tiny_epoxy: actually use log files

examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1

@@ -1,4 +1,24 @@
 LAMMPS (4 Nov 2022)
+# two molecules DGEBA (diepoxy) and one DETA (linker)
+# two crosslinking reactions
+
+units real
+
+boundary p p p
+
+atom_style full
+
+pair_style lj/class2 8
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_epoxy.data
 Reading data file ...
   orthogonal box = (10 -10 -15) to (30 20 10)
   1 by 1 by 1 MPI processor grid
@@ -33,7 +53,11 @@ Finding 1-2 1-3 1-4 neighbors ...
     19 = max # of 1-4 neighbors
     22 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.022 seconds
+  read_data CPU = 0.015 seconds
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_pre.molecule_template
 Read molecule template mol1:
   1 molecules
   0 fragments
@@ -42,6 +66,7 @@ Read molecule template mol1:
   53 angles with max type 29
   66 dihedrals with max type 39
   3 impropers with max type 5
+molecule mol2 rxn1_stp1_post.molecule_template
 Read molecule template mol2:
   1 molecules
   0 fragments
@@ -50,6 +75,7 @@ Read molecule template mol2:
   55 angles with max type 36
   75 dihedrals with max type 51
   2 impropers with max type 5
+molecule mol3 rxn1_stp2_post.molecule_template
 Read molecule template mol3:
   1 molecules
   0 fragments
@@ -58,6 +84,7 @@ Read molecule template mol3:
   53 angles with max type 37
   72 dihedrals with max type 53
   3 impropers with max type 5
+molecule mol4 rxn2_stp1_pre.molecule_template
 Read molecule template mol4:
   1 molecules
   0 fragments
@@ -66,6 +93,7 @@ Read molecule template mol4:
   73 angles with max type 41
   96 dihedrals with max type 54
   3 impropers with max type 5
+molecule mol5 rxn2_stp1_post.molecule_template
 Read molecule template mol5:
   1 molecules
   0 fragments
@@ -74,6 +102,7 @@ Read molecule template mol5:
   75 angles with max type 37
   108 dihedrals with max type 53
   2 impropers with max type 5
+molecule mol6 rxn2_stp2_post.molecule_template
 Read molecule template mol6:
   1 molecules
   0 fragments
@@ -82,14 +111,46 @@ Read molecule template mol6:
   73 angles with max type 50
   102 dihedrals with max type 66
   3 impropers with max type 22
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix rxns all bond/react stabilization yes statted_grp .03   react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map   react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map   react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map   react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
 dynamic group bond_react_MASTER_group defined
 dynamic group statted_grp_REACT defined
 
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
+
+run 2000
+
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
 Your simulation uses code contributions which should be cited:
+
 - fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
-The log file lists these citations in BibTeX format.
+
+@Article{Gissinger17,
+ author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
+ title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
+ journal = {Polymer},
+ year =    2017,
+ volume =  128,
+ pages =   {211--217}
+}
+
+@Article{Gissinger20,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
+ journal = {Macromolecules},
+ year =    2020,
+ volume =  53,
+ number =  22,
+ pages =   {9953--9961}
+}
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -111,10 +172,6 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Setting up Verlet run ...
-  Unit style    : real
-  Current step  : 0
-  Time step     : 1
 Per MPI rank memory allocation (min/avg/max) = 16.64 | 16.64 | 16.64 Mbytes
    Step          Temp        f_rxns[1]      f_rxns[2]      f_rxns[3]      f_rxns[4]   
          0   300            0              0              0              0            
@@ -158,21 +215,21 @@ Per MPI rank memory allocation (min/avg/max) = 16.64 | 16.64 | 16.64 Mbytes
       1900   315.3756       1              1              1              1            
       1950   260.65335      1              1              1              1            
       2000   354.03612      1              1              1              1            
-Loop time of 0.909774 on 1 procs for 2000 steps with 118 atoms
+Loop time of 0.910097 on 1 procs for 2000 steps with 118 atoms
 
