mdkits 1.0.2__tar.gz → 1.0.4__tar.gz

{mdkits-1.0.2 → mdkits-1.0.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mdkits
-Version: 1.0.2
+Version: 1.0.4
 Summary: kits for md or dft
 License: MIT
 Keywords: molecular dynamics,density functional theory

{mdkits-1.0.2 → mdkits-1.0.4}/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "mdkits"
-version = "1.0.2"
+version = "1.0.4"
 description = "kits for md or dft"
 readme = "README.md"
 authors = ["jxxcr <jixxcr@qq.com>"]

{mdkits-1.0.2 → mdkits-1.0.4}/src/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-1.0.2 → mdkits-1.0.4}/src/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-1.0.2 → mdkits-1.0.4}/src/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-1.0.2 → mdkits-1.0.4}/src/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-1.0.2 → mdkits-1.0.4}/src/mdkits/md_cli/msd.py

@@ -18,11 +18,17 @@ 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}")
+    o = f"msd_{type}_{'_'.join(group).replace(' ', '_')}.dat"
+    np.savetxt(o, data, fmt="%.5f", delimiter="\t", header=header)