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Tweak example and add reference logs

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This commit is contained in:
Stan Gerald Moore
2021-09-20 13:01:57 -06:00
parent 9feab449fb
commit d79b1b3145
7 changed files with 3320 additions and 6011 deletions
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9007
examples/reaxff/water/data.water
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10
examples/reaxff/water/in.water.acks2 Executable file → Normal file
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@ -2,10 +2,14 @@
boundary p p p
units real
atom_style full
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
@ -19,7 +23,7 @@ fix 1 all acks2/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 100
thermo 10
thermo_style custom step temp press density vol
run ${t}
run 20

10
examples/reaxff/water/in.water.qeq Executable file → Normal file
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@ -2,10 +2,14 @@
boundary p p p
units real
atom_style full
atom_style charge
read_data data.water
variable x index 1
variable y index 1
variable z index 1
replicate $x $y $z
pair_style reaxff NULL safezone 3.0 mincap 150
@ -19,7 +23,7 @@ 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 100
thermo 10
thermo_style custom step temp press density vol
run ${t}
run 20

76
examples/reaxff/water/log.20Sep21.reaxff.water-acks2.g++.1 Normal file
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LAMMPS (31 Aug 2021)
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
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)
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:
- fix acks2/reaxff command:
The log file lists these citations in BibTeX format.
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
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
Performance: 0.034 ns/day, 704.533 hours/ns, 0.789 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
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11077.0 ave 11077 max 11077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 971815.0 ave 971815 max 971815 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 971815
Ave neighs/atom = 323.93833
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:27

76
examples/reaxff/water/log.20Sep21.reaxff.water-acks2.g++.4 Normal file
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LAMMPS (31 Aug 2021)
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
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)
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:
- fix acks2/reaxff command:
The log file lists these citations in BibTeX format.
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
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
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
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
Nlocal: 750.000 ave 760 max 735 min
Histogram: 1 0 0 0 1 0 0 0 0 2
Nghost: 6231.50 ave 6255 max 6192 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Neighs: 277006.0 ave 280567 max 271394 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Total # of neighbors = 1108026
Ave neighs/atom = 369.34200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09

76
examples/reaxff/water/log.20Sep21.reaxff.water-qeq.g++.1 Normal file
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LAMMPS (31 Aug 2021)
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
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)
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:
- fix qeq/reaxff command:
The log file lists these citations in BibTeX format.
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
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
Performance: 0.050 ns/day, 477.262 hours/ns, 1.164 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
Nlocal: 3000.00 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11077.0 ave 11077 max 11077 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 971826.0 ave 971826 max 971826 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 971826
Ave neighs/atom = 323.94200
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:18

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examples/reaxff/water/log.20Sep21.reaxff.water-qeq.g++.4 Normal file
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LAMMPS (31 Aug 2021)
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
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)
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:
- fix qeq/reaxff command:
The log file lists these citations in BibTeX format.
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
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
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
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
Nlocal: 750.000 ave 759 max 735 min
Histogram: 1 0 0 0 0 1 0 0 0 2
Nghost: 6230.50 ave 6256 max 6190 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 277008.0 ave 280943 max 271394 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 1108032
Ave neighs/atom = 369.34400
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:10