surface-construct 0.8.2__tar.gz → 0.9__tar.gz

{surface_construct-0.8.2/surface_construct.egg-info → surface_construct-0.9}/PKG-INFO

@@ -1,26 +1,32 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.8.2
+Version: 0.9
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
 Author-email: 0403114076@163.com
 License: GPL
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Operating System :: OS Independent
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase
 Requires-Dist: networkx
-Requires-Dist: numpy
 Requires-Dist: spglib
 Requires-Dist: pandas
 Requires-Dist: tqdm
-Requires-Dist: matplotlib
-Requires-Dist: scipy
 Requires-Dist: scikit-learn
 Requires-Dist: scikit-image
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
 
 # 基于分层采样策略的催化剂表面位点全局分析
 

{surface_construct-0.8.2 → surface_construct-0.9}/setup.py

@@ -6,19 +6,16 @@ with open("README.md", "r", encoding='utf-8') as f:
 install_requires = [
     'ase',
     'networkx',
-    'numpy',
     'spglib',
     'pandas',
     'tqdm',
-    'matplotlib',
-    'scipy',
     'scikit-learn',
     'scikit-image'
 ]
 
 setup(
     name='surface_construct',
-    version='0.8.2',
+    version='0.9',
     packages=['surface_construct'],
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',
@@ -30,7 +27,6 @@ setup(
     install_requires=install_requires,
     classifiers=[
         "Programming Language :: Python :: 3",
-        "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)",
         "Operating System :: OS Independent",
     ],
 )

surface_construct-0.9/surface_construct/__init__.py

@@ -0,0 +1,12 @@
+from surface_construct.structures.surface import Crystal, Surface, Slab, Termination
+from surface_construct.structures.surface import get_terminations_score
+from surface_construct.structures.surface_grid import SurfaceGrid, GridGenerator
+
+
+__all__ = ['SurfaceGrid',
+           'GridGenerator',
+           'Crystal',
+           'Surface',
+           'Slab',
+           'Termination',
+           ]

{surface_construct-0.8.2 → surface_construct-0.9}/surface_construct/db.py

@@ -6,7 +6,7 @@ from ase.db.core import now
 from ase.io.jsonio import write_json, read_json
 import os
 from ase.db.row import AtomsRow, row2dct
-from surface_construct.atoms import get_atoms_topo_id
+from surface_construct.utils.atoms import get_atoms_topo_id
 from surface_construct.utils import calc_hull_vertices, get_calc_info
 
 """

