ion-CSP 2.1.3__py3-none-any.whl → 2.1.5__py3-none-any.whl

ion_CSP/__init__.py

@@ -1,8 +1,8 @@
 __author__ = "Ze Yang"
 __contact__ = "yangze1995007@163.com"
 __license__ = "MIT"
-__version__ = "2.1.3"
-__date__ = "2025-06-11"
+__version__ = "2.1.5"
+__date__ = "2025-06-16"
 
 
 try:

ion_CSP/gen_opt.py

@@ -4,11 +4,12 @@ import time
 import shutil
 import logging
 import subprocess
+import importlib.resources
+from typing import List
 from ase.io import read
+from dpdispatcher import Machine
 from pyxtal import pyxtal
 from pyxtal.msg import Comp_CompatibilityError, Symm_CompatibilityError
-from dpdispatcher import Machine
-from typing import List
 from ion_CSP.log_and_time import redirect_dpdisp_logging
 
 
@@ -18,30 +19,32 @@ class CrystalGenerator:
         Initialize the class based on the provided ionic crystal composition structure files and corresponding composition numbers.
         """
         redirect_dpdisp_logging(os.path.join(work_dir, "dpdispatcher.log"))
-        self.script_dir = os.path.dirname(__file__)
-        self.mlp_opt_file = os.path.join(self.script_dir, "mlp_opt.py")
-        self.model_file = os.path.join(self.script_dir, "../../model/model.pt")
+        # self.script_dir = os.path.dirname(__file__)
+        # self.mlp_opt_file = os.path.join(self.script_dir, "mlp_opt.py")
+        # self.model_file = os.path.join(self.script_dir, "../../model/model.pt")
+        self.mlp_opt_file = importlib.resources.files("ion_CSP").joinpath("mlp_opt.py")
+        self.model_file = importlib.resources.files("ion_CSP.model").joinpath("model.pt")
         # 获取当前脚本的路径以及同路径下离子晶体组分的结构文件, 并将这一路径作为工作路径来避免可能的错误
         self.base_dir = work_dir
         os.chdir(self.base_dir)
         self.ion_numbers = ion_numbers
         self.species = species
         self.species_paths = []
-        ion_atomss, species_atomss = [], []
+        ion_atomss, species_atoms = [], []
         # 读取离子晶体各组分的原子数，并在日志文件中记录
         for ion, number in zip(self.species, self.ion_numbers):
             species_path = os.path.join(self.base_dir, ion)
             self.species_paths.append(species_path)
             species_atom = len(read(species_path))
-            species_atomss.append(species_atom)
-            species_atoms = species_atom * number
-            ion_atomss.append(species_atoms)
+            species_atoms.append(species_atom)
+            ion_atoms = species_atom * number
+            ion_atomss.append(ion_atoms)
         self.cell_atoms = sum(ion_atomss)
         logging.info(
             f"The components of ions {self.species} in the ionic crystal are {self.ion_numbers}"
         )
         logging.info(
-            f"The number of atoms for each ion is: {species_atomss}, and the total number of atoms is {self.cell_atoms}"
+            f"The number of atoms for each ion is: {species_atoms}, and the total number of atoms is {self.cell_atoms}"
         )
         self.generation_dir = os.path.join(self.base_dir, "1_generated")
         os.makedirs(self.generation_dir, exist_ok=True)
@@ -199,14 +202,10 @@ class CrystalGenerator:
             logging.info("Start running phonopy processing ...")
             for _, filename in POSCAR_file_index_pairs:
                 self._single_phonopy_processing(filename=filename)
-            # 准备dpdispatcher运行所需的文件，将其复制到primitive_cell文件夹中
-            self.required_files = [self.mlp_opt_file, self.model_file]
-            for file in self.required_files:
-                shutil.copy(file, self.primitive_cell_dir)
+            # 在 phonopy 成功进行对称化处理后，删除 1_generated/POSCAR_Files 文件夹以节省空间
             logging.info(
                 "The phonopy processing has been completed!!\nThe symmetrized primitive cells have been saved in POSCAR format to the primitive_cell folder."
             )
-            # 在 phonopy 成功进行对称化处理后，删除 1_generated/POSCAR_Files 文件夹以节省空间
             shutil.rmtree(self.POSCAR_dir)
         except FileNotFoundError:
             logging.error(
@@ -215,6 +214,7 @@ class CrystalGenerator:
             raise FileNotFoundError(
                 "There are no POSCAR structure files after generating.\nPlease check the error during generation"
             )
+        
 
