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tiny_epoxy: actually use log files

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This commit is contained in:
Jacob Gissinger
2022-12-15 13:22:15 -05:00
parent 35eff624ab
commit f0af982d09
2 changed files with 152 additions and 33 deletions
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92
examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.1
View File

@ -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
100.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 189.870 ns/day, 0.126 hours/ns, 2197.568 timesteps/s, 259.313 katom-step/s
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
Bond | 0.63695 | 0.63695 | 0.63695 | 0.0 | 70.01
Neigh | 0.013916 | 0.013916 | 0.013916 | 0.0 | 1.53
Comm | 0.0057214 | 0.0057214 | 0.0057214 | 0.0 | 0.63
Output | 0.0005856 | 0.0005856 | 0.0005856 | 0.0 | 0.06
Modify | 0.14641 | 0.14641 | 0.14641 | 0.0 | 16.09
Other | | 0.003576 | | | 0.39
Pair | 0.10286 | 0.10286 | 0.10286 | 0.0 | 11.30
Bond | 0.63714 | 0.63714 | 0.63714 | 0.0 | 70.01
Neigh | 0.013949 | 0.013949 | 0.013949 | 0.0 | 1.53
Comm | 0.0056606 | 0.0056606 | 0.0056606 | 0.0 | 0.62
Output | 0.00055825 | 0.00055825 | 0.00055825 | 0.0 | 0.06
Modify | 0.14629 | 0.14629 | 0.14629 | 0.0 | 16.07
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

93
examples/PACKAGES/reaction/tiny_epoxy/log.4Nov2022.tiny_epoxy.stabilized.g++.4
View File

@ -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
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 366.420 ns/day, 0.065 hours/ns, 4240.970 timesteps/s, 500.434 katom-step/s
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
Bond | 0.072805 | 0.16458 | 0.21783 | 13.9 | 34.78
Neigh | 0.0056701 | 0.0057265 | 0.0057792 | 0.1 | 1.21
Comm | 0.028105 | 0.095922 | 0.19546 | 20.3 | 20.27
Output | 0.00034311 | 0.00041507 | 0.0006278 | 0.0 | 0.09
Modify | 0.17725 | 0.17761 | 0.17826 | 0.1 | 37.54
Other | | 0.004064 | | | 0.86
Pair | 0.016546 | 0.024458 | 0.038858 | 5.5 | 5.19
Bond | 0.072622 | 0.16458 | 0.21778 | 13.9 | 34.90
Neigh | 0.0056307 | 0.0056812 | 0.0057292 | 0.1 | 1.20
Comm | 0.028022 | 0.095922 | 0.19526 | 20.3 | 20.34
Output | 0.00034591 | 0.00041633 | 0.00062378 | 0.0 | 0.09
Modify | 0.17613 | 0.17649 | 0.17711 | 0.1 | 37.43
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