surface_construct-0.9/surface_construct/sg_sampler.py

@@ -0,0 +1,314 @@
+import numpy as np
+from scipy.spatial import cKDTree
+from scipy.spatial.distance import cdist
+from sklearn.cluster import KMeans as Cluster
+import random
+
+
+def name2sampler(name):
+    return globals()[name]
+
+
+def addition_samples(sg_obj, size=None, probability=None, **kwargs):
+    if 'seed' in kwargs:
+        seed = kwargs['seed']
+    else:
+        seed = None
+    if probability is None:
+        probability = {
+            "max_sigma": 0.2,  # 采样方法的概率
+            "max_diversity": 0.8,
+        }
+    if size is None:
+        size = 1
+
+    # 归一化
+    total = sum(probability.values())
+    if total != 1.0:
+        probability = {k: v / total for k, v in probability.items()}
+
+    rng = np.random.default_rng(seed)
+    method_list = rng.choice(list(probability.keys()), size=size, p=list(probability.values()))
+
+    point_idx = np.array([], dtype=int)
+    for method in method_list:
+        method_lower = method.lower()
+        if method_lower == 'max_sigma':
+            sampling_obj = MaxSigmaSGSampler(sg_obj)
+        elif method_lower == 'max_diversity':
+            sampling_obj = MaxDiversitySGSampler(sg_obj)
+        else:
+            raise NotImplementedError
+        point_idx = np.concatenate([point_idx, sampling_obj.samples(size=1, **kwargs)])  # 每种方法只采一个
+
+    return point_idx
+
+
+class SGSamplerBase:
+    def __init__(self, sg_obj, **kwargs):
+        self.sg_obj = sg_obj
+        self.threshold = kwargs.get('threshold', 0.37)  # 0.37 is half of H-H bond
+        self.weight = kwargs.get('weight', 1.0)  # 采样的几率，最后进行归一化处理
+        self.kwargs = kwargs
+
+    @property
+    def _pop_size(self):
+        return len(self.sg_obj.points)
+
+    @property
+    def _population(self):
+        """
+        默认的全体是 sg_obj.points 的 index
+        :return:
+        """
+        return range(self._pop_size)
+
+    def _append_sample_to_sg(self, point_idx=None):
+        """
+        将采样点加入到 sg_obj.sample_points 和相应的 vector
+
+        :return:
+        """
+        if point_idx is None:
+            point_idx = []
+        elif type(point_idx) is int:
+            point_idx = [point_idx]
+
+        for p in point_idx:
+            self.sg_obj.sample_idx = p
+
+    def _samples(self, size, **kwargs):
+        raise NotImplementedError
+
+    def samples(self, size=1, **kwargs):
+        result = []
+        curr_size = size
+        loop = 0
+        while len(result) < size and loop < 10:
+            point_idx = self._samples(size=curr_size, **kwargs)
+            filtered_idx = self.exclude_too_close_sample(point_idx)
+            self._append_sample_to_sg(point_idx=filtered_idx)
+            result += filtered_idx
+            curr_size = size - len(filtered_idx)
+            loop += 1
+        return result
+
+    def exclude_too_close_sample(self, idx_list, threshold=None):
+        if threshold is None:
+            threshold = self.threshold
+        if self.sg_obj.sample_idx is not None:
+            unique_idx_list = [i for i in idx_list if i not in self.sg_obj.sample_idx]
+            points = list(self.sg_obj.sample_points)
+        else:
+            unique_idx_list = idx_list[:]
+            points = []
+        new_idx_list = []
+        for idx in unique_idx_list:
+            p = self.sg_obj.points[idx]
+            if len(points) == 0:
+                points.append(p)
+                new_idx_list.append(idx)
+                continue
+            tree = cKDTree(points)
+            if len(tree.query_ball_point(x=p, r=threshold,p=2))==0:
+                points.append(p)
+                new_idx_list.append(idx)
+
+        if len(new_idx_list) != len(idx_list):
+            print(f"Exclude too close sample {set(idx_list)-set(new_idx_list)}")
+        return new_idx_list
+
+class KeyPointSGSampler(SGSamplerBase):
+    """
+    关键点采样，使用 vip_id
+    """
+    def _samples(self, **kwargs):
+        sample_idx = self.sg_obj.unique_vip_id
+        clusters = Cluster(n_clusters=len(sample_idx)).fit(self.sg_obj.vector)
+        self.sg_obj._clusters = clusters
+        return sample_idx
+
+    def samples(self, size=None, **kwargs):
+        point_idx = self._samples(**kwargs)
+        filtered_idx = self.exclude_too_close_sample(point_idx)
+        self._append_sample_to_sg(point_idx=filtered_idx)
+        return filtered_idx
+
+class RandomSGSampler(SGSamplerBase):
+    """
+    完全随机的选择点，仅用于测试，效率太低。
+    """
+    def __init__(self, sg_obj, **kwargs):
+        super().__init__(sg_obj, **kwargs)
+        if 'seed' in kwargs:
+            self.seed = kwargs['seed']
+        else:
+            self.seed = None
+
+    def _samples(self, size, **kwargs):
+        idx = random.sample(self._population, size)
+        return idx
+
+
+class MaxSigmaSGSampler(SGSamplerBase):
+    """
+    对最大误差的点进行采样
+    """
+    def _samples(self, size, **kwargs):
+        if 'energy' in self.sg_obj.grid_property:
+            # 如果已经读入了一些能量，则返回误差最大的点
+            sigma_array = self.sg_obj.grid_property['energy']
+            sigma0 = sigma_array.max()
+            idx_list = np.argwhere(sigma_array <= sigma0-0.1).flatten().tolist()
+            idx = random.sample(idx_list, size)
+            return idx
+        else:
+            raise "No energy for all population, pls do initial sampling first!"
+
+
+class MinEnergySGSampler(SGSamplerBase):