-Performance: 189.937 ns/day, 0.126 hours/ns, 2198.347 timesteps/s, 259.405 katom-step/s
+Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s
-100.0% CPU use with 1 MPI tasks x no OpenMP threads
+99.9% CPU use with 1 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.10261    | 0.10261    | 0.10261    |   0.0 | 11.28
+Pair    | 0.10286    | 0.10286    | 0.10286    |   0.0 | 11.30
-Bond    | 0.63695    | 0.63695    | 0.63695    |   0.0 | 70.01
+Bond    | 0.63714    | 0.63714    | 0.63714    |   0.0 | 70.01
-Neigh   | 0.013916   | 0.013916   | 0.013916   |   0.0 |  1.53
+Neigh   | 0.013949   | 0.013949   | 0.013949   |   0.0 |  1.53
-Comm    | 0.0057214  | 0.0057214  | 0.0057214  |   0.0 |  0.63
+Comm    | 0.0056606  | 0.0056606  | 0.0056606  |   0.0 |  0.62
-Output  | 0.0005856  | 0.0005856  | 0.0005856  |   0.0 |  0.06
+Output  | 0.00055825 | 0.00055825 | 0.00055825 |   0.0 |  0.06
-Modify  | 0.14641    | 0.14641    | 0.14641    |   0.0 | 16.09
+Modify  | 0.14629    | 0.14629    | 0.14629    |   0.0 | 16.07
-Other   |            | 0.003576   |            |       |  0.39
+Other   |            | 0.003637   |            |       |  0.40
 
 Nlocal:            118 ave         118 max         118 min
 Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -186,4 +243,7 @@ Ave neighs/atom = 29.550847
 Ave special neighs/atom = 10.576271
 Neighbor list builds = 68
 Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data nofix
 Total wall time: 0:00:01

examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4

@@ -1,5 +1,24 @@
 LAMMPS (4 Nov 2022)
-WARNING: Using I/O redirection is unreliable with parallel runs. Better use -in switch to read input file. (../lammps.cpp:529)
+# two molecules DGEBA (diepoxy) and one DETA (linker)
+# two crosslinking reactions
+
+units real
+
+boundary p p p
+
+atom_style full
+
+pair_style lj/class2 8
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_epoxy.data
 Reading data file ...
   orthogonal box = (10 -10 -15) to (30 20 10)
   1 by 2 by 2 MPI processor grid
@@ -34,7 +53,11 @@ Finding 1-2 1-3 1-4 neighbors ...
     19 = max # of 1-4 neighbors
     22 = max # of special neighbors
   special bonds CPU = 0.000 seconds
-  read_data CPU = 0.009 seconds
+  read_data CPU = 0.013 seconds
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_pre.molecule_template
 Read molecule template mol1:
   1 molecules
   0 fragments
@@ -43,6 +66,7 @@ Read molecule template mol1:
   53 angles with max type 29
   66 dihedrals with max type 39
   3 impropers with max type 5
+molecule mol2 rxn1_stp1_post.molecule_template
 Read molecule template mol2:
   1 molecules
   0 fragments
@@ -51,6 +75,7 @@ Read molecule template mol2:
   55 angles with max type 36
   75 dihedrals with max type 51
   2 impropers with max type 5
+molecule mol3 rxn1_stp2_post.molecule_template
 Read molecule template mol3:
   1 molecules
   0 fragments
@@ -59,6 +84,7 @@ Read molecule template mol3:
   53 angles with max type 37
   72 dihedrals with max type 53
   3 impropers with max type 5
+molecule mol4 rxn2_stp1_pre.molecule_template
 Read molecule template mol4:
   1 molecules
   0 fragments
@@ -67,6 +93,7 @@ Read molecule template mol4:
   73 angles with max type 41
   96 dihedrals with max type 54
   3 impropers with max type 5
+molecule mol5 rxn2_stp1_post.molecule_template
 Read molecule template mol5:
   1 molecules
   0 fragments
@@ -75,6 +102,7 @@ Read molecule template mol5:
   75 angles with max type 37
   108 dihedrals with max type 53
   2 impropers with max type 5
+molecule mol6 rxn2_stp2_post.molecule_template
 Read molecule template mol6:
   1 molecules
   0 fragments
@@ -83,14 +111,46 @@ Read molecule template mol6:
   73 angles with max type 50
   102 dihedrals with max type 66
   3 impropers with max type 22
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix rxns all bond/react stabilization yes statted_grp .03   react rxn1_stp1 all 1 0.0 5 mol1 mol2 rxn1_stp1.map   react rxn1_stp2 all 1 0.0 5 mol2 mol3 rxn1_stp2.map   react rxn2_stp1 all 1 0.0 5 mol4 mol5 rxn2_stp1.map   react rxn2_stp2 all 1 0.0 5 mol5 mol6 rxn2_stp2.map
 dynamic group bond_react_MASTER_group defined
 dynamic group statted_grp_REACT defined
 
