surface-construct 0.9.3__tar.gz → 0.10.1__tar.gz

{surface_construct-0.9.3/surface_construct.egg-info → surface_construct-0.10.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.9.3
+Version: 0.10.1
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
@@ -158,6 +158,8 @@ $$
 
 **TODO**
 
+* 计算位点 SALI （Structure-Activity Landscape Index），量化 activity cliffs，SALI = |ΔActivity| / (1 − Similarity)
+* 新增 PathSampler，用于在相邻的关键格点之间的扩散路径进行采样，使用 ase.neb.idpp 方法进行采样，使用 Delaunay 剖分找到相邻位点的路径。
 * 表面位点数据库
 * 多原子体系（内坐标受限体系）
 * 完善用户界面、例子、教程
@@ -167,5 +169,6 @@ $$
 
 [^Duvenaud]: [The Kernel Cookbook: Advice on Covariance functions](https://www.cs.toronto.edu/~duvenaud/)]
 [^BASC]: Shane Carr, Roman Garnett, Cynthia LoBASC: Applying Bayesian Optimization to the Search for Global Minima on Potential Energy Surfaces.
+
 [^向量空间转化]: 计算实空间和向量空间的相邻格点距离的映射系数，根据此系数将实空间的距离转化为向量空间距离。
 

{surface_construct-0.9.3 → surface_construct-0.10.1}/README.md

@@ -128,6 +128,8 @@ $$
 
 **TODO**
 
+* 计算位点 SALI （Structure-Activity Landscape Index），量化 activity cliffs，SALI = |ΔActivity| / (1 − Similarity)
+* 新增 PathSampler，用于在相邻的关键格点之间的扩散路径进行采样，使用 ase.neb.idpp 方法进行采样，使用 Delaunay 剖分找到相邻位点的路径。
 * 表面位点数据库
 * 多原子体系（内坐标受限体系）
 * 完善用户界面、例子、教程
@@ -137,5 +139,6 @@ $$
 
 [^Duvenaud]: [The Kernel Cookbook: Advice on Covariance functions](https://www.cs.toronto.edu/~duvenaud/)]
 [^BASC]: Shane Carr, Roman Garnett, Cynthia LoBASC: Applying Bayesian Optimization to the Search for Global Minima on Potential Energy Surfaces.
+
 [^向量空间转化]: 计算实空间和向量空间的相邻格点距离的映射系数，根据此系数将实空间的距离转化为向量空间距离。
 

{surface_construct-0.9.3 → surface_construct-0.10.1}/setup.py

@@ -15,7 +15,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.9.3',
+    version='0.10.1',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.9.3 → surface_construct-0.10.1}/surface_construct/structures/surface.py

@@ -7,7 +7,7 @@ import pandas as pd
 import spglib
 from tqdm import tqdm
 
-from surface_construct.utils.atoms import topo_identity, bondvalence, \
+from surface_construct.utils.atoms import topo_identity,dist_identity, get_atoms_topo_id, bondvalence, \
     refined_atoms, atoms2spg, coprime_factor, adj_matrix, topodist_matrix, atoms2graph, coordnum_adj
 
 
@@ -103,43 +103,31 @@ class Crystal(object):
 
 
 class Surface:
-    def __init__(self, crystal, hkl, refine=None):
+    def __init__(self, crystal, hkl):
         self.crystal = crystal
         self.hkl = hkl
         self.reduced_hkl = reduce_miller_indices(hkl)
         self.primary_hkl, self.peer_hkl = get_symmetry_miller(crystal.atoms,
                                                               self.reduced_hkl)
-        self._refine = bool(refine)  # 是否进行 refine
+        self._refine = None
         self._area = None
         self._surface_parameter = None
+        self.original_surface_parameter = None
 
     @property
-    def surface_parameter(self):
-        if self._surface_parameter is None:
-            slab = self.create_slab()
+    def surface_parameter(self, refine=False):
+        if refine != self._refine or self._surface_parameter is None:
+            slab = self.create_slab(refine=refine)
             len_ang = slab.atoms.cell.cellpar()
             self._surface_parameter = len_ang
         return self._surface_parameter
 