+    """
+    对最大误差的点进行采样
+    """
+    def _samples(self, size, **kwargs):
+        if 'energy' in self.sg_obj.grid_property:
+            E_array = self.sg_obj.grid_property['energy']
+            # 如果已经读入了一些能量，则返回能量最低的点 (<0.1eV 以内，然后随机选一个)
+            E0 = E_array.min()
+            idx_list = np.argwhere(E_array <= E0+0.1).flatten().tolist()
+            idx = random.sample(idx_list, size)
+            return idx
+        else:
+            raise "No energy for all population, pls do initial sampling first!"
+
+
+class InitialSGSampler(SGSamplerBase):
+    """
+    结合使用 KeyPointSampling 和 MaxDiversitySampling
+    """
+    def _samples(self, size=None, **kwargs):
+        # 先进行 KeyPoint sampling，数量不够再进行 Max diversity sampling
+        vip_idx = self.sg_obj.unique_vip_id
+        if size is None:
+            size = len(vip_idx)
+
+        if size == len(vip_idx):
+            # 已经排除了距离过近的点，而且已经加入到了sg_obj
+            sample_idx = KeyPointSGSampler(self.sg_obj, **self.kwargs).samples(**kwargs)
+        elif size < len(vip_idx):
+            print(f"The initial sampling size {size} is smaller than the number of key points {len(vip_idx)}.")
+            sample_idx = random.sample(vip_idx, size)
+            self._append_sample_to_sg(point_idx=sample_idx)
+        else:
+            sample_idx = KeyPointSGSampler(self.sg_obj, **self.kwargs).samples(**kwargs)
+            while len(sample_idx) < size:
+                adding_sample = MaxDiversitySGSampler(self.sg_obj).samples(size=size-len(sample_idx),**kwargs)
+                sample_idx = np.concatenate([sample_idx, adding_sample])
+        return sample_idx
+
+    def samples(self, size=1, **kwargs):
+        return self._samples(size=size, **kwargs)
+
+
+class MaxDiversitySGSampler(SGSamplerBase):
+    """
+    对当前采样结构差异最大的点进行采样
+    基本思路是这样的：
+        * 重新进行聚类，
+        * 判断已经采样点属于的类别，找出没有点的类别，空类
+        * 如果空类不止一个，比较这些空类中心与旧点的距离，选择距离最大的点。
+    """
+    def _samples(self, size, center=True, **kwargs):
+        """
+        :param size:
+        :param center: 是否取中心。如果不是，则取能量最小值的点。如果没有能量则报错。
+        :param kwargs:
+        :return:
+        """
+        # 判断是否有过往的采样点，如果没有，调用 InitialSampling
+        if len(self.sg_obj.sample_idx) == 0:
+            clusters = Cluster(n_clusters=size).fit(self.sg_obj.vector)
+            virgin = list(set(clusters.labels_))
+        else:
+            cluster_size = len(self.sg_obj.sample_idx) + size
+            nvirgin = 0
+            larger_clusters = None
+            larger_virgin = None
+            virgin = None
+            clusters = None
+            # 如果等于则停止，并保存 cluster
+            while nvirgin != size:
+                # 以 len(sample_idx) + size 作为新的聚类的size
+                clusters = Cluster(n_clusters=cluster_size).fit(self.sg_obj.vector)
+                labels = clusters.labels_[self.sg_obj.sample_idx]
+                labels_set = set(labels)
+                virgin = set(range(cluster_size)) - labels_set
+                nvirgin = len(virgin)
+                # 判断分类以后空类数目与size的大小
+                # 如果大于size，则减小size，并记录空类的数目
+                if nvirgin > size:
+                    cluster_size -= 1
+                    larger_clusters = clusters
+                    larger_virgin = virgin
+                # 如果小于 size 则增大size，检查上一个size是否有记录，如果有记录则使用上个size 的记录。从中随机选择size个点作为采样点。
+                elif nvirgin < size:
+                    cluster_size += 1
+                    if larger_clusters is not None:
+                        clusters = larger_clusters
+                        virgin = larger_virgin
+                        break
+        # 从 virgin 里面选取 size 个点
+        cluster_idx = random.sample(list(virgin), size)
+        if (not center) and 'energy' not in self.sg_obj.grid_property:
+            center = True
+            print("Warning: Can't get cluster minimum energy, use cluster center instead!")
+        if center:
+            # 取中心位置的格点
+            centers = clusters.cluster_centers_[cluster_idx]
+            center_dist = cdist(centers, self.sg_obj.vector)  # 计算每个点到中心的距离
+            point_idx = np.argmin(center_dist, axis=-1)
+        else:
+            # 取这些 clusters 中能量最小值点
+            point_idx = []
+            for c_id in cluster_idx:
+                p_idx = np.arange(len(self.sg_obj.points))[clusters.labels_ == c_id]
+                # 求这些点的能量最小值
+                p_energy = self.sg_obj.grid_energy[p_idx]
+                point_idx.append(p_idx[p_energy.argmin()])
+        # assign cluster to sg_obj
+        self.sg_obj._clusters = clusters
+        return point_idx
+
+
+class NewtonSGSampler(SGSamplerBase):
+    """
+    沿着受力方向进行采样
+    """
+
+    def _samples(self, size, **kwargs):
+        raise NotImplementedError
+
+
+class RandomWalk(SGSamplerBase):
+    """
+    从给定点出发随机行走进行采样
+    """
+    def _samples(self, size, **kwargs):
+        raise NotImplementedError
+
+
+class SystematicSGSampler(SGSamplerBase):
+    """
+    等距采样。主要用于测试。
+    """
+    def _samples(self, size, **kwargs):
+        if 'start' in kwargs:
+            start = kwargs['start']
+        else:
+            start = random.randint(0, self._pop_size)
+        stop = self._pop_size
+        indices = list(range(start, stop)) + list(range(0, start))
+        step = int(self._pop_size / size)
+        point_idx = [indices[i + n * step] for n, i in enumerate(range(size))]
+
+        return point_idx

