surface-construct 0.9__tar.gz → 0.9.1__tar.gz

{surface_construct-0.9/surface_construct.egg-info → surface_construct-0.9.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.9
+Version: 0.9.1
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.9 → surface_construct-0.9.1}/setup.py

@@ -1,4 +1,4 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 
 with open("README.md", "r", encoding='utf-8') as f:
     long_description = f.read()
@@ -15,8 +15,8 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.9',
-    packages=['surface_construct'],
+    version='0.9.1',
+    packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',
     author='ren',

surface_construct-0.9.1/surface_construct/structures/__init__.py

@@ -0,0 +1,50 @@
+class AdsGridCombiner:
+    def __init__(self, sg_obj, ads_obj,
+                 **kwargs):
+        """
+        :param sg_obj: 表面格点
+        :param ads_obj: 吸附分子，包含Atoms，主轴，内坐标列表，根据这些参数可以得到分子坐标
+        :param kwargs:
+        """
+        self.atoms = None
+        self.sg_obj = sg_obj
+        self.ads_obj = ads_obj
+        self.kwargs = kwargs
+        if self.sg_obj.atoms.calc is not None:
+            self.calc = self.sg_obj.atoms.calc
+        else:
+            if self.ads_obj.atoms.calc is not None:
+                self.calc = self.ads_obj.atoms.calc
+            else:
+                self.calc = None
+
+    def get_atoms(self, grid_idx=None,**kwargs):
+        """
+        将分子放置于 grid_idx 格点上
+        :param grid_idx: 格点序号。默认是随机idx。
+        :return: 组合后的 Atoms
+        """
+        attitude = kwargs.get('attitude') # 分子姿态，分子主轴的夹角
+        internal_coord = kwargs.get('internal_coord')  # 分子内坐标
+        ads_atoms = self.ads_obj.atoms.copy()
+        # TODO: 先进性 rotate and 改变分子构象
+        site = self.sg_obj.points[grid_idx]
+        # TODO: get_z 去更新 site 的坐标
+        site = self._get_z(site, ads_atoms)
+        ads_atoms.set_positions(ads_atoms.get_positions() +
+                                (site - ads_atoms.get_center_of_mass()))
+
+        atoms = self.sg_obj.atoms.copy()
+        atoms += ads_atoms
+        atoms.calc = self.calc
+        self.atoms = atoms
+        return atoms
+
+    def _get_z(self, xyz0, ads_atoms):
+        """
+        由于分子可能会与表面冲突，调整分子的高度可以避免
+        事实上调整的是沿着格点法向向量的距离 xyz = xyz0 + r×d
+        :return:
+        """
+        xyz = xyz0
+        return xyz

surface_construct-0.9.1/surface_construct/structures/adsorbate.py

@@ -0,0 +1,38 @@
+import numpy as np
+from ase import Atoms
+
+class Adsorbate:
+    """
+    吸附分子的类，包含质心，内坐标，主轴
+    """
+    def __init__(self, atoms, **kwargs):
+        # TODO：加上半径的参数，计算分子半径
+        self.atoms = atoms
+        self.internal_coords = dict()
+        self.kwargs = kwargs
+        self._rads = 0.76 # 默认是碳原子的共价半径
+
+    @property
+    def com(self):
+        return self.atoms.center_of_mass()
+
+    @property
+    def principal_axis(self):
+        # 分子主轴向量
+        evals, evecs = self.atoms.get_moments_of_inertia(vectors=True)
+        return evecs[np.argmin(np.abs(evals))]
+
+    @property
+    def rads(self):
+        # 分子的半径，sg_obj 构造时作为参考
+        # TODO: 计算分子半径
+        return self._rads
+
+    @rads.setter
+    def rads(self, value):
+        self._rads = value
+
+    @property
+    def natoms(self):
+        return len(self.atoms)
+