Commit: 5feb556a0a6ec4a1f923650e35046a47ec72d4fe - myprojects-hg-reborn (hg)

Commit MetaInfo

• Revision: 5feb556a0a6ec4a1f923650e35046a47ec72d4fe (tree)
• Zeit: 2008-04-16 07:20:32
• Autor: iselllo
• Commiter: iselllo

Log Message

Now diffusion_many_clusters.py also works out the trajectory-averaged
diffusion coefficient, but it does not seem very useful. I also
re-calculate the effective radius using the ensemble-averaged diffusion
coefficient.

Ändern Zusammenfassung

• modified: Python-codes/diffusion_many_clusters.py

Diff

diff -r 7a7995b1bc4a -r 5feb556a0a6e Python-codes/diffusion_many_clusters.py
--- a/Python-codes/diffusion_many_clusters.py	Tue Apr 15 15:27:54 2008 +0000
+++ b/Python-codes/diffusion_many_clusters.py	Tue Apr 15 22:20:32 2008 +0000
@@ -964,6 +964,7 @@
 my_delta_r_sq=pos_results[:,6]
 delta_r_sq_formed=my_delta_r_sq[cluster_formed]
 
+p.save("delta_r_sq_time.dat",delta_r_sq_formed)
 
 lin_fit=stats.linregress(time_formed,delta_r_sq_formed)
 
@@ -1243,6 +1244,55 @@
     print "delta_v_sq_time_aver is, ", delta_v_sq_time_aver
 
 
+
+
+
+
+
+
+
+def Diff(kT,mu,r_eff):
+    D=kT/(6.*s.pi*mu*r_eff)
+    return D
+
+def R_mob(kT,mu, D):
+    r_eff=kT/(6.*s.pi*mu*D)
+
+    return r_eff
+
+
+
+
+kT=0.5
+mu=1./(3.*s.pi)
+
+Diff_R_h=Diff(kT,mu,R_h_mean)
+
+
+Diff_R_gyr=Diff(kT,mu,R_gyr_mean)
+
+print "D calculated with R_gyr is, ", Diff_R_gyr
+
+print "D calculated with R_h is, ", Diff_R_h
+
+R_mobility=R_mob(kT,mu,Diff_coeff)
+
+print "The effective mobility radius is ", R_mobility
+
+print "the ratio R_mobility/R_gyration is, ", R_mobility/R_gyr_mean
+
+print "the ratio R_mobility/R_hydro_mean is, ", R_mobility/R_h_mean
+
+# now I re-calculate the displacement for a given configuration as 
+
+
+
+
+
+
+
+
+
 #Now I calculate the diffusion coefficient from the collected cluster positions
 
 print "s.shape(R_cm_arr) is, ", s.shape(R_cm_arr)
@@ -1289,39 +1339,29 @@
 
 
 
+#delta_r_sq_formed
 
-def Diff(kT,mu,r_eff):
-    D=kT/(6.*s.pi*mu*r_eff)
-    return D
+i=70
 
-def R_mob(kT,mu, D):
-    r_eff=kT/(6.*s.pi*mu*D)
+print "I select time configuration (numbered from 0!!!), ", i
 
-    return r_eff
+test_x_cm=R_cm_arr[:,(i*3)]
+test_y_cm=R_cm_arr[:,(i*3+1)]
+test_z_cm=R_cm_arr[:,(i*3+2)]
+    
+delta_x_sq_test=test_x_cm.var()
+delta_y_sq_test=test_y_cm.var()
+delta_z_sq_test=test_z_cm.var()
+
+delta_r_sq_test=delta_x_sq_test+delta_y_sq_test+delta_z_sq_test
+
+print "delta_r_sq_test is, ", delta_r_sq_test
 
 
 
 
-kT=0.5
-mu=1./(3.*s.pi)
-
-Diff_R_h=Diff(kT,mu,R_h_mean)
-
-
-Diff_R_gyr=Diff(kT,mu,R_gyr_mean)
-
-print "D calculated with R_gyr is, ", Diff_R_gyr
-
-print "D calculated with R_h is, ", Diff_R_h
-
-R_mobility=R_mob(kT,mu,D_mean)
-
-print "The effective mobility radius is ", R_mobility
-
-print "the ratio R_mobility/R_gyration is, ", R_mobility/R_gyr_mean
-
-print "the ratio R_mobility/R_hydro_mean is, ", R_mobility/R_h_mean
 
 
 
 print "So far so good"
+