{surface_construct-0.8.2 → surface_construct-0.9/surface_construct.egg-info}/PKG-INFO

@@ -1,26 +1,32 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.8.2
+Version: 0.9
 Summary: Surface termination construction especially for complex model, such as oxides or carbides.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
 Author-email: 0403114076@163.com
 License: GPL
 Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)
 Classifier: Operating System :: OS Independent
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: ase
 Requires-Dist: networkx
-Requires-Dist: numpy
 Requires-Dist: spglib
 Requires-Dist: pandas
 Requires-Dist: tqdm
-Requires-Dist: matplotlib
-Requires-Dist: scipy
 Requires-Dist: scikit-learn
 Requires-Dist: scikit-image
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: summary
 
 # 基于分层采样策略的催化剂表面位点全局分析
 

{surface_construct-0.8.2 → surface_construct-0.9}/surface_construct.egg-info/SOURCES.txt

@@ -2,16 +2,15 @@ LICENSE
 README.md
 setup.py
 surface_construct/__init__.py
-surface_construct/atoms.py
 surface_construct/db.py
 surface_construct/default_parameter.py
-surface_construct/sampling.py
-surface_construct/structure.py
-surface_construct/surface.py
-surface_construct/surface_grid.py
-surface_construct/utils.py
+surface_construct/sg_sampler.py
 surface_construct.egg-info/PKG-INFO
 surface_construct.egg-info/SOURCES.txt
 surface_construct.egg-info/dependency_links.txt
 surface_construct.egg-info/requires.txt
-surface_construct.egg-info/top_level.txt
+surface_construct.egg-info/top_level.txt
+tests/test_sampling1.py
+tests/test_sampling2.py
+tests/test_surface_grid.py
+tests/test_task.py