-    @property
-    def refine(self):
-        return self._refine
-
-    @refine.setter
-    def refine(self, v):
-        v = bool(v)
-        if v != self._refine:
-            self._refine = v
-            # 重设surface_parameter，重新计算
-            self._surface_parameter = None
-            self._area = None
-        else:  # do nothing
-            pass
+    @surface_parameter.setter
+    def surface_parameter(self, v):
+        self._surface_parameter = v
 
-    def create_slab(self, layers=3, vacuum=15.0, atoms=None, refine=None):
-        if refine is None:
-            refine = self.refine
-        slab = Slab(self, layers, vacuum, atoms=atoms, refine=refine)
+    def create_slab(self, layers=3, vacuum=15.0, atoms=None, refine=None, from_last=False):
+        slab = Slab(self, layers, vacuum, atoms=atoms, refine=refine, from_last=from_last)
         return slab
 
     @property
@@ -151,15 +139,25 @@ class Surface:
 
         return self._area
 
+    @area.setter
+    def area(self,v):
+        self._area = v
 
 class Slab(object):
-    """
-    TODO: 判断是否 refine 起到作用了？
-    """
-    def __init__(self, surface, layers=3, vacuum=15.0, atoms=None, refine=None):
+    def __init__(self, surface, layers=3, vacuum=15.0, atoms=None, refine=False, from_last=False):
+        """
+        TODO: construct from atoms without surface
+        :param surface:
+        :param layers:
+        :param vacuum:
+        :param atoms:
+        :param refine:
+        :param from_last: peel atoms from last index, default is from first.
+        """
         self.surface = surface
         self.layers = layers
         self.vacuum = vacuum
+        self.from_last = from_last
         if not atoms:
             atoms = ase.build.surface(surface.crystal.atoms,
                                       surface.primary_hkl,
@@ -169,7 +167,7 @@ class Slab(object):
         if refine:
             atoms = refined_atoms(atoms)
 
-        self.refine = bool(refine)  # 构造好了就要再更改了
+        self.refine = refine  # 构造好了就要再更改了
         self.atoms = atoms
         self.natoms = len(self.atoms)
         self.natoms_per_layer = int(self.natoms / layers)  # Dirty: atoms 变量必须包含整数倍的层
@@ -213,14 +211,19 @@ class Slab(object):
             self._adj_matrix = adj_matrix(self.atoms)
         return self._adj_matrix
 
-    def supercell(self, size=(1, 1, 1)):
-        multiple = size[0] * size[1] * size[2]
+    def supercell(self, size=(1, 1)):
+        """
+        TODO: super size the surface too.
+        :param size:
+        :return:
+        """
+        multiple = size[0] * size[1]
         if multiple == 1:
             return self
         # make supercell
         P = [[size[0], 0, 0],
              [0, size[1], 0],
-             [0, 0, size[2]]]
+             [0, 0, 1]]
         extended_atoms = ase.build.make_supercell(self.atoms, P, wrap=False)  # Note: wrap may change the atoms order.
         # reorder atoms
         new_atoms = ase.Atoms(cell=extended_atoms.cell, pbc=extended_atoms.pbc)
@@ -230,8 +233,10 @@ class Slab(object):
                 atoms_id = [i + self.natoms_per_layer * ilayer + self.natoms * icell
                             for i in range(self.natoms_per_layer)]
                 new_atoms.extend(extended_atoms[atoms_id])
-
-        super_slab = Slab(self.surface, self.layers, vacuum=self.vacuum, atoms=new_atoms)
+        # TODO: create new super surface
+        super_slab = Slab(self.surface, self.layers, vacuum=self.vacuum, atoms=new_atoms, from_last=self.from_last)
+        super_slab.surface.surface_parameter = new_atoms.cell.cellpar()
+        super_slab.surface.area = None
         super_slab.refine = True  # 不能在初始化时定义，否则会重构成单胞。但是这里为什么要定义为 True 呢？
         return super_slab
 
