWPtn5ta5Q0ndJVheskSG_kHWhHC4fVcr6Q,6314
+ion_csp-2.2.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+ion_csp-2.2.2.dist-info/entry_points.txt,sha256=NexQJDs9f69kJA2DgoU6tsA3V8a66nadJRem1U_c_6g,54
+ion_csp-2.2.2.dist-info/top_level.txt,sha256=aYZa43dDebjLpWPN6bDIlBb6BVwA8gk4ajEjDDK9b9I,8
+ion_csp-2.2.2.dist-info/RECORD,,