improved coloring of LJ-evolution

Author: simongravelle

figures/LJ-evolution.png

@@ -23,6 +23,7 @@ solution/improved.min.png
 solution/improved.md.lmp
 solution/improved.md.log
 solution/improved.md.dat
+solution/improved.md.png
 solution/min_coords.data
 
 # 3) folders not known to LAMMPS GUI will be skipped

files/tutorial1/.manifest

@@ -31,7 +31,7 @@ thermo          1000
 thermo_style    custom step temp pe ke etotal press v_n1_in v_n2_in c_sumcoor12
 
 dump            mydmp    all      image 100 dump.md.*.ppm type type shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes
-dump_modify     mydmp adiam 1 1 adiam 2 3 acolor 1 darkturquoise acolor 2 darkblue backcolor white
+dump_modify     mydmp adiam 1 1 adiam 2 3 acolor 1 turquoise acolor 2 royalblue backcolor white
 
 # 5) Run
 velocity        all create 1.0 49284 mom yes dist gaussian

files/tutorial1/solution/improved.md.lmp

@@ -7,7 +7,7 @@ Reading data file ...
   1150 atoms
   reading velocities ...
   1150 velocities
-  read_data CPU = 0.008 seconds
+  read_data CPU = 0.016 seconds
 1000 atoms in group grp_t1
 150 atoms in group grp_t2
 165 atoms in group grp_in
@@ -351,20 +351,20 @@ Per MPI rank memory allocation (min/avg/max) = 12.62 | 12.62 | 12.62 Mbytes
     298000   0.99957512    -0.21748891     1.4979859      1.2804969      0.016812985    200            59             0.054054054  
     299000   1.0174594     -0.24203802     1.5247876      1.2827496      0.016035544    202            60             0.045738046  
     300000   0.99574358    -0.22448684     1.4922438      1.267757       0.015433292    191            59             0.043659044  
-Loop time of 524.734 on 8 procs for 300000 steps with 1089 atoms
+Loop time of 611.436 on 8 procs for 300000 steps with 1089 atoms
 
-Performance: 246982.373 tau/day, 571.718 timesteps/s, 622.601 katom-step/s
-438.2% CPU use with 1 MPI tasks x 8 OpenMP threads
+Performance: 211959.960 tau/day, 490.648 timesteps/s, 534.316 katom-step/s
+456.3% CPU use with 1 MPI tasks x 8 OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 17.781     | 17.781     | 17.781     |   0.0 |  3.39
-Neigh   | 8.0319     | 8.0319     | 8.0319     |   0.0 |  1.53
-Comm    | 6.3951     | 6.3951     | 6.3951     |   0.0 |  1.22
-Output  | 429.93     | 429.93     | 429.93     |   0.0 | 81.93
-Modify  | 60.066     | 60.066     | 60.066     |   0.0 | 11.45
-Other   |            | 2.532      |            |       |  0.48
+Pair    | 19.164     | 19.164     | 19.164     |   0.0 |  3.13
+Neigh   | 9.4899     | 9.4899     | 9.4899     |   0.0 |  1.55
+Comm    | 7.3851     | 7.3851     | 7.3851     |   0.0 |  1.21
+Output  | 504.32     | 504.32     | 504.32     |   0.0 | 82.48
+Modify  | 68.283     | 68.283     | 68.283     |   0.0 | 11.17
+Other   |            | 2.798      |            |       |  0.46
 
 Nlocal:           1089 ave        1089 max        1089 min
 Histogram: 1 0 0 0 0 0 0 0 0 0

files/tutorial1/solution/improved.md.log

@@ -1,4 +1,4 @@
-LAMMPS data file via write_data, version 27 Jun 2024, timestep = 1000, units = lj
+LAMMPS data file via write_data, version 29 Aug 2024, timestep = 1000, units = lj
 
 1150 atoms
 2 atom types

files/tutorial1/solution/improved.md.png

@@ -845,7 +845,7 @@ \subsubsection{My first input}
     size 800 800 zoom 1.452 shiny 0.7 fsaa yes &
     view 80 10 box yes 0.025 axes no 0.0 0.0 &
     center s 0.483725 0.510373 0.510373
-dump_modify viz pad 9 boxcolor darkblue &
+dump_modify viz pad 9 boxcolor royalblue &
     backcolor white adiam 1 1.6 adiam 2 4.8
 \end{lstlisting}
 This command tells LAMMPS to generate NetPBM format images every 100
@@ -1057,9 +1057,8 @@ \subsubsection{Improving the script}
 \end{figure}
 
 Finally, let us complete the script by adding the following lines to
-\flecmd{improved.md.lmp}.  Note that there is no
-need for a \lmpcmd{Settings} section, because the settings are taken
-from the \flecmd{.data} file.
+\flecmd{improved.md.lmp}.  Note that there is no need for a \lmpcmd{Settings}
+section, as the settings are taken from the \flecmd{.data} file.
 \begin{lstlisting}
 # 4) Visualization
 thermo 1000
@@ -1068,12 +1067,13 @@ \subsubsection{Improving the script}
 
 dump mydmp all image 100 dump.md.*.ppm type type &
   shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes
-dump_modify mydmp  adiam 1 1 adiam 2 3 acolor 1 &
-  darkturquoise acolor 2 darkblue backcolor white
+dump_modify mydmp adiam 1 1 adiam 2 3 acolor 1 &
+  turquoise acolor 2 royalblue backcolor white
 \end{lstlisting}
-The two variables, \lmpcmd{n1\_in}, \lmpcmd{n2\_in}, along with the compute
+The two variables \lmpcmd{n1\_in}, \lmpcmd{n2\_in}, along with the compute
 \lmpcmd{sumcoor12}, were added to the list of information printed during
-the simulation.
+the simulation. Additionally, images of the system will be created with
+slightly less saturated colors than the default ones. 
 
 Finally, add the following lines to \flecmd{improved.md.lmp}:
 \begin{lstlisting}