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This commit is contained in:
Stan Gerald Moore
2021-10-13 14:03:50 -06:00
parent 9cfb822847
commit 74219585f3
10 changed files with 772 additions and 66 deletions
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1
examples/reaxff/water/in.water.acks2.field
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@ -22,6 +22,7 @@ velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10

1
examples/reaxff/water/in.water.qeq.field
View File

@ -22,6 +22,7 @@ velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10

129
examples/reaxff/water/log.13Oct21.reaxff.water-acks2-field.g++.1 Normal file
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@ -0,0 +1,129 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 361.2 | 361.2 | 361.2 Mbytes
Step Temp Press Density Volume
0 300 -20762.954 0.99996859 29916.212
10 396.27588 -18423.747 1.0000143 29914.844
20 518.59361 -10010.691 1.0000209 29914.647
Loop time of 29.8896 on 1 procs for 20 steps with 3000 atoms
Performance: 0.029 ns/day, 830.268 hours/ns, 0.669 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.611 | 11.611 | 11.611 | 0.0 | 38.85
Neigh | 0.6729 | 0.6729 | 0.6729 | 0.0 | 2.25
Comm | 0.0020791 | 0.0020791 | 0.0020791 | 0.0 | 0.01
Output | 0.00015777 | 0.00015777 | 0.00015777 | 0.0 | 0.00
Modify | 17.602 | 17.602 | 17.602 | 0.0 | 58.89
Other | | 0.001149 | | | 0.00
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5438.00 ave 5438 max 5438 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 787357.0 ave 787357 max 787357 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 787357
Ave neighs/atom = 262.45233
Neighbor list builds = 7
Dangerous builds = 0
Total wall time: 0:00:32

129
examples/reaxff/water/log.13Oct21.reaxff.water-acks2-field.g++.4 Normal file
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@ -0,0 +1,129 @@
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.011 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
2 by 1 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 198.5 | 199.3 | 199.9 Mbytes
Step Temp Press Density Volume
0 300 -20761.724 0.99996859 29916.212
10 396.27588 -18420.441 1.0000144 29914.843
20 518.59146 -10012.622 1.0000207 29914.652
Loop time of 11.3556 on 4 procs for 20 steps with 3000 atoms
Performance: 0.076 ns/day, 315.433 hours/ns, 1.761 timesteps/s
94.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7511 | 3.8123 | 3.9245 | 3.4 | 33.57
Neigh | 0.36492 | 0.3767 | 0.39023 | 1.5 | 3.32
Comm | 0.12022 | 0.23202 | 0.29307 | 13.8 | 2.04
Output | 8.0451e-05 | 0.00017452 | 0.00045489 | 0.0 | 0.00
Modify | 6.9172 | 6.9312 | 6.9431 | 0.4 | 61.04
Other | | 0.003189 | | | 0.03
Nlocal: 750.000 ave 758 max 737 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 4219.50 ave 4233 max 4198 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Neighs: 230733.0 ave 233431 max 225531 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Total # of neighbors = 922931
Ave neighs/atom = 307.64367
Neighbor list builds = 7
Dangerous builds = 0
Total wall time: 0:00:12

78
examples/reaxff/water/log.20Sep21.reaxff.water-acks2.g++.1 → examples/reaxff/water/log.13Oct21.reaxff.water-acks2.g++.1
View File

@ -1,23 +1,75 @@
LAMMPS (31 Aug 2021)
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:295)
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
The log file lists these citations in BibTeX format.
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -38,29 +90,25 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 574.5 | 574.5 | 574.5 Mbytes
Step Temp Press Density Volume
0 300 1572.3474 1 29915.273
10 300.61522 8252.7686 1 29915.273
20 294.7387 2502.6624 1 29915.273
Loop time of 25.3632 on 1 procs for 20 steps with 3000 atoms
Loop time of 25.9579 on 1 procs for 20 steps with 3000 atoms
Performance: 0.034 ns/day, 704.533 hours/ns, 0.789 timesteps/s
Performance: 0.033 ns/day, 721.052 hours/ns, 0.770 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.789 | 13.789 | 13.789 | 0.0 | 54.37
Neigh | 0.33364 | 0.33364 | 0.33364 | 0.0 | 1.32
Comm | 0.002672 | 0.002672 | 0.002672 | 0.0 | 0.01
Output | 0.00013542 | 0.00013542 | 0.00013542 | 0.0 | 0.00
Modify | 11.237 | 11.237 | 11.237 | 0.0 | 44.30
Other | | 0.000942 | | | 0.00
Pair | 14.081 | 14.081 | 14.081 | 0.0 | 54.24
Neigh | 0.34284 | 0.34284 | 0.34284 | 0.0 | 1.32
Comm | 0.0027799 | 0.0027799 | 0.0027799 | 0.0 | 0.01
Output | 0.00012876 | 0.00012876 | 0.00012876 | 0.0 | 0.00
Modify | 11.53 | 11.53 | 11.53 | 0.0 | 44.42
Other | | 0.001007 | | | 0.00
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

