surface-construct 0.11__tar.gz → 0.12__tar.gz

{surface_construct-0.11/surface_construct.egg-info → surface_construct-0.12}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.11
-Summary: Surface termination construction especially for complex model, such as oxides or carbides.
+Version: 0.12
+Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
 Author-email: 0403114076@163.com

{surface_construct-0.11 → surface_construct-0.12}/setup.py

@@ -15,13 +15,13 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.11',
+    version='0.12',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',
     author='ren',
     author_email='0403114076@163.com',
-    description='Surface termination construction especially for complex model, such as oxides or carbides.',
+    description='Surface construction and surface reaction sampling tools.',
     long_description=long_description,
     long_description_content_type="text/markdown",
     install_requires=install_requires,

{surface_construct-0.11 → surface_construct-0.12}/surface_construct/structures/adsorbate.py

@@ -5,7 +5,7 @@ from ase.geometry.analysis import Analysis as ase_Analysis
 from ase.geometry.distance import distance as ase_distance
 from scipy.spatial import cKDTree
 
-from surface_construct.utils.atoms import atoms2graph, atoms_regulate, set_dihedrals
+from surface_construct.utils.atoms import atoms2graph, atoms_regulate, set_dihedrals, topodist_matrix, topo_identity
 from surface_construct.utils.geometry import dih_grid, sample_rotations_with_symmetry, view_samples, \
     estimate_rotation_samples
 from surface_construct.utils.pymsym_wrapper import get_pure_rotations, get_point_group, get_Cn
@@ -64,9 +64,12 @@ class Adsorbate:
                 f"    Point Group: {self.point_group}",
                 f"    Radius: {self.rads}",
                 f"    Principal axis: [{px:8.3f}, {py:8.3f}, {pz:8.3f}] ",
-                f"    Number of dihedral: {len(self.all_dihedrals)}"]
+                ]
         if self.dihedral_delta:
-            info.append(f"    Number of dihedral grid: {len(self.dihedral_grid)}",)
+            info+=[
+                f"    Number of dihedral grid: {len(self.dihedral_grid)}",
+                f"    Number of dihedral: {len(self.all_dihedrals)}",
+            ]
         info += [f"    Number of symmetry rotation operations: {len(self.symmetry_rotation_operations)}",
                 f"    Number of symmetry rotations: {len(self._symmetry_rotations)}",]
         if self.rotation_delta:
@@ -90,11 +93,14 @@ class Adsorbate:
         将分子旋转到主轴 = z, 次主轴=x, 第三轴 = y
         """
         # com to 0,0,0
+        constraints = self.atoms.constraints.copy()  # 需要先消除限制，因为会影响set_com 和旋转
+        self.atoms.constraints = []
         if len(self.atoms) > 1:
             atoms_regulate(self.atoms)
         else:
             self.atoms.set_center_of_mass([0.,0.,0.])
         self.is_regulated = True
+        self.atoms.constraints = constraints
 
     @property
     def com(self):
@@ -106,8 +112,8 @@ class Adsorbate:
     @property
     def principal_axis(self):
         # 分子主轴向量
-        if not self.is_regulated:
-            self.regulate()
+        #if not self.is_regulated:
+        #    self.regulate()
         evals, evecs = self.atoms.get_moments_of_inertia(vectors=True)
         return evecs[np.argmin(np.abs(evals))]
 
@@ -216,6 +222,12 @@ class Adsorbate:
 
         return self._atoms_graph
 
+    @property
+    def topo_id(self):
+        dm = topodist_matrix(self._adj_matrix)
+        ids = topo_identity(dm)
+        return ids
+
     def get_dihedral_mask(self, dihedral: Tuple[int, int, int, int]) -> set:
         """
         为二面角生成移动的 mask indices

{surface_construct-0.11 → surface_construct-0.12}/surface_construct/structures/combiner.py

