mdkits 0.2.0__tar.gz → 0.2.2__tar.gz

{mdkits-0.2.0 → mdkits-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.2.0
+Version: 0.2.2
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-0.2.0 → mdkits-0.2.2}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.2.0"
+version = "0.2.2"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-0.2.0 → 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
@@ -118,14 +119,20 @@ class Density_distribution(AnalysisBase):
 @click.option('--group', type=str, help='group to analysis')
 @click.option('--atomic_mass', type=float, help='output density unit (g/cm3), should give atomic mass of element, else is concentration unit (mol/L)')
 @click.option('-o', type=str, help='output file name', default='density_{element}.dat', show_default=True)
-def main(filename, cell, o, element, atomic_mass, update_water, distance, angle, surface):
+def main(filename, cell, o, group, atomic_mass, update_water, distance, angle, surface, r):
     """
     analysis density or concentration of element in a trajectory file
     """
 
-    density_dist = Density_distribution(filename, cell, o=o, distance_judg=distance, angle_judg=angle, element=element, atomic_mass=atomic_mass, update_water=update_water, surface=surface)
+    density_dist = Density_distribution(filename, cell, o=o, distance_judg=distance, angle_judg=angle, element=group, atomic_mass=atomic_mass, update_water=update_water, surface=surface)
 
-    density_dist.run()
+    if r is not None:
+        if len(r) == 2:
+            density_dist.run(start=r[0], stop=r[1])
+        elif len(r) == 3:
+            density_dist.run(start=r[0], stop=r[1], step=r[2])
+    else:
+        density_dist.run()
 
 
 if __name__ == '__main__':

{mdkits-0.2.0 → mdkits-0.2.2}/src/mdkits/md_cli/vac.py

@@ -33,10 +33,9 @@ class Velocity_AutoCorrelation(AnalysisBase):
         self.cvv = np.array(self.cvv)
 
         sf = self.cvv.shape[0]
-        t = 1/sf
-        f = np.fft.fft(self.cvv).real
+        f = np.abs(np.fft.fft(self.cvv))
 
-        faxis = np.fft.fftfreq(sf, d=t)
+        faxis = np.fft.fftfreq(sf, d=1/sf)
         pf = np.where(faxis>0)
         faxis = faxis[pf]
         f = f[pf]

{mdkits-0.2.0 → 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])