mdkits 0.2.0__tar.gz → 0.2.1__tar.gz

{mdkits-0.2.0 → mdkits-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 0.2.0
+Version: 0.2.1
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-0.2.0 → mdkits-0.2.1}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "0.2.0"
+version = "0.2.1"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-0.2.0 → mdkits-0.2.1}/src/mdkits/md_cli/density.py

@@ -118,14 +118,20 @@ 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-0.2.1}/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]