{surface_construct-0.8.2 → surface_construct-0.9}/surface_construct.egg-info/requires.txt

@@ -1,10 +1,7 @@
 ase
 networkx
-numpy
 spglib
 pandas
 tqdm
-matplotlib
-scipy
 scikit-learn
 scikit-image

surface_construct-0.9/tests/test_sampling1.py

@@ -0,0 +1,38 @@
+import pytest
+import ase.io
+
+from surface_construct.sg_sampler import InitialSGSampler, KeyPointSGSampler, MaxDiversitySGSampler
+from surface_construct import SurfaceGrid
+
+
+class TestSampling1:
+    """
+    Simple Ru 0001 suface
+    """
+    def setup_method(self):
+        self.atoms = ase.io.read('atoms_files/ru_0001_POSCAR')
+        self.sg_obj = SurfaceGrid(self.atoms, interval=0.1, ads_num=6, lpca=True)
+        self.sg_obj.initialize()
+
+    def teardown_method(self):
+        pass
+
+    def test_initial_sampling(self):
+        for size in range(1, 6):
+            sample_obj = InitialSGSampler(self.sg_obj)
+            samples = sample_obj.samples(size=size)
+            self.sg_obj.plot_cluster(figname=f'sampling_{size}')
+            self.sg_obj.del_sample()
+
+    def test_keypoint_sampling(self):
+        sample_obj = KeyPointSGSampler(self.sg_obj)
+        samples = sample_obj.samples()
+        self.sg_obj.plot_cluster(figname=f'KeyPoint_sampling')
+
+    def test_max_diversity_sampling(self):
+        sample_obj = MaxDiversitySGSampler(self.sg_obj)
+        samples = sample_obj.samples(size=4)
+        self.sg_obj.plot_cluster(figname=f'MaxDiversity_sampling')
+
+    def test_max_sigma_sampling(self):
+        pass

surface_construct-0.9/tests/test_sampling2.py

@@ -0,0 +1,44 @@
+import pytest
+import ase.io
+
+from surface_construct import SurfaceGrid
+from surface_construct.sg_sampler import InitialSGSampler, KeyPointSGSampler, MaxDiversitySGSampler
+
+class TestSampling2:
+    """
+    Cu-CuO interface
+    """
+    def setup_method(self):
+        atoms = ase.io.read('atoms_files/CuOx-Cu100-CONTCAR')
+        self.sg_obj = SurfaceGrid(atoms, interval=0.2, ads_num=6, lpca=False)
+        self.sg_obj.initialize()
+
+    def teardown_method(self):
+        pass
+
+    def test_initial_sampling(self):
+        for size in [4, 8, 16]:
+            sample_obj = InitialSGSampler(self.sg_obj)
+            samples = sample_obj.samples(size=size)
+            self.sg_obj.plot_cluster(figname=f'sampling_{size}')
+            self.sg_obj.del_sample()
+
+    def test_keypoint_sampling(self):
+        sample_obj = KeyPointSGSampler(self.sg_obj)
+        samples = sample_obj.samples()
+        self.sg_obj.plot_cluster(figname=f'KeyPoint_sampling')
+
+    def test_max_diversity_sampling(self):
+        sample_obj = MaxDiversitySGSampler(self.sg_obj)
+        samples = sample_obj.samples(size=10)
+        self.sg_obj.plot_cluster(figname=f'MaxDiversity_sampling')
+
+    def test_max_sigma_sampling(self):
+        pass
+
+    def test_exclude_too_close_sampling(self):
+        samples = [0,1,2,3]
+        sample_obj = KeyPointSGSampler(self.sg_obj)
+        result_sample = sample_obj.exclude_too_close_sample(samples)
+        print(self.sg_obj.points[samples])
+        print(result_sample)

