ion-CSP 2.1.9__py3-none-any.whl → 2.2.1__py3-none-any.whl

ion_CSP/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.1.9"
-__date__ = "2025-06-27"
+__version__ = "2.2.1"
+__date__ = "2025-06-30"
 
 
 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/empirical_estimate.py

@@ -79,11 +79,11 @@ class EmpiricalEstimation:
         self.folders = folders
         self.ratios = ratios
         self.sort_by = sort_by
-        if sort_by not in ("density", "nitrogen"):
-            raise ValueError(f"The sort_by parameter must be either 'density' or 'nitrogen', but got '{sort_by}'")
+        if sort_by not in ("density", "nitrogen", "NC_ratio"):
+            raise ValueError(f"The sort_by parameter must be either 'density' 'nitrogen' or 'NC_ratio', but got '{sort_by}'")
         self.density_csv = "sorted_density.csv"
         self.nitrogen_csv = "sorted_nitrogen.csv"
-        self.carbon_nitrogen_csv = "specific_C_N_ratio.csv"
+        self.NC_ratio_csv = "specific_NC_ratio.csv"
         # 检查Multiwfn可执行文件是否存在
         self.multiwfn_path = self._check_multiwfn_executable()
     
@@ -487,7 +487,7 @@ class EmpiricalEstimation:
         filtered_data.sort(key=lambda x: (-x[1], -x[2]))
 
         # 写入排序后的 .csv 文件
-        with open(self.carbon_nitrogen_csv, "w", newline="", encoding="utf-8") as csv_file:
+        with open(self.NC_ratio_csv, "w", newline="", encoding="utf-8") as csv_file:
             writer = csv.writer(csv_file)
             # 动态生成表头
             num_components = len(combinations[0]) if combinations else 0
@@ -642,6 +642,8 @@ class EmpiricalEstimation:
             base_csv = self.density_csv
         elif self.sort_by == 'nitrogen':
             base_csv = self.nitrogen_csv
+        elif self.sort_by == "NC_ratio":
+            base_csv = self.NC_ratio_csv
         if not target_dir:
             target_dir = f'../2_{self.sort_by}_combos'
         with open(base_csv, mode='r', newline='') as file:

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}")

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"

ion_CSP/vasp_processing.py

@@ -140,9 +140,7 @@ class VaspProcessing:
             task_dir = os.path.join(self.for_vasp_opt_dir, f"{parent}pop{pop}")
             for job_i in node_jobs[pop]:
                 vasp_dir = mlp_contcar_files[job_i].split("CONTCAR_")[1]
-                shutil.copytree(
-                    f"{task_dir}/{vasp_dir}", f"{self.vasp_optimized_dir}/{vasp_dir}"
-                )
+                shutil.copytree(f"{task_dir}/{vasp_dir}", f"{self.vasp_optimized_dir}/{vasp_dir}", dirs_exist_ok=True)
             # 在成功完成 VASP 分步优化后，删除 3_for_vasp_opt/{parent}/pop{n} 文件夹以节省空间
             shutil.rmtree(task_dir)
         if machine_inform["context_type"] == "SSHContext":
@@ -256,10 +254,16 @@ class VaspProcessing:
             task_dir = os.path.join(self.vasp_optimized_dir, f"{parent}pop{pop}")
             for job_i in node_jobs[pop]:
                 vasp_dir = vasp_optimized_folders[job_i]
-                shutil.copytree(
-                    f"{task_dir}/{vasp_dir}/fine/final",
-                    f"{self.vasp_optimized_dir}/{vasp_dir}/fine/final",
-                )
+                try:
+                    shutil.copytree(
+                        f"{task_dir}/{vasp_dir}/fine/final",
+                        f"{self.vasp_optimized_dir}/{vasp_dir}/fine/final", 
+                        dirs_exist_ok=True,
+                    )
+                except FileNotFoundError:
+                    logging.error(
+                        f"No final optimization results found for {vasp_dir} in {task_dir}"
+                    )
             # 在成功完成 VASP 分步优化后，删除 4_vasp_optimized /{parent}/pop{n} 文件夹以节省空间
             shutil.rmtree(task_dir)
         if machine_inform["context_type"] == "SSHContext":
@@ -267,127 +271,6 @@ class VaspProcessing:
             shutil.rmtree(os.path.join(self.vasp_optimized_dir, parent))
         logging.info("Batch VASP optimization completed!!!")
 
