fixed free sampling code and figures

Author: simongravelle

figures/US-density-evolution.png

@@ -1,54 +0,0 @@
-# Chunk-averaged data for fix myac and group all
-# Timestep Number-of-chunks Total-count
-# Chunk Coord1 Ncount density/number
-4000000 50 200.00000000000006
-  1 -24.5 4.74 0.00948
-  2 -23.5 4.7831 0.00956619
-  3 -22.5 4.7604 0.0095208
-  4 -21.5 4.86592 0.00973184
-  5 -20.5 4.86826 0.00973651
-  6 -19.5 4.76565 0.0095313
-  7 -18.5 4.79443 0.00958886
-  8 -17.5 4.85737 0.00971473
-  9 -16.5 4.89866 0.00979732
-  10 -15.5 4.82998 0.00965996
-  11 -14.5 4.90789 0.00981579
-  12 -13.5 4.93531 0.00987062
-  13 -12.5 4.91643 0.00983286
-  14 -11.5 4.86221 0.00972442
-  15 -10.5 4.96515 0.00993031
-  16 -9.5 4.93611 0.00987222
-  17 -8.5 4.47913 0.00895826
-  18 -7.5 4.73773 0.00947546
-  19 -6.5 5.79113 0.0115823
-  20 -5.5 4.64622 0.00929243
-  21 -4.5 1.05415 0.00210829
-  22 -3.5 0.72657 0.00145314
-  23 -2.5 0.751093 0.00150219
-  24 -1.5 0.73587 0.00147174
-  25 -0.5 0.721085 0.00144217
-  26 0.5 0.736407 0.00147281
-  27 1.5 0.760687 0.00152137
-  28 2.5 0.73136 0.00146272
-  29 3.5 0.63102 0.00126204
-  30 4.5 0.936882 0.00187376
-  31 5.5 4.4201 0.0088402
-  32 6.5 5.55349 0.011107
-  33 7.5 4.67568 0.00935137
-  34 8.5 4.50497 0.00900995
-  35 9.5 4.65875 0.0093175
-  36 10.5 4.73779 0.00947558
-  37 11.5 4.78154 0.00956308
-  38 12.5 4.7601 0.0095202
-  39 13.5 4.7299 0.0094598
-  40 14.5 4.7456 0.0094912
-  41 15.5 4.7732 0.00954639
-  42 16.5 4.71844 0.00943687
-  43 17.5 4.65763 0.00931525
-  44 18.5 4.59819 0.00919637
-  45 19.5 4.739 0.009478
-  46 20.5 4.79002 0.00958004
-  47 21.5 4.76412 0.00952823
-  48 22.5 4.71521 0.00943042
-  49 23.5 4.71839 0.00943677
-  50 24.5 4.83169 0.00966339

figures/US-density.png

@@ -2,16 +2,16 @@
 variable sigma equal 3.405
 variable epsilon equal 0.238
 variable U0 equal 1.5*${epsilon}
-variable dlt equal 0.5
-variable x0 equal 5.0
+variable dlt equal 1.0
+variable x0 equal 10.0
 
 units real
 atom_style atomic
 pair_style lj/cut 3.822
 pair_modify shift yes
 boundary p p p
 
-region myreg block -25 25 -5 5 -25 25
+region myreg block -50 50 -15 15 -50 50
 create_box 1 myreg
 create_atoms 1 random 200 34134 myreg overlap 3 maxtry 50
 
@@ -23,23 +23,25 @@ variable F atom ${U0}/((x-${x0})^2/${dlt}^2+1)/${dlt}-${U0}/((x+${x0})^2/${dlt}^
 fix myadf all addforce v_F 0.0 0.0 energy v_U
 
 fix mynve all nve
-fix mylgv all langevin 119.8 119.8 50 30917
+fix mylgv all langevin 119.8 119.8 500 30917
 
 region mymes block -${x0} ${x0} INF INF INF INF
 variable n_center equal count(all,mymes)
 thermo_style custom step temp etotal v_n_center
-thermo 10000
+thermo 2000
 
 dump viz all image 50000 myimage-*.ppm type type &
-    shiny 0.1 box yes 0.01 view 180 90 zoom 7 size 1600 400
-dump_modify viz backcolor white acolor 1 cyan adiam 1 1 boxcolor black
+    shiny 0.1 box yes 0.01 view 180 90 zoom 6 size 1600 500 fsaa yes
+dump_modify viz backcolor white acolor 1 cyan adiam 1 3 boxcolor black
 
 timestep 2.0
-run 500000
+run 50000
 reset_timestep 0
 
-compute cc1 all chunk/atom bin/1d x 0.0 1.0
-fix myac all ave/chunk 10 400000 4000000 &
+thermo 200000
+
+compute cc1 all chunk/atom bin/1d x 0.0 2.0
+fix myac all ave/chunk 100 20000 2000000 &
     cc1 density/number file free-sampling.dat
 
-run 4000000
+run 2000000

figures/US-potential.png

@@ -3573,7 +3573,7 @@ \subsubsection{Method 1: Free sampling}
 \begin{lstlisting}
 variable sigma equal 3.405
 variable epsilon equal 0.238
-variable U0 equal 2.0*${epsilon}
+variable U0 equal 1.5*${epsilon}
 variable dlt equal 0.5
 variable x0 equal 5.0
 
@@ -3740,9 +3740,9 @@ \subsubsection{Method 1: Free sampling}
 \begin{figure}
 \centering
 \includegraphics[width=\linewidth]{US-density}
-\caption{Fluid density $\rho$ along the $x$ direction. Here,
+\caption{Fluid density $\rho$ along the $x$ direction.  Here,
 $U_0 = 0.36~\text{kcal/mol}$, $\delta = 0.5~\mathrm{\AA{}}$, $x_0 = 5~\mathrm{\AA{}}$,
-and reference density $\rho_\text{bulk} = 0.0033~\text{\AA{}}^{-3}$.}
+and the reference density is $\rho_\text{bulk} = 0.0033~\text{\AA{}}^{-3}$.}
 \label{fig:US-density}
 \end{figure}