@@ -120,6 +120,10 @@ class AdsGridCombiner:
                 rotation:Sequence=None,
                 dock_point:int=None) -> ase.Atoms:
         from scipy.spatial.transform import Rotation as R
+
+        atoms = self.ads_obj.atoms.copy()
+        constraints = atoms.constraints.copy()  # 需要先消除限制，因为会影响set_com 和旋转
+        atoms.constraints = []
         if dih_value is not None:
             dih_dict = self.ads_obj.get_dihedrals(dih_value=dih_value)
             atoms = set_dihedrals(self.ads_obj.atoms,dih_dict)
@@ -134,6 +138,7 @@ class AdsGridCombiner:
             atoms.positions = R.from_quat(rotation, scalar_first=True).apply(atoms.positions)
 
         atoms.positions += xyz # move atoms
+        atoms.constraints = constraints  # 重新找回 constraints
         return atoms
 
     def get_vip_rot(self)->Sequence:

{surface_construct-0.11 → surface_construct-0.12}/surface_construct/tasks/__init__.py

@@ -11,4 +11,5 @@
 3. obj.run 运行任务
 4. 分析和作图
 """
-from .sitesampling import SurfaceSiteSampleTask
+from .sitesampling import SurfaceSiteSampleTask
+from .afm import AFMTask

surface_construct-0.12/surface_construct/tasks/afm.py

@@ -0,0 +1,120 @@
+import datetime
+
+import ase.io
+import numpy as np
+from ase import Atoms
+from ase.constraints import FixAtoms, dict2constraint
+from .sitesampling import SurfaceSiteSampleTask
+
+def update_fixatoms_index(atoms:Atoms, idx:int):
+    c_list = []
+    for c in atoms.constraints:
+        if isinstance(c, FixAtoms):
+            dct = c.todict()
+            dct['kwargs']['indices'] = [i+idx for i in dct['kwargs']['indices']]
+            new_c = dict2constraint(dct)
+            c_list.append(new_c)
+    return c_list
+
+def get_topo_id(A,nl=None):  # 替代老的
+    from ase.geometry.analysis import Analysis as ase_Analysis
+    from surface_construct.utils.atoms import topodist_matrix, topo_identity
+    analysis = ase_Analysis(A, nl=nl)
+    adj_matrix = analysis.adjacency_matrix[0].toarray()
+    dm = topodist_matrix(adj_matrix)
+    ids = topo_identity(dm)
+    return ids
+
+class AFMTask(SurfaceSiteSampleTask):
+
+    def irun(self,grid_idx=None, **kwargs):
+        # 采样单元运行
+        self.grid_idx = grid_idx
+        x,y,z = self.sg_obj.points[grid_idx]
+        dock_point = self.combiner.ads_obj.dock_points[0]  # tip must define the dock_point
+        dz_range = (np.linspace(2.0,0.75,self.kwargs.get('nz',10)) *
+                    (max(self.sg_obj.rsub)+self.sg_obj.rads))  # from far to near
+        z0 = max(self.sg_obj.atoms.positions[:,2])
+        e0_list = []
+        dz_list = []
+        atoms_list = []
+        ads_topo_id0 = self.combiner.ads_obj.topo_id
+        for dz in dz_range:
+            ads_atoms = self.combiner.docking(
+                xyz=[x,y,z0+dz],
+                dock_point=dock_point,
+            )
+            atoms = self.sg_obj.atoms.copy()
+            atoms += ads_atoms
+            atoms.calc = self.combiner.calc
+
+            if self.optimizer is not None:
+                # 设置 constraint
+                idx0 = len(self.sg_obj.atoms)
+                new_constraint = (update_fixatoms_index(self.combiner.ads_obj.atoms, idx0)
+                                  + atoms.constraints)
+                atoms.constraints = new_constraint
+                opt_kwargs = self.kwargs.get('optimizer',dict())
+                output_name = f"opt_{grid_idx}-{dz:.2f}"
+                if 'logfile' not in opt_kwargs:
+                    opt_kwargs['logfile'] = f"{output_name}.log"
+                if 'trajectory' not in opt_kwargs:
+                    opt_kwargs['trajectory'] = f"{output_name}.traj"
+                if 'fmax' in opt_kwargs:
+                    fmax = opt_kwargs.pop('fmax')
+                else:
+                    fmax = 0.1
+                if 'steps' in opt_kwargs:
+                    steps = opt_kwargs.pop('steps')
+                else:
+                    steps = 100
+                opt = self.optimizer(atoms, **opt_kwargs)
+                converged = opt.run(fmax=fmax, steps=steps)
+                if converged:
+                    new_ads_atoms = atoms[len(self.sg_obj.atoms):]
+                    topo_id = get_topo_id(new_ads_atoms,nl=self.combiner.ads_obj.nl)
+                    if topo_id != ads_topo_id0:
+                        msg=f"Warning: The connectivity of tip is broken for dz={dz}"
+                        self.log(msg+'\n')
+                        converged = False
+            else:
+                converged = True
+
+            if converged:
+                e0=atoms.get_potential_energy()
+                e0_list.append(e0)
+                dz_list.append(dz)
+                atoms_list.append(atoms.copy())
+
+        if len(e0_list) == 0:
+            e0 = np.nan
+            converged = False  # re-define converged
+        else:
+            converged = True
+            e0_min_idx = np.argmin(e0_list)
+            e0 = e0_list[e0_min_idx]
+            dz = dz_list[e0_min_idx]
+            z = z0 + dz
+
+        # 打印信息到 log file：
+        used_time = (datetime.datetime.now() - self.stime).seconds
+        h = used_time // 3600
+        m = (used_time % 3600) // 60
+        s = (used_time % 60)
+        msg = (f"SAMPLE {h:02}:{m:02}:{s:02} {grid_idx:7} "
+               f"{x:8.3f} {y:8.3f} {z:8.3f} {e0:.4f}  {str(converged)[0]}")
+        self.log(msg+'\n')
+        # 输出 优化完的结构
+        if converged:
+            ase.io.write(f"atoms_{grid_idx}.traj", atoms_list)
+            # 更新 sg_obj
+            self.sg_obj.set_energy(grid_idx, e0)
+            for iz, ie in zip(dz_list, e0_list):
+                self.sg_obj.set_property(grid_idx, ie, key=iz)
+            self.to_pkl()
+            # 是否画图？
+            if kwargs.get('fit', False):
+                self.sg_obj.fit()
+                self.sg_obj.plot_energy()
+        else:
+            self.sg_obj.del_sample(grid_idx)

