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replace planar logs

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This commit is contained in:
srtee
2022-12-01 11:48:26 +10:00
parent a733e4ddf9
commit 793987e0c3
10 changed files with 386 additions and 162 deletions
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50
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.1 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-7
kspace_modify slab ew2d
@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.006 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.005 seconds
group bot molecule 1
144 atoms in group bot
@ -67,6 +67,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 1.2145309e-07
KSpace vectors: actual max1d max3d = 90 5 665
kxmax kymax kzmax = 3 3 5
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -94,7 +112,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes
Per MPI rank memory allocation (min/avg/max) = 15.94 | 15.94 | 15.94 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703
@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.93 | 15.93 | 15.93 Mbytes
8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704
9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704
10 2 -0.30920491 0.30920491 0.31376826 -1.4543704
Loop time of 0.0912872 on 1 procs for 10 steps with 288 atoms
Loop time of 0.0451804 on 1 procs for 10 steps with 288 atoms
Performance: 9.465 ns/day, 2.536 hours/ns, 109.544 timesteps/s
400.1% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 19.123 ns/day, 1.255 hours/ns, 221.335 timesteps/s, 63.744 katom-step/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 | 0.0086713 | 0.0086713 | 0.0086713 | 0.0 | 9.50
Bond | 3.759e-06 | 3.759e-06 | 3.759e-06 | 0.0 | 0.00
Kspace | 0.04575 | 0.04575 | 0.04575 | 0.0 | 50.12
Pair | 0.0046814 | 0.0046814 | 0.0046814 | 0.0 | 10.36
Bond | 1.293e-06 | 1.293e-06 | 1.293e-06 | 0.0 | 0.00
Kspace | 0.028302 | 0.028302 | 0.028302 | 0.0 | 62.64
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00018224 | 0.00018224 | 0.00018224 | 0.0 | 0.20
Output | 0.0027569 | 0.0027569 | 0.0027569 | 0.0 | 3.02
Modify | 0.03386 | 0.03386 | 0.03386 | 0.0 | 37.09
Other | | 6.314e-05 | | | 0.07
Comm | 7.3611e-05 | 7.3611e-05 | 7.3611e-05 | 0.0 | 0.16
Output | 0.001128 | 0.001128 | 0.001128 | 0.0 | 2.50
Modify | 0.010919 | 0.010919 | 0.010919 | 0.0 | 24.17
Other | | 7.567e-05 | | | 0.17
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0

50
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew2d.g++.4 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew2d.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-7
kspace_modify slab ew2d
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.008 seconds
special bonds CPU = 0.003 seconds
read_data CPU = 0.009 seconds
group bot molecule 1
144 atoms in group bot
@ -68,6 +68,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 1.2145309e-07
KSpace vectors: actual max1d max3d = 90 5 665
kxmax kymax kzmax = 3 3 5
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -95,7 +113,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes
Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030920491 0.030920491 0.031376826 -1.4543703
@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.96 | 15.96 | 15.96 Mbytes
8 1.6 -0.24736393 0.24736393 0.25101461 -1.4543704
9 1.8 -0.27828442 0.27828442 0.28239144 -1.4543704
10 2 -0.30920491 0.30920491 0.31376826 -1.4543704
Loop time of 0.0456609 on 4 procs for 10 steps with 288 atoms
Loop time of 0.022489 on 4 procs for 10 steps with 288 atoms
Performance: 18.922 ns/day, 1.268 hours/ns, 219.006 timesteps/s
86.7% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 38.419 ns/day, 0.625 hours/ns, 444.661 timesteps/s, 128.062 katom-step/s
91.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0019389 | 0.0024013 | 0.0030807 | 0.9 | 5.26
Bond | 1.493e-06 | 1.7132e-06 | 1.935e-06 | 0.0 | 0.00
Kspace | 0.016165 | 0.016695 | 0.017072 | 0.3 | 36.56
Pair | 0.0011688 | 0.0013694 | 0.0016077 | 0.4 | 6.09
Bond | 6.72e-07 | 7.59e-07 | 9.02e-07 | 0.0 | 0.00
Kspace | 0.0077542 | 0.0093901 | 0.010384 | 1.0 | 41.75
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0030891 | 0.0037595 | 0.0040145 | 0.6 | 8.23
Output | 0.0024177 | 0.0027885 | 0.0037099 | 1.0 | 6.11
Modify | 0.01944 | 0.019746 | 0.020327 | 0.2 | 43.24
Other | | 0.0002691 | | | 0.59
Comm | 0.0015392 | 0.0016945 | 0.00183 | 0.3 | 7.53
Output | 0.00084374 | 0.0010929 | 0.0015437 | 0.8 | 4.86
Modify | 0.007495 | 0.0084669 | 0.010081 | 1.1 | 37.65
Other | | 0.0004745 | | | 2.11
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0