@@ -259,6 +264,10 @@ class Slab(object):
 
     @property
     def all_cn(self):
+        """
+        Slab 中所有原子的配位数
+        :return: 配位数列表，[{(原子序号，原子序号): 数量}]
+        """
         if self._all_cn is None:
             self._all_cn = coordnum_adj(self.adj_matrix)
 
@@ -266,19 +275,34 @@ class Slab(object):
 
     @property
     def bulk_cn(self):
+        """
+        Slab 中所有体相位置原子的配位数
+        :return: 配位数列表，[{(原子序号，原子序号): 数量}]
+        """
         if self._bulk_cn is None:
             self._bulk_cn = [self.all_cn[i] for i in self.bulk_id]
         return self._bulk_cn
 
     @property
     def skin_id(self):  # Dirty trick
+        """
+        表层 skin 的原子序号。假设体系有三层，以第一层为表层。
+        :return:
+        """
         if self._skin_id is None:
-            self._skin_id = list(range(0, self.natoms_per_layer))
-
+            if self.from_last:
+                self._skin_id = list(range(self.natoms_per_layer * (self.layers - 1),
+                                  self.natoms_per_layer * self.layers))
+            else:
+                self._skin_id = list(range(0, self.natoms_per_layer))
         return self._skin_id
 
     @property
     def bulk_id(self):  # Dirty trick
+        """
+        体相原子的原子序号。假设体系有三层，以中间层为表层。
+        :return:
+        """
         if self._bulk_id is None:
             self._bulk_id = list(range(self.natoms_per_layer,
                                        self.natoms_per_layer * (self.layers - 1)))
@@ -286,9 +310,16 @@ class Slab(object):
 
     @property
     def bottom_id(self):  # Dirty trick
+        """
+        底层原子的原子序号。假设体系有三层，以最下层为底层。
+        :return:
+        """
         if self._bottom_id is None:
-            self._bottom_id = list(range(self.natoms_per_layer * (self.layers - 1),
-                                         self.natoms_per_layer * self.layers))
+            if not self.from_last:
+                self._bottom_id = list(range(self.natoms_per_layer * (self.layers - 1),
+                                  self.natoms_per_layer * self.layers))
+            else:
+                self._bottom_id =  list(range(0, self.natoms_per_layer))
         return self._bottom_id
 
     def estimate_terminations(self, sheet_window=0.5):
@@ -324,18 +355,19 @@ class Slab(object):
             return self._sheet_list
 
         pos = self.atoms.positions
-        posz = pos[0:self.natoms_per_layer, 2]
+        skin_id = self.skin_id
+        posz = pos[skin_id, 2]
         zmin, zmax = pos[:, 2].min(), pos[:, 2].max()
         posz = posz - zmin if posz[0] - zmin < zmax - posz[0] else zmax - posz
-        enumerate_posz = sorted(enumerate(posz), key=lambda lst: lst[1])
-        posz = [i[1] for i in enumerate_posz]
-        posz_idx = [i[0] for i in enumerate_posz]  # 由小到大排列，从外表面到内部
+        sorted_posz = sorted(zip(skin_id,posz), key=lambda lst: lst[1])
+        posz = [i[1] for i in sorted_posz]
+        posz_idx = [i[0] for i in sorted_posz]  # 由小到大排列，从外表面到内部
         posz_mx, posz_my = np.meshgrid(posz, posz)
         posz_dist = np.abs(posz_mx - posz_my)
         idx_row, idx_col = np.argwhere(posz_dist < self.sheet_window).T
-        idx_row_set = set(idx_row)
+        idx_row_set = sorted([[i, posz[i]] for i in set(idx_row)], key=lambda lst: lst[1])  # 从外表面到內表面排序，否则在切除的时候会混乱
         sheet_list = []
-        for ir in idx_row_set:
+        for ir,_ in idx_row_set:
             idx_col_set = set([posz_idx[i] for i in idx_col[idx_row == ir]])
             if idx_col_set in sheet_list:
                 continue
@@ -357,6 +389,7 @@ class Slab(object):
         peel_list = []
         base_peel = set()
         for sheet in self.sheet_list:
+            base_peel.difference_update(sheet)  # 需要把本层相关的去掉
             peel_list += [base_peel.union(set(idx_list)) for n in range(1, len(sheet) + 1)
                           for idx_list in itertools.combinations(sheet, n)]
             base_peel.update(sheet)
@@ -365,7 +398,7 @@ class Slab(object):
 