     def dpdisp_mlp_tasks(self, machine: str, resources: str, nodes: int = 1):
         """
@@ -222,6 +222,10 @@ class CrystalGenerator:
         """
         # 调整工作目录，减少错误发生
         os.chdir(self.primitive_cell_dir)
+        # 准备dpdispatcher运行所需的文件，将其复制到primitive_cell文件夹中
+        self.required_files = [self.mlp_opt_file, self.model_file]
+        for file in self.required_files:
+            shutil.copy(file, self.primitive_cell_dir)
         # 读取machine和resources的参数
         if machine.endswith(".json"):
             machine = Machine.load_from_json(machine)

ion_CSP/model/options/README.md

@@ -0,0 +1,5 @@
+# 目录 ./model
+用于存放所调用的机器学习势文件，文件名必须为 model.pt。
+
+# 目录 ./model/options
+用于存放其他机器学习势文件，文件名任意。

ion_CSP/param/INCAR_0

@@ -0,0 +1,16 @@
+SYSTEM = ION_CSP
+NPAR = 4
+PREC = Accurate 
+ENCUT = 800
+EDIFF = 1e-4  # 1e-6
+IBRION = -1
+ISMEAR = 0 ; SIGMA = 0.05
+#No writing charge density and wavefunction 
+LCHARG = FALSE 
+LWAVE = FALSE 
+#Target Pressure 
+#PSTRESS = 100 
+#Finer optimization 
+EDIFFG = -0.05  # 1e-4
+KSPACING = 0.25 
+IVDW = 11

ion_CSP/param/INCAR_1

@@ -0,0 +1,19 @@
+SYSTEM = ION_CSP
+NPAR = 4
+PREC = Accurate 
+ENCUT = 600  # 800
+EDIFF = 1e-4  # 1e-6
+IBRION = 2 
+ISIF = 8 
+NSW = 300  # 200
+ISMEAR = 0 ; SIGMA = 0.05 
+POTIM = 0.05 
+#No writing charge density and wavefunction 
+LCHARG = FALSE 
+LWAVE = FALSE 
+#Target Pressure 
+#PSTRESS = 100 
+#Finer optimization 
+EDIFFG = -0.05  # 1e-4
+KSPACING = 0.7  # 0.25 
+IVDW = 12

ion_CSP/param/INCAR_2

@@ -0,0 +1,19 @@
+SYSTEM = ION_CSP
+NPAR = 4
+PREC = Accurate 
+ENCUT = 800
+EDIFF = 1e-6
+IBRION = 2 
+ISIF = 8 
+NSW = 300  # 200
+ISMEAR = 0 ; SIGMA = 0.05 
+POTIM = 0.05 
+#No writing charge density and wavefunction 
+LCHARG = FALSE 
+LWAVE = FALSE 
+#Target Pressure 
+#PSTRESS = 100 
+#Finer optimization 
+EDIFFG = -0.02
+KSPACING = 0.5
+IVDW = 12

ion_CSP/param/INCAR_3

@@ -0,0 +1,19 @@
+SYSTEM = ION_CSP
+NPAR = 4
+PREC = Accurate 
+ENCUT = 800
+EDIFF = 1e-6
+IBRION = 2 
+ISIF = 3 
+NSW = 300  # 200
+ISMEAR = 0 ; SIGMA = 0.05 
+POTIM = 0.05 
+#No writing charge density and wavefunction 
+LCHARG = FALSE 
+LWAVE = FALSE 
+#Target Pressure 
+#PSTRESS = 100 
+#Finer optimization 
+EDIFFG = -0.02
+KSPACING = 0.5
+IVDW = 12