{surface_construct-0.11 → surface_construct-0.12}/surface_construct/tasks/sitesampling.py

@@ -81,7 +81,6 @@ class SurfaceSiteSampleTask(TaskBase):
             msg.append(f"    Size: {s.get('size')}")
             msg.append(f"    Surface Sampler: {s.get('surface')}")
             msg.append(f"    Surface Sampler weight: {s.get('weight',1.0)}")
-            msg.append(f"    Conformation Sampler: {s.get('conformation')}")
         msg.append("Other kwargs:")
         for k,v in self.kwargs.items():
             msg.append(f'    {k} : {v}')
@@ -113,8 +112,7 @@ class SurfaceSiteSampleTask(TaskBase):
                                             cidx=cidx,
                                             ridx=ridx,
                                             dp_idx=dp_idx,
-                                            opt_z=True,
-                                            **kwargs)
+                                            opt_z=True)
             if atoms is None:
                 continue
             if self.optimizer is not None:
@@ -181,7 +179,6 @@ class SurfaceSiteSampleTask(TaskBase):
             sg_sampler = isampler.get("surface")
             if type(sg_sampler) in (tuple, list) and len(sg_sampler) == 1:
                 sg_sampler = sg_sampler[0]
-            conf_sampler = isampler.get("conformation", None)  # TODO: 这个需要重新设计和调试
             if type(sg_sampler) == str:
                 sg_sampler_obj = name2sampler(sg_sampler)
                 if sg_sampler in ('InitialSGSampler', 'KeyPointSGSampler'):  # 一次性采N样，其余都是一次一个点