-    def dpdisp_vasp_complete_tasks(
-        self,
-        machine: str,
-        resources: str,
-        nodes: int = 1,
-    ):
-        """
-        Based on the dpdispatcher module, prepare and submit files for optimization on remote server or local machine.
-        """
-        # 调整工作目录，减少错误发生
-        os.chdir(self.for_vasp_opt_dir)
-        # 读取machine.json和resources.json的参数
-        if machine.endswith(".json"):
-            machine = Machine.load_from_json(machine)
-        elif machine.endswith(".yaml"):
-            machine = Machine.load_from_yaml(machine)
-        else:
-            raise KeyError("Not supported machine file type")
-        if resources.endswith(".json"):
-            resources = Resources.load_from_json(resources)
-        elif resources.endswith(".yaml"):
-            resources = Resources.load_from_yaml(resources)
-        else:
-            raise KeyError("Not supported resources file type")
-        # 由于dpdispatcher对于远程服务器以及本地运行的forward_common_files的默认存放位置不同，因此需要预先进行判断，从而不改动优化脚本
-        machine_inform = machine.serialize()
-        if machine_inform["context_type"] == "SSHContext":
-            # 如果调用远程服务器，则创建二级目录
-            parent = "data/"
-        elif machine_inform["context_type"] == "LocalContext":
-            # 如果在本地运行作业，则只在后续创建一级目录
-            parent = ""
-
-        # 获取dir文件夹中所有以prefix_name开头的文件，在此实例中为POSCAR_
-        mlp_contcar_files = [
-            f for f in os.listdir(self.for_vasp_opt_dir) if f.startswith("CONTCAR_")
-        ]
-        # 创建一个嵌套列表来存储每个节点的任务并将文件平均依次分配给每个节点
-        # 例如：对于10个结构文件任务分发给4个节点的情况，则4个节点领到的任务分别[0, 4, 8], [1, 5, 9], [2, 6], [3, 7]
-        node_jobs = [[] for _ in range(nodes)]
-        for index, file in enumerate(mlp_contcar_files):
-            node_index = index % nodes
-            node_jobs[node_index].append(index)
-        task_list = []
-        for pop in range(nodes):
-            forward_files = [
-                "INCAR_1",
-                "INCAR_2",
-                "INCAR_3",
-                "POTCAR_H",
-                "POTCAR_C",
-                "POTCAR_N",
-                "POTCAR_O",
-                "sub_final.sh",
-            ]
-            backward_files = ["log", "err"]
-            # 将所有参数文件各复制一份到每个 task_dir 目录下
-            task_dir = os.path.join(self.for_vasp_opt_dir, f"{parent}pop{pop}")
-            os.makedirs(task_dir, exist_ok=True)
-            for file in forward_files:
-                shutil.copyfile(self.param_dir.joinpath(file), f"{task_dir}/{file}")
-            for job_i in node_jobs[pop]:
-                # 将分配好的POSCAR文件添加到对应的上传文件中
-                forward_files.append(mlp_contcar_files[job_i])
-                vasp_dir = mlp_contcar_files[job_i].split("CONTCAR_")[1]
-                # 每个POSCAR文件在优化后都取回对应的CONTCAR和OUTCAR输出文件
-                backward_files.append(f"{vasp_dir}/*")
-                backward_files.append(f"{vasp_dir}/fine/*")
-                backward_files.append(f"{vasp_dir}/fine/final/*")
-                shutil.copyfile(
-                    f"{self.for_vasp_opt_dir}/{mlp_contcar_files[job_i]}",
-                    f"{task_dir}/{mlp_contcar_files[job_i]}",
-                )
-
-            remote_task_dir = f"{parent}pop{pop}"
-            command = "chmod +x sub_final.sh && ./sub_final.sh"
-            task = Task(
-                command=command,
-                task_work_path=remote_task_dir,
-                forward_files=forward_files,
-                backward_files=backward_files,
-            )
-            task_list.append(task)
-
-        submission = Submission(
-            work_base=self.for_vasp_opt_dir,
-            machine=machine,
-            resources=resources,
-            task_list=task_list,
-        )
-        submission.run_submission()
-
-        # 创建用于存放优化后文件的 4_vasp_optimized 目录
-        os.makedirs(self.vasp_optimized_dir, exist_ok=True)
-        mlp_outcar_files = [
-            f for f in os.listdir(self.for_vasp_opt_dir) if f.startswith("OUTCAR_")
-        ]
-        for mlp_contcar, mlp_outcar in zip(mlp_contcar_files, mlp_outcar_files):
-            shutil.copyfile(
-                f"{self.for_vasp_opt_dir}/{mlp_contcar}",
-                f"{self.vasp_optimized_dir}/{mlp_contcar}",
-            )
-            shutil.copyfile(
-                f"{self.for_vasp_opt_dir}/{mlp_outcar}",
-                f"{self.vasp_optimized_dir}/{mlp_outcar}",
-            )
-        for pop in range(nodes):
-            # 从传回的 pop 文件夹中将结果文件取到 4_vasp_optimized 目录
-            task_dir = os.path.join(self.for_vasp_opt_dir, f"{parent}pop{pop}")
-            for job_i in node_jobs[pop]:
-                vasp_dir = mlp_contcar_files[job_i].split("CONTCAR_")[1]
-                shutil.copytree(
-                    f"{task_dir}/{vasp_dir}", f"{self.vasp_optimized_dir}/{vasp_dir}"
-                )
-            # 在成功完成 VASP 分步优化后，删除 3_for_vasp_opt/{parent}/pop{n} 文件夹以节省空间
-            shutil.rmtree(task_dir)
-        if machine_inform["context_type"] == "SSHContext":
-            # 如果调用远程服务器，则删除data级目录
-            shutil.rmtree(os.path.join(self.for_vasp_opt_dir, parent))
-        logging.info("Batch VASP optimization completed!!!")
-
     def read_vaspout_save_csv(self, molecules_prior: bool, relaxation: bool = False):
         """
         Read VASP output files in batches and save energy and density to corresponding CSV files in the directory
@@ -626,6 +509,17 @@ class VaspProcessing:
             writer.writerow(header)
             for data in datas:
                 writer.writerow(data)
+                
+        logging.info(
+            f"Maximum MLP Density: {max(mlp_densities)}, Structure Number: {numbers[mlp_densities.index(max(mlp_densities))]}"
+        )
+        logging.info(
+            f"Maximum Fine Density: {max(fine_densities)}, Structure Number: {numbers[fine_densities.index(max(fine_densities))]}"
+        )
+        if relaxation:
+            logging.info(
+                f"Maximum Final Density: {max(final_densities)}, Structure Number: {numbers[final_densities.index(max(final_densities))]}"
+            )
 