surface_construct-0.9/tests/test_surface_grid.py

@@ -0,0 +1,105 @@
+import ase.io
+import pytest
+
+import numpy as np
+from ase.visualize import view
+from ase import Atoms
+import ase
+from surface_construct import GridGenerator
+from ase.cluster.cubic import FaceCenteredCubic
+from surface_construct import SurfaceGrid
+
+class TestSurfaceGrid:
+    def test_Cu_cluster(self):
+        """
+        GridGenerator.
+        Runtime is about 9s
+        :return:
+        """
+        surfaces = [(1, 0, 0), (1, 1, 0), (1, 1, 1)]
+        layers = [4, 4, 4]
+        lc = 3.61000
+        atoms = FaceCenteredCubic('Cu', surfaces, layers, latticeconstant=lc)
+
+        atoms.cell = [35, 35, 35]
+        atoms.pbc = False  # True is very slow
+        atoms.center()
+
+        gridgen = GridGenerator(atoms, interval=0.1)
+        grid = gridgen.grid
+        print(len(grid))
+
+    def test_Ag_cluster(self):
+        # Ag55
+        # Time: 4.23s
+        atoms = ase.io.read('atoms_files/Ag.xyz')
+        gridgen = GridGenerator(atoms, interval=0.2, subtype='cluster')
+        grid = gridgen.grid
+        print(len(grid))
+
+    def test_Ru0001_slab(self):
+        # Ru(0001)
+        # Time: 4.23s
+        atoms = ase.io.read('atoms_files/ru_0001_POSCAR')
+        gridgen = GridGenerator(atoms, interval=0.1, subtype='slab')
+        grid = gridgen.grid
+        print(len(grid))
+
+    def test_Ru0001_grid_graph(self):
+        # Ru(0001)
+        atoms = ase.io.read('atoms_files/ru_0001_POSCAR')
+        sg_obj = SurfaceGrid(atoms, interval=0.1, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        sg_obj.vectorize()
+        graph = sg_obj.grid_graph
+        vip = sg_obj.vip_id
+        print(len(vip))
+        print(sg_obj.vector_unit)
+        print(len(sg_obj.vector))
+
+    def test_In2O3_slab(self):
+        # In2O3. Should use larger scale.
+        atoms = ase.io.read('atoms_files/POSCAR_In2O3_110')
+        sg_obj = SurfaceGrid(atoms, interval=0.1, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        sg_obj.vectorize()
+        graph = sg_obj.grid_graph
+        vip = sg_obj.vip_id
+        print(len(vip))
+        print(sg_obj.vector_unit)
+
+    def test_Fe3C_slab(self):
+        atoms = ase.io.read('atoms_files/Fe3C001_07_CONTCAR')
+        sg_obj = SurfaceGrid(atoms, interval=0.1, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        sg_obj.vectorize()
+        graph = sg_obj.grid_graph
+        grid_site_label, site_dict = sg_obj.get_grid_site_type()
+        grid_index_label, index_dict = sg_obj.get_grid_index_type()
+        vip = sg_obj.vip_id
+        print(len(vip))
+        print(list(site_dict.keys()))
+
+    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)
+        grid = gridgen.grid
+        print(len(grid))
+
+    def test_interface1(self):
+        atoms = ase.io.read('atoms_files/CuOx-Cu100-CONTCAR')
+        sg_obj = SurfaceGrid(atoms, interval=0.2, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        sg_obj.vectorize()
+        vip = sg_obj.vip_id
+        uvip = sg_obj.unique_vip_id
+        print(len(vip), len(uvip))
+
+    def test_In2O3_4x4(self):
+        # This a large surface, contain about 75K points.
+        atoms = ase.io.read('atoms_files/POSCAR_In2O3_110')
+        superatoms = atoms.repeat([2,2,1])
+        sg_obj = SurfaceGrid(superatoms, interval=0.1, ads_num=6, lpca=False)
+        sg_obj.gridize(subtype='slab')
+        Lga = sg_obj._Lga
+        print(Lga.shape)