updated figures tutorial 1

Author: simongravelle

figures/LJ-energy.png

@@ -10,20 +10,20 @@ improved.md.lmp
 
 # 2) solution files
 # only downloaded on request
+solution/improved.md.dat
+solution/improved.md.lmp
+solution/improved.md.log
+solution/improved.md.mp4
+solution/improved.md.png
+solution/improved.min.data
+solution/improved.min.lmp
+solution/improved.min.log
+solution/improved.min.png
 solution/initial.lmp
 solution/initial.log
-solution/initial.parta.dat
-solution/initial.partb.dat
-solution/initial.run0.png
 solution/initial.min.png
 solution/initial.mp4
-solution/improved.min.lmp
-solution/improved.min.log
-solution/improved.min.png
-solution/improved.md.lmp
-solution/improved.md.log
-solution/improved.md.dat
-solution/improved.md.png
-solution/min_coords.data
+solution/initial.png
+
 
 # 3) folders not known to LAMMPS GUI will be skipped

figures/chart-1.png

@@ -8,6 +8,7 @@ units lj
 dimension 3
 atom_style atomic
 boundary p p p
+
 # 2) System definition
 pair_style lj/cut 4.0
 read_data improved.min.data
@@ -30,13 +31,17 @@ variable n1_in equal count(grp_t1,cyl_in)
 variable n2_in equal count(grp_t2,cyl_in)
 compute coor12 grp_t1 coord/atom cutoff 2.0 group grp_t2
 compute sumcoor12 grp_t1 reduce ave c_coor12
+
 # 3) Settings
+
 # 4) Visualization
 thermo 1000
-thermo_style custom step temp pe ke etotal press v_n1_in v_n2_in c_sumcoor12
-
-dump viz all image 100 myimage.md.*.ppm type type shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes
-dump_modify viz adiam 1 1 adiam 2 3 acolor 1 turquoise acolor 2 royalblue backcolor white
+thermo_style custom step temp pe ke etotal &
+  press v_n1_in v_n2_in c_sumcoor12
+dump viz all image 100 myimage-*.ppm type type &
+  shiny 0.1 box no 0.01 view 0 0 zoom 1.8 fsaa yes size 800 800
+dump_modify viz 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

figures/chart-and-output.png

@@ -8,6 +8,7 @@ units lj
 dimension 3
 atom_style atomic
 boundary p p p
+
 # 2) System definition
 region simbox block -20 20 -20 20 -20 20
 create_box 2 simbox
@@ -16,17 +17,21 @@ region cyl_in cylinder z 0 0 10 INF INF side in
 region cyl_out cylinder z 0 0 10 INF INF side out
 create_atoms 1 random 1000 34134 cyl_out
 create_atoms 2 random 150 12756 cyl_in
+
 # 3) Settings
 mass 1 1.0
 mass 2 10.0
 pair_style lj/cut 4.0
 pair_coeff 1 1 1.0 1.0
 pair_coeff 2 2 0.5 3.0
+
 # 4) Visualization
 thermo 10
 thermo_style custom step etotal press
+
 # 5) Run
 minimize 1.0e-6 1.0e-6 1000 10000
+
 # 6) Save system
 write_data improved.min.data
 

figures/output-1.png

@@ -4,7 +4,7 @@ Created orthogonal box = (-20 -20 -20) to (20 20 20)
   1 by 1 by 1 MPI processor grid
 Created 1000 atoms
   using lattice units in orthogonal box = (-20 -20 -20) to (20 20 20)
-  create_atoms CPU = 0.002 seconds
+  create_atoms CPU = 0.001 seconds
 Created 150 atoms
   using lattice units in orthogonal box = (-20 -20 -20) to (20 20 20)
   create_atoms CPU = 0.000 seconds
@@ -128,9 +128,9 @@ Per MPI rank memory allocation (min/avg/max) = 10.44 | 10.44 | 10.44 Mbytes
        980  -1.3509009     -0.00062855692
        990  -1.3621364     -0.00057827024
       1000  -1.3722835     -0.00049492281
-Loop time of 0.756427 on 8 procs for 1000 steps with 1150 atoms
+Loop time of 0.126597 on 8 procs for 1000 steps with 1150 atoms
 
-869.8% CPU use with 1 MPI tasks x 8 OpenMP threads
+884.9% CPU use with 1 MPI tasks x 8 OpenMP threads
 
 Minimization stats:
   Stopping criterion = max iterations
@@ -144,12 +144,12 @@ Minimization stats:
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.2483     | 0.2483     | 0.2483     |   0.0 | 32.83
-Neigh   | 0.11973    | 0.11973    | 0.11973    |   0.0 | 15.83
-Comm    | 0.10413    | 0.10413    | 0.10413    |   0.0 | 13.77
-Output  | 0.0049911  | 0.0049911  | 0.0049911  |   0.0 |  0.66
-Modify  | 0.091781   | 0.091781   | 0.091781   |   0.0 | 12.13
-Other   |            | 0.1875     |            |       | 24.79
+Pair    | 0.045      | 0.045      | 0.045      |   0.0 | 35.55
+Neigh   | 0.022573   | 0.022573   | 0.022573   |   0.0 | 17.83
+Comm    | 0.015767   | 0.015767   | 0.015767   |   0.0 | 12.45
+Output  | 0.000642   | 0.000642   | 0.000642   |   0.0 |  0.51
+Modify  | 0.014301   | 0.014301   | 0.014301   |   0.0 | 11.30
+Other   |            | 0.02832    |            |       | 22.37
 
 Nlocal:           1150 ave        1150 max        1150 min
 Histogram: 1 0 0 0 0 0 0 0 0 0