mdkits 0.2.0__py3-none-any.whl → 0.2.2__py3-none-any.whl

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/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/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])

{mdkits-0.2.0.dist-info → mdkits-0.2.2.dist-info}/METADATA

@@ -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.dist-info → mdkits-0.2.2.dist-info}/RECORD

@@ -19,7 +19,7 @@ mdkits/dft_cli/cube.py,sha256=G-QNup8W6J1-LCcEl1EHsV3nstd23byePDOcE_95t18,1176
 mdkits/dft_cli/dft_cli.py,sha256=Ou9-e4uGhDJJk2Gdg7tcj6iKApkAJZFSbN1hr7SlCMc,281
 mdkits/dft_cli/pdos.py,sha256=ALAZ5uOaoT0UpCyKYleWxwmk569HMzKTTK-lMJeicM8,1411
 mdkits/md_cli/angle.py,sha256=cfhI6dsn_hIy-YXSTXemu1m1O_l2HuL_x6zx_3uL-Uw,5450
-mdkits/md_cli/density.py,sha256=_w6UunY6alTp0jLa8cyqR8sSYubN0XbM-PDF4SkzsJU,5058
+mdkits/md_cli/density.py,sha256=br8jq_qlkKwJr_wkdKGHCYbg16TmGPjasX5LI9E55yk,5312
 mdkits/md_cli/dipole.py,sha256=tXTO8CZAQTVY55GwuXWJNGo7EQ4Tb2611g5IHucdlec,4836
 mdkits/md_cli/hb_distribution.py,sha256=ForMmNjfJxpXHqo1Au0OXOmwgvHxIuVR8qnpu3iS7Eg,7897
 mdkits/md_cli/md_cli.py,sha256=2vH04o_3d5kCJsn3qEq-iUPhebKJOrS-e7HJtyiZTiQ,571
@@ -27,7 +27,7 @@ mdkits/md_cli/monitor.py,sha256=JNEgz5RGbFn4x_E85pAiPUY1NVIyZ3b2vjpBk_d1dR8,4536
 mdkits/md_cli/msd.py,sha256=v-9TPKBGHz6ce2PUwexrekVq_9eiutIOQYaw582yN30,965
 mdkits/md_cli/rdf.py,sha256=p4HMMYZLfFRPnGx7YHQU6kZnMAfoL6vOyOVpZhfdBfM,1712
 mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
-mdkits/md_cli/vac.py,sha256=9YZ9QviJ9VPfF29_cFKUYPwxkszYZ7cHTB7AMgUV4go,2147
+mdkits/md_cli/vac.py,sha256=eIVRF5ADHLwWp50gv0VoAxT0UCXpzLcD57f3TQM6Hxs,2135
 mdkits/md_cli/wrap.py,sha256=YdUpvhRyKn7bYnIAVgP39qItPdrEoTeJl55TmbS7Qqk,1044
 mdkits/mdkits.py,sha256=EiAt7dxGTaHuuj7bCNxgAqZbX0i3sldO0mBxOG-aMnY,595
 mdkits/util/.fig_operation.py.swp,sha256=iZYqdYMj4UKS1rmbXv8Ve2FcVBcNljX7Y43-neMdPSk,12288
@@ -37,12 +37,12 @@ mdkits/util/cp2k_input_parsing.py,sha256=7NMVOYEGycarokLJlhLoWWilciM7sd8MWp5FVTF
 mdkits/util/encapsulated_ase.py,sha256=uhqIhsALxzwJYuFrfOYGGC6U0QLm_dcZNridvfl_XGc,4339
 mdkits/util/encapsulated_mda.py,sha256=m3i-XrcscMcM5V7JzLnor3JtAOfuDx3LLMl0tZt0n-w,2325
 mdkits/util/fig_operation.py,sha256=FwffNUtXorMl6qE04FipgzcVljEQii7wrNJUCJMyY3E,1045
-mdkits/util/numpy_geo.py,sha256=zkh3uNC3HGHIwtHOmiDXborab5_40PmaJF54jSQ-njU,3874
+mdkits/util/numpy_geo.py,sha256=B2QVADl1M8iixZrIOre2UUhHqvAeghvM8Q2woEQsH3Q,3880
 mdkits/util/os_operation.py,sha256=ErN2ExjX9vZRfPe3ypsj4eyoQTEePqzlEX0Xm1N4lL4,980
 mdkits/util/out_err.py,sha256=7vGDI7wVoJWe1S0BDbcq-UC2KAhblCzg-NAYZKBZ4lo,900
 mdkits/util/structure_parsing.py,sha256=mRPMJeih3O-ST7HeETDvBEkfV-1psT-XgxyYgDadV0U,4152
-mdkits-0.2.0.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-0.2.0.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-0.2.0.dist-info/METADATA,sha256=tDq50lJJD0-8TPS7UKxZiXVD7EaK7n4xf_RuZheZldY,10963
-mdkits-0.2.0.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-0.2.0.dist-info/RECORD,,
+mdkits-0.2.2.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-0.2.2.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-0.2.2.dist-info/METADATA,sha256=GWbzewK2VIqfZ0HatG6WAlKQX_V20ZDlh-ZMK_o7HIM,10963
+mdkits-0.2.2.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-0.2.2.dist-info/RECORD,,