50
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.1 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-7
kspace_modify slab 3.0 # ew3dc
@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.004 seconds
group bot molecule 1
144 atoms in group bot
@ -67,6 +67,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 9.3919471e-08
KSpace vectors: actual max1d max3d = 266 12 7812
kxmax kymax kzmax = 3 3 12
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -94,7 +112,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes
Per MPI rank memory allocation (min/avg/max) = 27.29 | 27.29 | 27.29 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194
@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.27 | 27.27 | 27.27 Mbytes
8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195
9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195
10 2 -0.30925182 0.30925182 0.31376826 -1.4394195
Loop time of 0.0672288 on 1 procs for 10 steps with 288 atoms
Loop time of 0.0243868 on 1 procs for 10 steps with 288 atoms
Performance: 12.852 ns/day, 1.867 hours/ns, 148.746 timesteps/s
400.4% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 35.429 ns/day, 0.677 hours/ns, 410.058 timesteps/s, 118.097 katom-step/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 | 0.0071442 | 0.0071442 | 0.0071442 | 0.0 | 10.63
Bond | 2.976e-06 | 2.976e-06 | 2.976e-06 | 0.0 | 0.00
Kspace | 0.0097903 | 0.0097903 | 0.0097903 | 0.0 | 14.56
Pair | 0.0041504 | 0.0041504 | 0.0041504 | 0.0 | 17.02
Bond | 8.92e-07 | 8.92e-07 | 8.92e-07 | 0.0 | 0.00
Kspace | 0.0046942 | 0.0046942 | 0.0046942 | 0.0 | 19.25
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00023514 | 0.00023514 | 0.00023514 | 0.0 | 0.35
Output | 0.0029795 | 0.0029795 | 0.0029795 | 0.0 | 4.43
Modify | 0.047009 | 0.047009 | 0.047009 | 0.0 | 69.92
Other | | 6.809e-05 | | | 0.10
Comm | 6.7942e-05 | 6.7942e-05 | 6.7942e-05 | 0.0 | 0.28
Output | 0.0010799 | 0.0010799 | 0.0010799 | 0.0 | 4.43
Modify | 0.014311 | 0.014311 | 0.014311 | 0.0 | 58.69
Other | | 8.199e-05 | | | 0.34
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0

50
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ew3dc.g++.4 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ew3dc.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style ewald/electrode 1.0e-7
kspace_modify slab 3.0 # ew3dc
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.008 seconds
read_data CPU = 0.123 seconds
special bonds CPU = 0.003 seconds
read_data CPU = 0.007 seconds
group bot molecule 1
144 atoms in group bot
@ -68,6 +68,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -77,9 +95,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 9.3919471e-08
KSpace vectors: actual max1d max3d = 266 12 7812
kxmax kymax kzmax = 3 3 12
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -95,7 +113,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes
Per MPI rank memory allocation (min/avg/max) = 27.32 | 27.32 | 27.32 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030925182 0.030925182 0.031376826 -1.4394194
@ -108,22 +126,22 @@ Per MPI rank memory allocation (min/avg/max) = 27.31 | 27.31 | 27.31 Mbytes
8 1.6 -0.24740146 0.24740146 0.25101461 -1.4394195
9 1.8 -0.27832664 0.27832664 0.28239144 -1.4394195
10 2 -0.30925182 0.30925182 0.31376826 -1.4394195
Loop time of 0.0459561 on 4 procs for 10 steps with 288 atoms
Loop time of 0.0200123 on 4 procs for 10 steps with 288 atoms
Performance: 18.801 ns/day, 1.277 hours/ns, 217.599 timesteps/s
95.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 43.173 ns/day, 0.556 hours/ns, 499.692 timesteps/s, 143.911 katom-step/s
90.2% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021527 | 0.0026891 | 0.0037845 | 1.3 | 5.85
Bond | 1.303e-06 | 1.9462e-06 | 3.206e-06 | 0.0 | 0.00
Kspace | 0.0066254 | 0.0077509 | 0.0083577 | 0.8 | 16.87
Pair | 0.0014059 | 0.0015013 | 0.0015856 | 0.2 | 7.50
Bond | 7.12e-07 | 8.9675e-07 | 1.19e-06 | 0.0 | 0.00
Kspace | 0.0036091 | 0.0037586 | 0.0039024 | 0.2 | 18.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00285 | 0.0057275 | 0.0067088 | 2.2 | 12.46
Output | 0.0024325 | 0.0034682 | 0.0065316 | 3.0 | 7.55
Modify | 0.025911 | 0.025969 | 0.026007 | 0.0 | 56.51
Other | | 0.0003494 | | | 0.76
Comm | 0.0017095 | 0.0017404 | 0.001775 | 0.1 | 8.70
Output | 0.00092975 | 0.0010846 | 0.0015398 | 0.8 | 5.42
Modify | 0.011292 | 0.011375 | 0.011438 | 0.1 | 56.84
Other | | 0.0005509 | | | 2.75
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0

