mdkits 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

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/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 = "_"

{mdkits-1.0.6.dist-info → mdkits-1.0.8.dist-info}/METADATA

@@ -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.dist-info → mdkits-1.0.8.dist-info}/RECORD

@@ -20,12 +20,12 @@ 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=EjZ1oWJHHUocZAZe8dgJUu6bkLPVwgrKkggidF3yduE,1445
 mdkits/md_cli/angle.py,sha256=EvsW4lmNDM2iyFj8YZcrikGVvYeyP6WIzu269-ZI4iw,5468
-mdkits/md_cli/density.py,sha256=rvM2LuQS3m5I6KGmdbs8MHHLqeZPH5FLvVfTGJ1-euM,5332
+mdkits/md_cli/density.py,sha256=Y2rJU1qJQq3OBb64_-pPhywm7eMdd0ywc8zuuw5XYYs,5392
 mdkits/md_cli/dipole.py,sha256=u_22-vMlzSEqGSpC6c5PG5t3uyjxaRKUvybgytovMk0,5027
 mdkits/md_cli/hb_distribution.py,sha256=lADOBiJYHCHPutXimXVDQpPdRKasBpldhiIl9SKf39o,7950
 mdkits/md_cli/md_cli.py,sha256=2vH04o_3d5kCJsn3qEq-iUPhebKJOrS-e7HJtyiZTiQ,571
 mdkits/md_cli/monitor.py,sha256=JNEgz5RGbFn4x_E85pAiPUY1NVIyZ3b2vjpBk_d1dR8,4536
-mdkits/md_cli/msd.py,sha256=yzBOeiVrYlTGwtttKNDr7kgooUEFoFCEhc7UZoWpXDM,1179
+mdkits/md_cli/msd.py,sha256=xg_c2sxNDOlxwK8jsNsQ4nbdqQAUvPGhOqFA6TXBTfs,1515
 mdkits/md_cli/rdf.py,sha256=p4HMMYZLfFRPnGx7YHQU6kZnMAfoL6vOyOVpZhfdBfM,1712
 mdkits/md_cli/setting.py,sha256=mxMTYpm6DUjMt9hOKsJbBSKwCqzMilOR0bo1azSdJP0,846
 mdkits/md_cli/vac.py,sha256=MJi_uftl0UUqhWvqDtcr14qtcRgYRd6X0VSg4J5MFN8,2133
@@ -42,8 +42,8 @@ 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-1.0.6.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-1.0.6.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-1.0.6.dist-info/METADATA,sha256=SXacPjE1ra_doe2JEw56eKdyUxz34L42gpBNnzJKvqU,13539
-mdkits-1.0.6.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-1.0.6.dist-info/RECORD,,
+mdkits-1.0.8.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-1.0.8.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-1.0.8.dist-info/METADATA,sha256=I8CmwQEDphRQRmtmhp0b6GJ76W54pIPLufV8SdWNXes,13539
+mdkits-1.0.8.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-1.0.8.dist-info/RECORD,,