surface-construct 0.12.6__tar.gz → 0.12.7__tar.gz

{surface_construct-0.12.6/surface_construct.egg-info → surface_construct-0.12.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.6
+Version: 0.12.7
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren

{surface_construct-0.12.6 → surface_construct-0.12.7}/setup.py

@@ -15,7 +15,7 @@ install_requires = [
 
 setup(
     name='surface_construct',
-    version='0.12.6',
+    version='0.12.7',
     packages=find_packages(),
     url='https://gitee.com/pjren/surface_construct/',
     license='GPL',

{surface_construct-0.12.6 → surface_construct-0.12.7}/surface_construct/sg_sampler.py

@@ -174,10 +174,12 @@ class MaxSigmaSGSampler(SGSamplerBase):
             else:
                 delta = 0.01
                 idx_list = []
-                while len(idx_list) >= size:
+                while len(idx_list) < size:
                     idx_list = np.argwhere(sigma_array > sigma0-delta).flatten().tolist()
+                    # 排除掉已经采过的点
+                    idx_list = [i for i in idx_list if i not in self.sg_obj.calculated_sample]
                     delta += 0.01
-                idx = random.sample(idx_list, size)
+                idx = random.sample(idx_list, min(size, len(idx_list)))
                 return idx
         else:
             raise "No energy for all population, pls do initial sampling first!"
@@ -194,10 +196,15 @@ class MinEnergySGSampler(SGSamplerBase):
                 raise ValueError("Number of points should greater than sample!")
             elif len(E_array) == size:
                 return np.asarray(range(len(E_array)))
-            # 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)
+            delta = 0.1
+            idx_list = []
+            while len(idx_list) < size:
+                # 如果已经读入了一些能量，则返回能量最低的点 (<delta eV 以内，然后随机选一个)
+                idx_list = np.argwhere(E_array <= E0+0.1).flatten().tolist()
+                idx_list = [i for i in idx_list if i not in self.sg_obj.calculated_sample]
+                delta += 0.1
+            idx = random.sample(idx_list, min(size, len(idx_list)))
             return idx
         else:
             raise "No energy for all population, pls do initial sampling first!"

{surface_construct-0.12.6 → surface_construct-0.12.7}/surface_construct/tasks/sitesampling.py

@@ -171,6 +171,11 @@ class SurfaceSiteSampleTask(TaskBase):
             self.sg_obj.del_sample(grid_idx)
 
     def run(self):
+        # 在新的采样之前先进行已经采到但是未计算的点
+        uncalc_samples = [idx for idx in self.sg_obj.sample_idx if not self.sg_obj.sample_dct[idx]['calculated']]
+        for grid_idx in uncalc_samples:
+            self.irun(grid_idx, fit=False)
+
         for isampler in self.sampler:
             size = isampler.get("size", 1)
             sg_sampler = isampler.get("surface")

{surface_construct-0.12.6 → surface_construct-0.12.7}/surface_construct/tasks/vipsitetask.py

@@ -1,3 +1,5 @@
+import os
+
 from matplotlib import pyplot as plt
 from matplotlib.patches import Circle
 
@@ -6,41 +8,43 @@ from .sitesampling import SurfaceSiteSampleTask
 class VIPSiteTask(SurfaceSiteSampleTask):
     def __init__(self, exclude=None, include=None, **kwargs):
         super().__init__(**kwargs)
+        if not os.path.isfile(self.hist_pkl):
+            vip_id = self.sg_obj.vip_id
+            grid_site_type, site_type_dict = self.sg_obj.get_grid_site_type()
+            if exclude is None and include is None:
+                msg = [f"Either exclude or include must be specified"]
+                msg += [f"Possible site types are {len(site_type_dict)} in total:"]
+                msg += [f"{k}: {v}" for k,v in site_type_dict.items() if type(k) in (int,)]
+                raise ValueError('\n'.join(msg))
+            elif exclude is not None and include is not None:
+                raise ValueError("Can not specified exclude and include at the same time")
+            elif exclude is not None and include is None:
+                filtered = [i for i in vip_id if site_type_dict[grid_site_type[i]] not in exclude]
+            else:
+                filtered = [i for i in vip_id if site_type_dict[grid_site_type[i]] in include]
 
-        vip_id = self.sg_obj.vip_id
-        grid_site_type, site_type_dict = self.sg_obj.get_grid_site_type()
-        if exclude is None and include is None:
-            msg = [f"Either exclude or include must be specified"]
-            msg += [f"Possible site types are {len(site_type_dict)} in total:"]
-            msg += [f"{k}: {v}" for k,v in site_type_dict.items() if type(k) in (int,)]
-            raise ValueError('\n'.join(msg))
-        elif exclude is not None and include is not None:
-            raise ValueError("Can not specified exclude and include at the same time")
-        elif exclude is not None and include is None:
-            filtered = [i for i in vip_id if site_type_dict[grid_site_type[i]] not in exclude]
-        else:
-            filtered = [i for i in vip_id if site_type_dict[grid_site_type[i]] in include]
-
-        points = self.sg_obj.points[filtered]
-        vector = self.sg_obj.vector[filtered]
-        raw_vector = self.sg_obj._raw_vector[filtered]
-        _ = self.sg_obj.vector_interval  # 此处call 一下，用于后面的 fit 中的参数
-        self.sg_obj.points = points
-        self.sg_obj.vector = vector
-        self.sg_obj._raw_vector = raw_vector
-        self.sg_obj.vectorgen = None
+            points = self.sg_obj.points[filtered]
+            vector = self.sg_obj.vector[filtered]
+            raw_vector = self.sg_obj._raw_vector[filtered]
+            _ = self.sg_obj.vector_interval  # 此处call 一下，用于后面的 fit 中的参数
+            self.sg_obj.points = points
+            self.sg_obj.vector = vector
+            self.sg_obj._raw_vector = raw_vector
+            self.sg_obj.vectorgen = None
 
-        sampler_size = 0
+        sampler_size = len(self.sg_obj.calculated_sample)
         new_sampler = []
         for isampler in self.sampler:  # 不需要初始采样和key 点采样
             if isampler['surface'] not in ('InitialSGSampler', 'KeyPointSGSampler'):
                 sampler_size += isampler.get('size', 0)
                 new_sampler.append(isampler)
+            else:
+                print("Warning: InitialSGSampler or KeyPointSGSampler should not applied in VIP sampling.")
 
         # 如果 filter 之后的点小于等于 self.sampler['size'], 重新定义sampler
-        if sampler_size >= len(points):
+        if sampler_size >= len(self.sg_obj.points):
             self.sampler = [{
-                'size': len(points),  # 采样大小
+                'size': len(self.sg_obj.points)-len(self.sg_obj.calculated_sample),  # 采样大小
                 'surface': "RandomSGSampler",  # 表面采样方法
             }]
         else:

{surface_construct-0.12.6 → surface_construct-0.12.7/surface_construct.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: surface_construct
-Version: 0.12.6
+Version: 0.12.7
 Summary: Surface construction and surface reaction sampling tools.
 Home-page: https://gitee.com/pjren/surface_construct/
 Author: ren