         return self._peel_set
 
-    def get_all_terminations(self, sheet_window=0.5, unique=False):
+    def get_all_terminations(self, sheet_window=0.5, unique=False, id_type='topo'):
         """
         Extract all the termination for given miller indices
 
@@ -379,7 +412,7 @@ class Slab(object):
         terminations = [self.create_terminations(peel) for peel in peel_set]
 
         if unique:
-            terminations_dict = {termination.get_identity(): termination
+            terminations_dict = {termination.get_identity(id_type=id_type): termination
                                  for termination in tqdm(terminations)}
             print("Unique terminations count, ", len(terminations_dict))
             return terminations_dict
@@ -422,18 +455,22 @@ class Termination(object):
         self.bulk_id = slab.bulk_id
         self.bottom_id = slab.bottom_id
         self.dermis_id = sorted(list(set(self.skin_id) - set(peel_id)))  # 真皮层，为什么要排序？
-        self.termination_id = self.dermis_id + self.bulk_id + self.bottom_id
+        self.termination_id = [idx for idx in range(self.slab.natoms) if idx not in peel_id]
 
         self.atoms = atoms
         if atoms is None:
             self.atoms = self.slab.atoms[self.termination_id]
 
         # 根据 termination.atoms 重新对原子编号
-        self.atoms_dermis_id = np.arange(len(self.dermis_id))
-        self.atoms_bulk_id = np.arange(len(self.dermis_id),
-                                       len(self.dermis_id + self.bulk_id))
-        self.atoms_bottom_id = np.arange(len(self.dermis_id + self.bulk_id),
-                                         len(self.atoms))
+        if self.slab.from_last:
+            # TODO: dirty, add the case for both side, or disordered the index
+            self.atoms_dermis_id = np.arange(len(self.atoms)-len(self.dermis_id), len(self.atoms))
+            self.atoms_bulk_id = self.bulk_id[:]
+            self.atoms_bottom_id = self.bottom_id[:]
+        else:
+            self.atoms_dermis_id = np.arange(len(self.dermis_id))
+            self.atoms_bulk_id = np.arange(len(self.dermis_id), len(self.dermis_id + self.bulk_id))
+            self.atoms_bottom_id = np.arange(len(self.dermis_id + self.bulk_id), len(self.atoms))
 
         self._adj_matrix = None
         self._all_cn = None
@@ -445,6 +482,7 @@ class Termination(object):
 
         self._thickness = None
         self.identity = None
+        self.identity_type = None
         self.dsuc = None
 
     @property
@@ -488,7 +526,9 @@ class Termination(object):
         :return:
         """
         if self._atoms_cus_id is None:
-            _ = self.cus_cn  # 求 cus_cn 的过程中，顺带求 atoms_cus_id
+            skin_idx = list(self.atoms_dermis_id) + list(self.atoms_bulk_id)
+            self._atoms_cus_id = [idx for idx, item in zip(skin_idx, self.cus_cn)
+                                  if any([i != 0 for i in item.values()])]
         return self._atoms_cus_id
 