+
+fix 1 statted_grp_REACT nvt temp 300 300 100
+
+thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
+
+run 2000
+
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
 Your simulation uses code contributions which should be cited:
+
 - fix bond/react: reacter.org doi:10.1016/j.polymer.2017.09.038, doi:10.1021/acs.macromol.0c02012
-The log file lists these citations in BibTeX format.
+
+@Article{Gissinger17,
+ author = {J. R. Gissinger and B. D. Jensen and K. E. Wise},
+ title = {Modeling Chemical Reactions in Classical Molecular Dynamics Simulations},
+ journal = {Polymer},
+ year =    2017,
+ volume =  128,
+ pages =   {211--217}
+}
+
+@Article{Gissinger20,
+ author = {J. R. Gissinger, B. D. Jensen, K. E. Wise},
+ title = {{REACTER}: A Heuristic Method for Reactive Molecular Dynamics},
+ journal = {Macromolecules},
+ year =    2020,
+ volume =  53,
+ number =  22,
+ pages =   {9953--9961}
+}
 
 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
 
@@ -112,10 +172,6 @@ Neighbor list info ...
       pair build: copy
       stencil: none
       bin: none
-Setting up Verlet run ...
-  Unit style    : real
-  Current step  : 0
-  Time step     : 1
 Per MPI rank memory allocation (min/avg/max) = 16.63 | 16.63 | 16.64 Mbytes
    Step          Temp        f_rxns[1]      f_rxns[2]      f_rxns[3]      f_rxns[4]   
          0   300            0              0              0              0            
@@ -159,21 +215,21 @@ Per MPI rank memory allocation (min/avg/max) = 16.63 | 16.63 | 16.64 Mbytes
       1900   315.3756       1              1              1              1            
       1950   260.65334      1              1              1              1            
       2000   354.03612      1              1              1              1            
-Loop time of 0.473184 on 4 procs for 2000 steps with 118 atoms
+Loop time of 0.47159 on 4 procs for 2000 steps with 118 atoms
 
-Performance: 365.186 ns/day, 0.066 hours/ns, 4226.686 timesteps/s, 498.749 katom-step/s
+Performance: 366.420 ns/day, 0.065 hours/ns, 4240.970 timesteps/s, 500.434 katom-step/s
-100.0% CPU use with 4 MPI tasks x no OpenMP threads
+99.9% CPU use with 4 MPI tasks x no OpenMP threads
 
 MPI task timing breakdown:
 Section |  min time  |  avg time  |  max time  |%varavg| %total
 ---------------------------------------------------------------
-Pair    | 0.01651    | 0.024868   | 0.039209   |   5.4 |  5.26
+Pair    | 0.016546   | 0.024458   | 0.038858   |   5.5 |  5.19
-Bond    | 0.072805   | 0.16458    | 0.21783    |  13.9 | 34.78
+Bond    | 0.072622   | 0.16458    | 0.21778    |  13.9 | 34.90
-Neigh   | 0.0056701  | 0.0057265  | 0.0057792  |   0.1 |  1.21
+Neigh   | 0.0056307  | 0.0056812  | 0.0057292  |   0.1 |  1.20
-Comm    | 0.028105   | 0.095922   | 0.19546    |  20.3 | 20.27
+Comm    | 0.028022   | 0.095922   | 0.19526    |  20.3 | 20.34
-Output  | 0.00034311 | 0.00041507 | 0.0006278  |   0.0 |  0.09
+Output  | 0.00034591 | 0.00041633 | 0.00062378 |   0.0 |  0.09
-Modify  | 0.17725    | 0.17761    | 0.17826    |   0.1 | 37.54
+Modify  | 0.17613    | 0.17649    | 0.17711    |   0.1 | 37.43
-Other   |            | 0.004064   |            |       |  0.86
+Other   |            | 0.00404    |            |       |  0.86
 
 Nlocal:           29.5 ave          45 max           7 min
 Histogram: 1 0 0 0 0 0 1 1 0 1
@@ -187,4 +243,7 @@ Ave neighs/atom = 29.550847
 Ave special neighs/atom = 10.576271
 Neighbor list builds = 68
 Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data nofix
 Total wall time: 0:00:00