{surface_construct-0.11 → surface_construct-0.12/surface_construct.egg-info}/PKG-INFO

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.11
-Summary: Surface termination construction especially for complex model, such as oxides or carbides.
+Version: 0.12
+Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren
 Author-email: 0403114076@163.com

{surface_construct-0.11 → surface_construct-0.12}/surface_construct.egg-info/SOURCES.txt

@@ -17,6 +17,7 @@ surface_construct/structures/pymsym_test.py
 surface_construct/structures/surface.py
 surface_construct/structures/surface_grid.py
 surface_construct/tasks/__init__.py
+surface_construct/tasks/afm.py
 surface_construct/tasks/sitesampling.py
 surface_construct/tasks/taskbase.py
 surface_construct/tasks/terminations.py

{surface_construct-0.11 → surface_construct-0.12}/tests/test_task.py

@@ -4,17 +4,18 @@ from random import randint
 
 import ase.io
 import pytest
-from ase import Atom
+from ase import Atom, Atoms
+from ase.constraints import FixAtoms
 from ase.visualize import view
 from lasp_ase.lasp import Lasp
 from surface_construct import SurfaceGrid
 from surface_construct import AdsGridCombiner
 from surface_construct import Adsorbate
-from surface_construct.tasks import SurfaceSiteSampleTask
+from surface_construct.tasks import SurfaceSiteSampleTask, AFMTask
 from ase.optimize import LBFGS, BFGS
 
 
-class TestSurfaceSiteSampling:
+class TestTask:
     """
     Simple Ru 0001 suface
     """
@@ -110,4 +111,39 @@ class TestSurfaceSiteSampling:
         ]
         task_obj = SurfaceSiteSampleTask(combiner=com_obj, sampler=sampler, optimizer=None)
         task_obj.run()
+        print('Done')
+
+    def test_afm(self):
+        tip_atoms = Atoms('Ru4CO',positions=[
+            [4.96420026, 5.33360004, 5.96179962],
+            [2.98259974, 6.51570022, 6.69340014],
+            [6.93529963, 6.55210018, 6.65879965],
+            [4.97309983, 3.62199992, 6.84219956],
+            [4.93830025, 5.30839980, 3.98790002],
+            [4.91949975, 5.28810024, 2.48350024],
+        ])
+
+        tip_atoms.constraints = FixAtoms(mask=tip_atoms.symbols == 'Ru')
+        tip_obj = Adsorbate(tip_atoms)
+        tip_obj.dock_point_indices = [[5]] # O atom as docker_point
+        shutil.copyfile('../atoms_files/RuCHO_lasp.in', 'lasp.in')
+        shutil.copyfile('../atoms_files/RuCHO_pf2.pot', 'RuCHO.pot')
+        satoms = ase.io.read('../atoms_files/ru_0001_POSCAR')
+        satoms.calc = Lasp()
+        sg_obj = SurfaceGrid(satoms, interval=0.1, rads=tip_obj.rads, lpca=False, subtype='slab')
+        sg_obj.gridize()
+        com_obj = AdsGridCombiner(sg_obj, tip_obj)
+
+        sampler =[
+            {
+                'surface': "KeyPointSGSampler",  # 表面采样方法
+            },  # 第一步采样
+            {
+                'size': 2,  # 采样大小
+                'surface': ("MaxDiversitySGSampler", "MaxSigmaSGSampler"),  # 表面采样方法
+                'weight': (0.5, 0.5),  # 表面采样方法的权重
+            }  # 第二步采样
+        ]
+        task_obj = AFMTask(combiner=com_obj, sampler=sampler, optimizer=LBFGS, nz=10) # nz 定义 z方向采多少样
+        task_obj.run()
         print('Done')