86
examples/reaxff/water/log.20Sep21.reaxff.water-acks2.g++.4 → examples/reaxff/water/log.13Oct21.reaxff.water-acks2.g++.4
View File

@ -1,23 +1,75 @@
LAMMPS (31 Aug 2021)
LAMMPS (29 Sep 2021)
# ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
read_data CPU = 0.013 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:295)
replicate CPU = 0.002 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * acks2_ff.water O H
Reading potential file acks2_ff.water with DATE: 2021-09-21
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
The log file lists these citations in BibTeX format.
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -38,29 +90,25 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 271.9 | 273.6 | 275.1 Mbytes
Step Temp Press Density Volume
0 300 1572.3807 1 29915.273
10 300.6152 8252.4834 1 29915.273
20 294.73868 2502.5661 1 29915.273
Loop time of 8.86017 on 4 procs for 20 steps with 3000 atoms
Loop time of 11.1133 on 4 procs for 20 steps with 3000 atoms
Performance: 0.098 ns/day, 246.116 hours/ns, 2.257 timesteps/s
98.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.078 ns/day, 308.702 hours/ns, 1.800 timesteps/s
92.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.4245 | 4.5176 | 4.5927 | 3.2 | 50.99
Neigh | 0.15776 | 0.15897 | 0.16001 | 0.2 | 1.79
Comm | 0.06196 | 0.13722 | 0.23035 | 18.5 | 1.55
Output | 7.534e-05 | 0.00010848 | 0.00019836 | 0.0 | 0.00
Modify | 4.0442 | 4.0453 | 4.0465 | 0.0 | 45.66
Other | | 0.0009994 | | | 0.01
Pair | 4.3609 | 4.7715 | 5.4812 | 19.5 | 42.94
Neigh | 0.15797 | 0.17176 | 0.19405 | 3.5 | 1.55
Comm | 0.21014 | 0.922 | 1.3353 | 44.6 | 8.30
Output | 8.815e-05 | 0.0002 | 0.00030501 | 0.0 | 0.00
Modify | 5.2267 | 5.2468 | 5.2584 | 0.5 | 47.21
Other | | 0.001074 | | | 0.01
Nlocal: 750.000 ave 760 max 735 min
Histogram: 1 0 0 0 1 0 0 0 0 2
@ -73,4 +121,4 @@ Total # of neighbors = 1108026
Ave neighs/atom = 369.34200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09
Total wall time: 0:00:12

128
examples/reaxff/water/log.13Oct21.reaxff.water-qeq-field.g++.1 Normal file
View File

@ -0,0 +1,128 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 332.3 | 332.3 | 332.3 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 15.4107 on 1 procs for 20 steps with 3000 atoms
Performance: 0.056 ns/day, 428.074 hours/ns, 1.298 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.413 | 11.413 | 11.413 | 0.0 | 74.06
Neigh | 0.57486 | 0.57486 | 0.57486 | 0.0 | 3.73
Comm | 0.0019709 | 0.0019709 | 0.0019709 | 0.0 | 0.01
Output | 0.00013211 | 0.00013211 | 0.00013211 | 0.0 | 0.00
Modify | 3.4192 | 3.4192 | 3.4192 | 0.0 | 22.19
Other | | 0.001104 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5439.00 ave 5439 max 5439 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 786591.0 ave 786591 max 786591 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 786591
Ave neighs/atom = 262.19700
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:16

128
examples/reaxff/water/log.13Oct21.reaxff.water-qeq-field.g++.4 Normal file
View File

@ -0,0 +1,128 @@
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p s
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (../atom.cpp:1208)
3000 atoms
read_data CPU = 0.017 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0012889577) to (31.043046 31.043046 31.045309)
2 by 1 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.002 seconds
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
fix 3 all efield 0.0 0.0 1.0
fix 4 all wall/reflect zlo EDGE zhi EDGE
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 6 6 6
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 188.9 | 189.5 | 190.1 Mbytes
Step Temp Press Density Volume
0 300 25015.837 0.99996859 29916.212
10 348.83356 31131.298 0.99964273 29925.965
20 414.67243 27564.999 0.99979791 29921.32
Loop time of 5.71549 on 4 procs for 20 steps with 3000 atoms
Performance: 0.151 ns/day, 158.764 hours/ns, 3.499 timesteps/s
94.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6678 | 3.8126 | 4.1402 | 9.8 | 66.71
Neigh | 0.31449 | 0.34639 | 0.38898 | 5.5 | 6.06
Comm | 0.032125 | 0.35935 | 0.50408 | 31.9 | 6.29
Output | 7.643e-05 | 0.00015959 | 0.00039876 | 0.0 | 0.00
Modify | 1.1534 | 1.1959 | 1.2283 | 3.0 | 20.92
Other | | 0.001099 | | | 0.02
Nlocal: 750.000 ave 757 max 738 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 4219.00 ave 4232 max 4198 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 230549.0 ave 233374 max 225849 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Total # of neighbors = 922196
Ave neighs/atom = 307.39867
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:06

77
examples/reaxff/water/log.20Sep21.reaxff.water-qeq.g++.1 → examples/reaxff/water/log.13Oct21.reaxff.water-qeq.g++.1
View File