     @property
@@ -500,7 +540,7 @@ class Termination(object):
         """
         if self._cus_id is None:
             slab_idx = self.dermis_id + self.bulk_id
-            self._cus_id = [idx for idx, item in zip(slab_idx, self._cus_cn)
+            self._cus_id = [idx for idx, item in zip(slab_idx, self.cus_cn)
                             if any([i != 0 for i in item.values()])]
 
         return self._cus_id
@@ -516,9 +556,13 @@ class Termination(object):
             slab_bulk_cn = self.slab.bulk_cn
             result = []  # idx is the id of self.atoms
             for idx, item in zip(self.dermis_id, self.dermis_cn):  # Must take all surface layer into account.
+                if self.slab.from_last:
+                    i = idx - (self.layers - 1) * self.natoms_per_layer
+                else:
+                    i = idx
                 cus_item = {}
                 for k in item:
-                    cus_item[k] = slab_bulk_cn[idx][k] - item[k]
+                    cus_item[k] = slab_bulk_cn[i][k] - item[k]
                 result.append(cus_item)
             for idx, item in zip(self.bulk_id, terminal_bulk_cn):
                 cus_item = {}
@@ -528,16 +572,10 @@ class Termination(object):
 
             self._cus_cn = result  # _cus_cn 中不仅有cus的cn，还有其他的cn，只是都是0而已
 
-        # self._atoms_cus_id 也在此处定义
-        if self._atoms_cus_id is None:
-            self._atoms_cus_id = [idx for idx, item in enumerate(self._cus_cn)
-                                  if any([i != 0 for i in item.values()])]
-
         # 接下来，我们构造新的 cus_cn
-        # cus_cn 是一个dict：{atoms_cus_id: cn_dict}
-        cus_cn = {idx: self._cus_cn[idx] for idx in self._atoms_cus_id}
-
-        return cus_cn
+        # cus_cn 是一个dict：{cus_id: cn_dict}
+        # cus_cn = {idx: self._cus_cn[idx] for idx in self.cus_id}
+        return self._cus_cn
 
     def pseudo_layer(self, fromslab=False):
         """
@@ -555,19 +593,28 @@ class Termination(object):
 
         return np.concatenate([dermis, complement])
 
-    def get_identity(self):
-        if not self.identity:
+    def get_identity(self, id_type='topo'):
+        if (not self.identity) or (self.identity_type!=id_type):
             pseudo_skin_atoms = self.atoms[self.atoms_cus_id]
             # add ghost at the top of the surface, in order to distinguish the surface
             pseudo_skin_z = pseudo_skin_atoms.positions[:, 2]
-            tips = np.concatenate(np.argwhere(pseudo_skin_z == pseudo_skin_z.min()))  # get the tip atoms id
-            ghost_xyz = pseudo_skin_atoms.positions[tips]
-            ghost_xyz[:, 2] = ghost_xyz[:, 2] - 0.5
+            if self.slab.from_last:  # dirty: index 0 at bottom and max index at top
+                tips = np.concatenate(np.argwhere(pseudo_skin_z == pseudo_skin_z.max()))  # get the tip atoms id
+                ghost_xyz = pseudo_skin_atoms.positions[tips]
+                ghost_xyz[:, 2] = ghost_xyz[:, 2] + 0.5
+            else:
+                tips = np.concatenate(np.argwhere(pseudo_skin_z == pseudo_skin_z.min()))  # get the tip atoms id
+                ghost_xyz = pseudo_skin_atoms.positions[tips]
+                ghost_xyz[:, 2] = ghost_xyz[:, 2] - 0.5
             pseudo_skin_atoms.extend(ase.Atoms('X' + str(len(ghost_xyz)), ghost_xyz))
-
-            identity = topo_identity(topodist_matrix(adj_matrix(pseudo_skin_atoms)))
-
+            if id_type == 'topo':
+                identity = get_atoms_topo_id(pseudo_skin_atoms)
+            elif id_type == 'dist':
+                identity = dist_identity(pseudo_skin_atoms)
+            else:
+                raise NotImplementedError
             self.identity = identity
+            self.identity_type = id_type
         return self.identity
 
     def get_identity_fast(self):

{surface_construct-0.9.3 → surface_construct-0.10.1}/surface_construct/structures/surface_grid.py

