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nylon_melt: actually use log files

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not output file
This commit is contained in:
Jacob Gissinger
2022-12-15 13:16:49 -05:00
parent b5eb64cc0c
commit 35eff624ab
2 changed files with 151 additions and 22 deletions
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75
examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.1
View File

@ -1,4 +1,25 @@
LAMMPS (4 Nov 2022)
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
1 by 1 by 1 MPI processor grid
@ -36,6 +57,10 @@ Finding 1-2 1-3 1-4 neighbors ...
41 = max # of special neighbors
special bonds CPU = 0.026 seconds
read_data CPU = 0.937 seconds
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
@ -44,6 +69,7 @@ Read molecule template mol1:
25 angles with max type 24
23 dihedrals with max type 33
2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
@ -52,6 +78,7 @@ Read molecule template mol2:
31 angles with max type 23
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
@ -60,6 +87,7 @@ Read molecule template mol3:
25 angles with max type 23
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
@ -68,15 +96,53 @@ Read molecule template mol4:
19 angles with max type 25
16 dihedrals with max type 29
2 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
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
@ -107,10 +173,6 @@ 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) = 209.8 | 209.8 | 209.8 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
@ -147,4 +209,7 @@ Ave neighs/atom = 196.80781
Ave special neighs/atom = 9.8480114
Neighbor list builds = 128
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:01:29

98
examples/PACKAGES/reaction/nylon,6-6_melt/log.4Nov2022.large_nylon_melt.g++.4
View File

@ -1,5 +1,25 @@
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)
# 35,000 atom nylon melt example
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data large_nylon_melt.data.gz extra/bond/per/atom 5 extra/angle/per/atom 15 extra/dihedral/per/atom 15 extra/improper/per/atom 25 extra/special/per/atom 25
Reading data file ...
orthogonal box = (-2.6834403 -2.0679138 -2.2198803) to (73.455228 73.244835 73.40648)
2 by 1 by 2 MPI processor grid
@ -36,7 +56,11 @@ Finding 1-2 1-3 1-4 neighbors ...
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.007 seconds
read_data CPU = 0.853 seconds
read_data CPU = 0.854 seconds
velocity all create 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.molecule_template
Read molecule template mol1:
1 molecules
0 fragments
@ -45,6 +69,7 @@ Read molecule template mol1:
25 angles with max type 24
23 dihedrals with max type 33
2 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.molecule_template
Read molecule template mol2:
1 molecules
0 fragments
@ -53,6 +78,7 @@ Read molecule template mol2:
31 angles with max type 23
39 dihedrals with max type 30
0 impropers with max type 0
molecule mol3 rxn1_stp2_unreacted.molecule_template
Read molecule template mol3:
1 molecules
0 fragments
@ -61,6 +87,7 @@ Read molecule template mol3:
25 angles with max type 23
30 dihedrals with max type 30
0 impropers with max type 0
molecule mol4 rxn1_stp2_reacted.molecule_template
Read molecule template mol4:
1 molecules
0 fragments
@ -69,15 +96,53 @@ Read molecule template mol4:
19 angles with max type 25
16 dihedrals with max type 29
2 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: Fix bond/react: Atom affected by reaction rxn2 is too close to template edge (../fix_bond_react.cpp:2624)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
# stable at 800K
fix 1 statted_grp_REACT nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
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
@ -108,10 +173,6 @@ 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) = 81.39 | 81.41 | 81.43 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
@ -119,22 +180,22 @@ Per MPI rank memory allocation (min/avg/max) = 81.39 | 81.41 | 81.43 Mbytes
100 694.36354 -2108.4881 0.80366765 57 22
150 716.5075 -12356.04 0.80366765 77 50
200 722.97306 -1308.3439 0.80366765 84 67
Loop time of 23.0703 on 4 procs for 200 steps with 35200 atoms
Loop time of 23.1041 on 4 procs for 200 steps with 35200 atoms
Performance: 0.749 ns/day, 32.042 hours/ns, 8.669 timesteps/s, 305.154 katom-step/s
Performance: 0.748 ns/day, 32.089 hours/ns, 8.656 timesteps/s, 304.708 katom-step/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.6778 | 6.8513 | 6.9896 | 5.2 | 29.70
Bond | 3.8962 | 3.9719 | 4.0488 | 3.0 | 17.22
Kspace | 1.1907 | 1.3846 | 1.6278 | 15.9 | 6.00
Neigh | 8.7963 | 8.7965 | 8.7967 | 0.0 | 38.13
Comm | 0.1468 | 0.15512 | 0.16131 | 1.6 | 0.67
Output | 0.00035931 | 0.00037432 | 0.00041707 | 0.0 | 0.00
Modify | 1.8808 | 1.8808 | 1.8809 | 0.0 | 8.15
Other | | 0.02973 | | | 0.13
Pair | 6.6935 | 6.8618 | 7.0049 | 5.1 | 29.70
Bond | 3.8936 | 3.9807 | 4.0626 | 3.5 | 17.23
Kspace | 1.1828 | 1.4033 | 1.6503 | 16.6 | 6.07
Neigh | 8.7942 | 8.7945 | 8.7946 | 0.0 | 38.06
Comm | 0.14682 | 0.15559 | 0.16441 | 1.8 | 0.67
Output | 0.00035959 | 0.00037472 | 0.00041627 | 0.0 | 0.00
Modify | 1.8787 | 1.8787 | 1.8788 | 0.0 | 8.13
Other | | 0.02917 | | | 0.13
Nlocal: 8800 ave 8911 max 8662 min
Histogram: 1 0 0 1 0 0 0 0 1 1
@ -148,4 +209,7 @@ Ave neighs/atom = 196.80838
Ave special neighs/atom = 9.8480114
Neighbor list builds = 128
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:24