@ -1,23 +1,74 @@
LAMMPS (31 Aug 2021)
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 1 by 1 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:295)
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
The log file lists these citations in BibTeX format.
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -38,29 +89,25 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 539.2 | 539.2 | 539.2 Mbytes
Step Temp Press Density Volume
0 300 780.33989 1 29915.273
10 301.29205 5433.7415 1 29915.273
20 297.90652 1572.6111 1 29915.273
Loop time of 17.1814 on 1 procs for 20 steps with 3000 atoms
Loop time of 17.5765 on 1 procs for 20 steps with 3000 atoms
Performance: 0.050 ns/day, 477.262 hours/ns, 1.164 timesteps/s
Performance: 0.049 ns/day, 488.237 hours/ns, 1.138 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.501 | 13.501 | 13.501 | 0.0 | 78.58
Neigh | 0.33379 | 0.33379 | 0.33379 | 0.0 | 1.94
Comm | 0.0026753 | 0.0026753 | 0.0026753 | 0.0 | 0.02
Output | 0.00013304 | 0.00013304 | 0.00013304 | 0.0 | 0.00
Modify | 3.3425 | 3.3425 | 3.3425 | 0.0 | 19.45
Other | | 0.0009654 | | | 0.01
Pair | 13.806 | 13.806 | 13.806 | 0.0 | 78.55
Neigh | 0.34211 | 0.34211 | 0.34211 | 0.0 | 1.95
Comm | 0.0028155 | 0.0028155 | 0.0028155 | 0.0 | 0.02
Output | 0.00012279 | 0.00012279 | 0.00012279 | 0.0 | 0.00
Modify | 3.4248 | 3.4248 | 3.4248 | 0.0 | 19.49
Other | | 0.001008 | | | 0.01
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

81
examples/reaxff/water/log.20Sep21.reaxff.water-qeq.g++.4 → examples/reaxff/water/log.13Oct21.reaxff.water-qeq.g++.4
View File

@ -1,23 +1,74 @@
LAMMPS (31 Aug 2021)
LAMMPS (29 Sep 2021)
# QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015)
boundary p p p
units real
atom_style charge
read_data data.water
Reading data file ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
reading atoms ...
3000 atoms
read_data CPU = 0.010 seconds
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
replicate 1 $y $z
replicate 1 1 $z
replicate 1 1 1
Replicating atoms ...
orthogonal box = (0.0000000 0.0000000 0.0000000) to (31.043046 31.043046 31.043046)
1 by 2 by 2 MPI processor grid
3000 atoms
replicate CPU = 0.001 seconds
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:295)
pair_style reaxff NULL safezone 3.0 mincap 150
pair_coeff * * qeq_ff.water O H
WARNING: Changed valency_val to valency_boc for X (../reaxff_ffield.cpp:296)
neighbor 0.5 bin
neigh_modify every 1 delay 0 check yes
velocity all create 300.0 4928459 rot yes dist gaussian
fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400
fix 2 all nvt temp 300 300 50.0
timestep 0.5
thermo 10
thermo_style custom step temp press density vol
run 20
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix qeq/reaxff command:
The log file lists these citations in BibTeX format.
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -38,29 +89,25 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 0.5
Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes
Step Temp Press Density Volume
0 300 780.34006 1 29915.273
10 301.29205 5433.7414 1 29915.273
20 297.90652 1572.6111 1 29915.273
Loop time of 9.57716 on 4 procs for 20 steps with 3000 atoms
Loop time of 6.79573 on 4 procs for 20 steps with 3000 atoms
Performance: 0.090 ns/day, 266.032 hours/ns, 2.088 timesteps/s
82.6% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.127 ns/day, 188.770 hours/ns, 2.943 timesteps/s
93.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.8491 | 5.0977 | 5.5111 | 11.0 | 53.23
Neigh | 0.19318 | 0.20407 | 0.22812 | 3.1 | 2.13
Comm | 0.91123 | 1.3208 | 1.5758 | 21.5 | 13.79
Output | 8.1778e-05 | 0.00012696 | 0.00025511 | 0.0 | 0.00
Modify | 2.8506 | 2.8668 | 2.8843 | 0.8 | 29.93
Other | | 0.08761 | | | 0.91
Pair | 4.4827 | 4.6649 | 4.866 | 6.6 | 68.64
Neigh | 0.16329 | 0.17253 | 0.18074 | 1.6 | 2.54
Comm | 0.44871 | 0.64804 | 0.82827 | 17.5 | 9.54
Output | 9.9269e-05 | 0.00013061 | 0.00022048 | 0.0 | 0.00
Modify | 1.3028 | 1.3091 | 1.3201 | 0.6 | 19.26
Other | | 0.001043 | | | 0.02
Nlocal: 750.000 ave 759 max 735 min
Histogram: 1 0 0 0 0 1 0 0 0 2
@ -73,4 +120,4 @@ Total # of neighbors = 1108032
Ave neighs/atom = 369.34400
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:10
Total wall time: 0:00:07