     def export_max_density_structure(self):
         """

{ion_csp-2.1.9.dist-info → ion_csp-2.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ion_CSP
-Version: 2.1.9
+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
@@ -28,7 +28,7 @@ Dynamic: home-page
 Dynamic: license-file
 Dynamic: requires-python
 
-# 基于分子/离子构型的晶体结构设计软件 V2.1
+# 基于分子/离子构型的晶体结构设计软件 V2.2
 
 ## 项目概述
 

{ion_csp-2.1.9.dist-info → ion_csp-2.2.1.dist-info}/RECORD

@@ -1,16 +1,16 @@
-ion_CSP/__init__.py,sha256=3in4RkuAl_VL3kDHDz_CHQn3zEBtH1Z-H8aFniQbQI8,356
+ion_CSP/__init__.py,sha256=r22zEoL_7sKE557XIpVNUnM5WcNc7i0k58ySIqd24_s,356
 ion_CSP/__main__.py,sha256=XlNCx5eMSrL7yld9ddSYXhjXvg2ZYGD_uk9LdqNabvs,74
-ion_CSP/convert_SMILES.py,sha256=HAexqf6HXZAqRuMww5BKmU68MIO3d7XIaUtPKv_QwMs,15595
-ion_CSP/empirical_estimate.py,sha256=oqZ-yPbcFCgc0MkOu2PU7JWRNm3fXHm6YRq-bozCZoo,37776
+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/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=JkgfkI7qHme1e8IxeYMTYum_vRXea7RzYfmmiAmO7KA,12125
 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=_mYlHpDVmSdIZR4SS5iglswY6NQoFJWzA2VLkt5JraE,16654
 ion_CSP/upload_download.py,sha256=HXxVQMUydEoHe2vV89wR7De4Ut1lEte6pmp8Q82decI,23800
-ion_CSP/vasp_processing.py,sha256=YhZxEg03n2lwDtoYzpXdUn329QzfOvp4XXm-qTIIIMA,33337
+ion_CSP/vasp_processing.py,sha256=Q4OotC5eK4RN4R3GZu5DnLk7wnkYSh-yC1oeGvrtT5U,28436
 ion_CSP/model/model.pt,sha256=5D9HTP5b7jUOv3kHltT71ORzhgt5p96awjbqC4oZVjQ,24649402
 ion_CSP/model/options/README.md,sha256=ifoeNXF2CfwqUjt3Xmh5qUl-e4hfP4eMV4EkqV7GU30,182
 ion_CSP/model/options/model.ckpt-4000000.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
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 ion_CSP/run/run_vasp_processing.py,sha256=hziE4cZwmIWvVaZtwHn9Dl35apYSLlMvSVIbCyd5mFg,1612
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