mdkits 1.0.6__tar.gz → 1.0.8__tar.gz

{mdkits-1.0.6 → mdkits-1.0.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 1.0.6
+Version: 1.0.8
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-1.0.6 → mdkits-1.0.8}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "1.0.6"
+version = "1.0.8"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-1.0.6 → mdkits-1.0.8}/src/mdkits/md_cli/density.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 
 import numpy as np
-import click
+import click, math
 from MDAnalysis import Universe
 from MDAnalysis.analysis.base import AnalysisBase
 from mdkits.util import (
@@ -88,7 +88,7 @@ class Density_distribution(AnalysisBase):
 
     def _conclude(self):
         if self.frame_count > 0:
-            V = self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size
+            V = self.u.dimensions[0] * self.u.dimensions[1] * math.sin(math.radians(180 - self.u.dimensions[-1])) * self.bin_size
 
             if self.atomic_mass:
                 density_distribution = (self.density_distribution * self.atomic_mass * 1.660539 / V) / self.frame_count

{mdkits-1.0.6 → mdkits-1.0.8}/src/mdkits/md_cli/msd.py

@@ -2,17 +2,25 @@ import click
 import MDAnalysis as mda
 import MDAnalysis.analysis.msd as msd
 import numpy as np
+from mdkits.util import arg_type
 
 
 @click.command(name="msd")
 @click.argument("filename", type=click.Path(exists=True))
 @click.argument('type', type=click.Choice(['xyz', 'xy', 'yz', 'xz', 'x', 'y', 'z']))
 @click.argument("group", type=str)
-def main(filename, type, group):
+@click.option('-r', type=arg_type.FrameRange, help='range of frame to analysis')
+def main(filename, type, group, r):
     """analysis msd along the given axis"""
     u = mda.Universe(filename)
     MSD = msd.EinsteinMSD(u, select=group, msd_type=type, fft=True)
-    MSD.run(verbose=True)
+    if r is not None:
+        if len(r) == 2:
+            MSD.run(start=r[0], stop=r[1], verbose=True)
+        elif len(r) == 3:
+            MSD.run(start=r[0], stop=r[1], step=r[2], verbose=True)
+    else:
+        MSD.run(verbose=True)
 
     data = np.arange(1, MSD.n_frames + 1).reshape(-1, 1)
     s = "_"