@@ -424,10 +424,13 @@ class SurfaceGrid:
         self.rcutoff = rcutoff
 
         if type(rsub) in (list, tuple, np.ndarray):
-            assert len(rsub) == len(atoms)
+            if not len(rsub) == len(atoms):
+                raise ValueError("Not all atoms have radius!")
             self.rsub = rsub
         elif type(rsub) == dict:
             self.rsub = [rsub.get(n) or rsub.get(chemical_symbols(n)) for n in atoms.numbers]
+            if None in self.rsub:
+                raise ValueError("Not all elements have radius!")
         elif type(rsub) == str:
             if rsub == 'covalent_radii' or rsub == 'natural_cutoff':
                 self.rsub = natural_cutoffs(atoms)
@@ -726,9 +729,8 @@ class SurfaceGrid:
         :return:
         """
         kwargs['pbc'] = kwargs.get('pbc',self.pbc)
-        kwargs['r0_dict'] = kwargs.get('r0_dict',
-                                       {atomnum:self.rads + self.rsub[atomnum]
-                                        for atomnum,_ in self.species})
+        kwargs['r0_dict'] = kwargs.get('r0_dict', {atomnum:self.rads+r
+                                                   for atomnum,r in zip(self.atoms.numbers, self.rsub)})
         vgen = MLATVectorGen(self.atoms, vlen=self.vlen, weight_func=wf,
                              lpca=self.lpca, pca_ratio=pca_ratio,
                              rcutoff=self.rcutoff, **kwargs)
@@ -765,7 +767,8 @@ class SurfaceGrid:
             sc = [min(vlen,c) for s,c in self.species]
             v0 = np.concatenate(np.array([[np.inf]*c for c in sc]))
             for idx, s in enumerate(self.species):
-                r = self.rsub[s[0]] + self.rads
+                num = list(self.atoms.numbers).index(s[0])
+                r = self.rsub[num] + self.rads
                 v1 = v0.copy()  # top
                 idx0 = sum(sc[:idx])
                 v1[idx0] = r

{surface_construct-0.9.3 → surface_construct-0.10.1}/surface_construct/utils/atoms.py

@@ -10,21 +10,6 @@ from hashlib import md5
 import spglib
 
 
-ATOM_COORDNUM = {
-    0: 1,
-    1: 1,
-    6: 4,
-    7: 3,
-    8: 2,
-    26: 12,
-}  # Maximum coordinate number for organic neutral mols.
-
-
-INITIAL_MAGMOM = {
-    26: 3,
-}
-
-
 def default_bv_parameter(atomnums=None):
     # 使用共价键长之和来生成
     radii = ase.data.covalent_radii.copy()
@@ -37,9 +22,6 @@ def default_bv_parameter(atomnums=None):
     return bv_parameter
 
 
-BONDVALENCE_PARAMETERS = default_bv_parameter()
-
-
 def round10(x):
     return round(x, 10)
 
@@ -209,6 +191,8 @@ def get_sub_matrix(mat, lst):
 def topo_identity(dm):
     """
     计算 topo 结构的标识。
+    If consider chirality of molecules, need add three non-collinear
+    points of cartesian coordinates. 通过主轴和二轴添加
     :param dm: topodist_matrix
     :return:
     """
@@ -231,6 +215,18 @@ def get_atoms_topo_id(atoms, *args, **kwargs):
     return ids
 
 
+def dist_identity(atoms, mic=True):
+    dm = atoms.get_all_distances(mic=mic)
+    n, m = dm.shape
+    I = np.identity(n)
+    dm = dm + atoms.get_atomic_numbers() * I  # set diagonal elements as atomic number
+    eigval = np.linalg.eigvalsh(dm).round(5)
+    content = ' '.join(map(str, np.sort(eigval)))
+    identity = md5(content.encode('utf-8')).hexdigest()
+
+    return identity
+
+
 def getghost(atoms):
     # get X index
     x = [idx for idx, i in enumerate(atoms.get_chemical_symbols()) if i == 'X']

{surface_construct-0.9.3 → surface_construct-0.10.1/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.9.3
+Version: 0.10.1
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
@@ -158,6 +158,8 @@ $$
 
