mdkits 1.0.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

mdkits/md_cli/angle.py

@@ -98,7 +98,7 @@ class Angle_distribution(AnalysisBase):
         if self.frame_count > 0:
             average_angle_w = self.angle_w_distribution / self.frame_count
             average_angle_oh = self.angle_oh_distribution / (self.frame_count*2)
-            bins_z = np.arange(len(average_angle_w)) * self.bin_size
+            bins_z = np.arange(len(average_angle_w)) * self.bin_size + self.bin_size / 2
             conbined_data = np.column_stack((bins_z, average_angle_w, average_angle_oh))
             np.savetxt("angle_distribution.dat", conbined_data, header="angle\tw_suf_dist\toh_suf_dist", fmt='%.5f', delimiter='\t')
 

mdkits/md_cli/density.py

@@ -95,7 +95,7 @@ class Density_distribution(AnalysisBase):
             else:
                 density_distribution = (self.density_distribution * (10000/6.02) / V) / self.frame_count
 
-            bins_z = np.arange(len(self.density_distribution)) * self.bin_size
+            bins_z = np.arange(len(self.density_distribution)) * self.bin_size + self.bin_size / 2
 
             if self.surface:
                 lower_z = self.surface_pos[0] / self.frame_count

mdkits/md_cli/dipole.py

@@ -86,7 +86,7 @@ class Dipole_distribution(AnalysisBase):
             average_dipole = self.dipole_distribution / self.o_count
             water_density = (self.o_count * (15.999+1.0008*2) * 1.660539 / (self.u.dimensions[0] * self.u.dimensions[1] * self.bin_size)) / self.frame_count
             average_dipole = average_dipole * water_density
-            bins_z = np.arange(len(average_dipole)) * self.bin_size
+            bins_z = np.arange(len(average_dipole)) * self.bin_size + self.bin_size / 2
 
             if self.surface:
                 lower_z = self.surface_pos[0] / self.frame_count

mdkits/md_cli/hb_distribution.py

@@ -134,7 +134,7 @@ class Hb_distribution(AnalysisBase):
             average_accepter = np.nan_to_num((self.accepter / self.frame_count) / average_od, nan=0)
             average_sum = average_donor + average_accepter
 
-            bins_z = np.arange(len(self.donor)) * self.bin_size
+            bins_z = np.arange(len(self.donor)) * self.bin_size + self.bin_size / 2
 
             if self.surface:
                 lower_z = self.surface_pos[0] / self.frame_count

mdkits/md_cli/msd.py

@@ -18,11 +18,16 @@ def main(filename, type, group):
     s = "_"
     name = f"{s.join(group.split(' '))}"
     header = ''
+    msd_cols = []
     for i in range(MSD.n_particles):
-        data = np.concatenate((data, MSD.results.msds_by_particle[:, i].reshape(-1, 1)), axis=1)
+        msd_cols.append(MSD.results.msds_by_particle[:, i].reshape(-1, 1))
         header += name + f"_{i}\t"
+    msd_array = np.concatenate(msd_cols, axis=1)
+    mean_col = np.mean(msd_array, axis=1, keepdims=True)
+    data = np.concatenate((data, mean_col, msd_array), axis=1)
+    header = "frame\tmean\t" + header
 
-    np.savetxt(f"msd_{type}.dat", data, fmt="%.5f", delimiter="\t", header=f"frame\t{header}")
+    np.savetxt(f"msd_{type}.dat", data, fmt="%.5f", delimiter="\t", header=header)
 
 
 

{mdkits-1.0.2.dist-info → mdkits-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 1.0.2
+Version: 1.0.3
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-1.0.2.dist-info → mdkits-1.0.3.dist-info}/RECORD

@@ -15,16 +15,17 @@ mdkits/cli/extract.py,sha256=dNf05CZuir98Z0EOjE33JrYK5_YBYLzuOauIt2Lwoh0,2944
 mdkits/cli/plot.py,sha256=1yh5dq5jnQDuyWlxV_9g5ztsnuFHVu4ouYQ9VJYSrUU,8938
 mdkits/config/__init__.py,sha256=ZSwmnPK02LxJLMgcYmNb-tIOk8fEuHf5jpqD3SDHWLg,1039
 mdkits/config/settings.yml,sha256=PY7u0PbFLuxSnd54H5tI9oMjUf-mzyADqSZtm99BwG0,71
+mdkits/dft_cli/check_neb.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 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=dS3qMreC-vIrwa5LAaZQ9lRPYuwUAe14_8ZDkntujl0,5448
-mdkits/md_cli/density.py,sha256=br8jq_qlkKwJr_wkdKGHCYbg16TmGPjasX5LI9E55yk,5312
-mdkits/md_cli/dipole.py,sha256=Q2Bp42gB00Q1mxrHgmYbhkLT1w3uVNHMmjA_93TF-V8,5007
-mdkits/md_cli/hb_distribution.py,sha256=aoB6Yk1a4agPLEravjkvJ3llNJAroZbSgQ8vNoNSex8,7930
+mdkits/md_cli/angle.py,sha256=EvsW4lmNDM2iyFj8YZcrikGVvYeyP6WIzu269-ZI4iw,5468
+mdkits/md_cli/density.py,sha256=rvM2LuQS3m5I6KGmdbs8MHHLqeZPH5FLvVfTGJ1-euM,5332
+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=v-9TPKBGHz6ce2PUwexrekVq_9eiutIOQYaw582yN30,965
+mdkits/md_cli/msd.py,sha256=UQUBNA08D_OxWv9xwbHQJdu2gya_km3JWaS44GXO9vw,1161
 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
@@ -41,8 +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-1.0.2.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
-mdkits-1.0.2.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
-mdkits-1.0.2.dist-info/METADATA,sha256=NoNCXVMUI1qGY6aXW6Hs9h2QKEIoLb6NLI-pUsGwcLM,13539
-mdkits-1.0.2.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
-mdkits-1.0.2.dist-info/RECORD,,
+mdkits-1.0.3.dist-info/entry_points.txt,sha256=xoWWZ_yL87S501AzCO2ZjpnVuYkElC6z-8J3tmuIGXQ,44
+mdkits-1.0.3.dist-info/LICENSE,sha256=VLaqyB0r_H7y3hUntfpPWcE3OATTedHWI983htLftcQ,1081
+mdkits-1.0.3.dist-info/METADATA,sha256=lx_xJ_iJm--f5XPy0K4Aa2tDXaAYGFOfTxIHzhikwBc,13539
+mdkits-1.0.3.dist-info/WHEEL,sha256=XbeZDeTWKc1w7CSIyre5aMDU_-PohRwTQceYnisIYYY,88
+mdkits-1.0.3.dist-info/RECORD,,