mdkits 0.2.1__tar.gz → 0.2.2__tar.gz

{mdkits-0.2.1 → mdkits-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.2.1
+Version: 0.2.2
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-0.2.1 → mdkits-0.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.2.1"
+version = "0.2.2"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-0.2.1 → mdkits-0.2.2}/src/mdkits/md_cli/density.py

@@ -82,8 +82,7 @@ class Density_distribution(AnalysisBase):
         if self.surface_group:
             surface = numpy_geo.find_surface(self.surface_group.positions[:, 2])
             self.surface_pos[0] += surface[0]
-            if len(surface) > 1:
-                self.surface_pos[1] += surface[1]
+            self.surface_pos[1] += surface[1]
 
         self.frame_count += 1
 
@@ -102,6 +101,8 @@ class Density_distribution(AnalysisBase):
                 lower_z = self.surface_pos[0] / self.frame_count
                 if self.surface_pos[1] == 0:
                     upper_z = np.inf
+                else:
+                    upper_z = self.surface_pos[1] / self.frame_count
 
                 mask = (bins_z >= lower_z) & (bins_z <= upper_z)
                 filtered_bins_z = bins_z[mask] - lower_z

{mdkits-0.2.1 → mdkits-0.2.2}/src/mdkits/util/numpy_geo.py

@@ -112,7 +112,7 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=0.05, surface_toleran
         layer_mean.append(np.mean(current_layer))
     
     if len(layer_mean) == 1:
-        return [layer_mean[0]]
+        return [layer_mean[0], 0]
 
     diff = np.diff(layer_mean)
     if np.any(diff > surface_tolerance):
@@ -120,5 +120,5 @@ def find_surface(surface_group:np.ndarray, layer_tolerance=0.05, surface_toleran
         return (layer_mean[index], layer_mean[index + 1])
     else:
         if layer_mean[-1] > layer_mean[0]:
-            return [layer_mean[-1]]
+            return [layer_mean[-1], 0]
         return (layer_mean[-1], layer_mean[0])