 **TODO**
 
+* 计算位点 SALI （Structure-Activity Landscape Index），量化 activity cliffs，SALI = |ΔActivity| / (1 − Similarity)
+* 新增 PathSampler，用于在相邻的关键格点之间的扩散路径进行采样，使用 ase.neb.idpp 方法进行采样，使用 Delaunay 剖分找到相邻位点的路径。
 * 表面位点数据库
 * 多原子体系（内坐标受限体系）
 * 完善用户界面、例子、教程
@@ -167,5 +169,6 @@ $$
 
 [^Duvenaud]: [The Kernel Cookbook: Advice on Covariance functions](https://www.cs.toronto.edu/~duvenaud/)]
 [^BASC]: Shane Carr, Roman Garnett, Cynthia LoBASC: Applying Bayesian Optimization to the Search for Global Minima on Potential Energy Surfaces.
+
 [^向量空间转化]: 计算实空间和向量空间的相邻格点距离的映射系数，根据此系数将实空间的距离转化为向量空间距离。
 

{surface_construct-0.9.3 → surface_construct-0.10.1}/surface_construct.egg-info/SOURCES.txt

@@ -23,5 +23,6 @@ surface_construct/utils/atoms.py
 surface_construct/utils/weight_functions.py
 tests/test_sampling1.py
 tests/test_sampling2.py
+tests/test_simple_surface.py
 tests/test_surface_grid.py
 tests/test_task.py

surface_construct-0.10.1/tests/test_simple_surface.py

@@ -0,0 +1,39 @@
+import pytest
+import ase.build
+from surface_construct.structures.surface import Surface, Crystal, Slab
+
+class TestSimpleSurface:
+    def test_Cu111_termination(self):
+        bulk = ase.build.bulk('Cu')
+        c = Crystal(bulk)
+        s = Surface(c, (1,1,1))
+
+        slab1 = Slab(s)
+        superslab1 = slab1.supercell((3,3))
+        terms = superslab1.get_all_terminations(unique=True)
+        atoms_list = [t.atoms for t in terms]
+
+        slab2 = Slab(s, from_last=True)
+        superslab2 = slab2.supercell((3,3))
+        terms_last = superslab2.get_all_terminations(unique=True)
+        assert len(terms) == len(terms_last) == 23
+        assert set(terms) == set(terms_last)
+
+    def test_Cu211_termination(self):
+        bulk = ase.build.bulk('Cu')
+        c = Crystal(bulk)
+        s = Surface(c, (2,1,1))
+
+        slab1 = Slab(s, layers=6)
+        slab1.set_layers(3)
+        superslab1 = slab1.supercell((2,3))
+        terms = superslab1.get_all_terminations(unique=True)
+
+        slab2 = Slab(s, from_last=True, layers=6)
+        slab2.set_layers(3)
+        superslab2 = slab2.supercell((2,3))
+        terms_last = superslab2.get_all_terminations(unique=True)
+        assert len(terms) == len(terms_last)
+        assert set(terms) == set(terms_last)
+
+

{surface_construct-0.9.3 → surface_construct-0.10.1}/tests/test_surface_grid.py

@@ -53,6 +53,8 @@ class TestSurfaceGrid:
         sg_obj.vectorize()
         graph = sg_obj.grid_graph
         vip = sg_obj.vip_id
+        uvip = sg_obj.unique_vip_id
+        uvip_points = sg_obj.points[uvip]  # [[x,y,z],....]  Nx3
         print(len(vip))
         print(sg_obj.vector_unit)
         print(len(sg_obj.vector))
@@ -92,7 +94,7 @@ class TestSurfaceGrid:
 
     def test_ZSM5(self):
         atoms = ase.io.read('atoms_files/zsm5.cif')
-        gridgen = GridGenerator(atoms, interval=0.2, subtype='bulk', rsub='vdw_radii', scale=1.0)
+        gridgen = GridGenerator(atoms, interval=0.5, subtype='bulk', rsub='vdw_radii', scale=1.0)
         grid = gridgen.grid
         print(len(grid))