48
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.1 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p p # finite field, fully periodic
kspace_style ewald/electrode 1.0e-7
@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.010 seconds
read_data CPU = 0.004 seconds
group bot molecule 1
144 atoms in group bot
@ -66,6 +66,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -75,9 +93,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 1.2145309e-07
KSpace vectors: actual max1d max3d = 95 5 665
kxmax kymax kzmax = 3 3 5
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -93,7 +111,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes
Per MPI rank memory allocation (min/avg/max) = 16.02 | 16.02 | 16.02 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893
@ -106,22 +124,22 @@ Per MPI rank memory allocation (min/avg/max) = 16.01 | 16.01 | 16.01 Mbytes
8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893
9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893
10 2 -0.30908718 0.30908718 0.31376826 -1.491893
Loop time of 0.0481838 on 1 procs for 10 steps with 288 atoms
Loop time of 0.0147727 on 1 procs for 10 steps with 288 atoms
Performance: 17.931 ns/day, 1.338 hours/ns, 207.539 timesteps/s
390.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 58.486 ns/day, 0.410 hours/ns, 676.926 timesteps/s, 194.955 katom-step/s
75.1% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0071719 | 0.0071719 | 0.0071719 | 0.0 | 14.88
Bond | 2.946e-06 | 2.946e-06 | 2.946e-06 | 0.0 | 0.01
Kspace | 0.0038758 | 0.0038758 | 0.0038758 | 0.0 | 8.04
Pair | 0.0035163 | 0.0035163 | 0.0035163 | 0.0 | 23.80
Bond | 9.61e-07 | 9.61e-07 | 9.61e-07 | 0.0 | 0.01
Kspace | 0.0018156 | 0.0018156 | 0.0018156 | 0.0 | 12.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00053561 | 0.00053561 | 0.00053561 | 0.0 | 1.11
Output | 0.0025385 | 0.0025385 | 0.0025385 | 0.0 | 5.27
Modify | 0.033951 | 0.033951 | 0.033951 | 0.0 | 70.46
Other | | 0.0001075 | | | 0.22
Comm | 0.00012717 | 0.00012717 | 0.00012717 | 0.0 | 0.86
Output | 0.00083495 | 0.00083495 | 0.00083495 | 0.0 | 5.65
Modify | 0.0083949 | 0.0083949 | 0.0083949 | 0.0 | 56.83
Other | | 8.273e-05 | | | 0.56
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0

50
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-ewald-ffield.g++.4 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-ewald-ffield.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p p # finite field, fully periodic
kspace_style ewald/electrode 1.0e-7
@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.026 seconds
special bonds CPU = 0.002 seconds
read_data CPU = 0.006 seconds
group bot molecule 1
144 atoms in group bot
@ -67,6 +67,24 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Ewald/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -76,9 +94,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 1.2145309e-07
KSpace vectors: actual max1d max3d = 95 5 665
kxmax kymax kzmax = 3 3 5
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -94,7 +112,7 @@ Neighbor list info ...
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes
Per MPI rank memory allocation (min/avg/max) = 15.98 | 15.98 | 15.98 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030908718 0.030908718 0.031376826 -1.491893
@ -107,22 +125,22 @@ Per MPI rank memory allocation (min/avg/max) = 15.97 | 15.97 | 15.97 Mbytes
8 1.6 -0.24726974 0.24726974 0.25101461 -1.491893
9 1.8 -0.27817846 0.27817846 0.28239144 -1.491893
10 2 -0.30908718 0.30908718 0.31376826 -1.491893
Loop time of 0.0294825 on 4 procs for 10 steps with 288 atoms
Loop time of 0.0151333 on 4 procs for 10 steps with 288 atoms
Performance: 29.306 ns/day, 0.819 hours/ns, 339.184 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 57.093 ns/day, 0.420 hours/ns, 660.794 timesteps/s, 190.309 katom-step/s
41.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0020718 | 0.0025674 | 0.0029431 | 0.7 | 8.71
Bond | 1.423e-06 | 2.0293e-06 | 2.615e-06 | 0.0 | 0.01
Kspace | 0.0028016 | 0.0031772 | 0.0035529 | 0.5 | 10.78
Pair | 0.0014606 | 0.0015586 | 0.0016093 | 0.1 | 10.30
Bond | 9.31e-07 | 1.0197e-06 | 1.084e-06 | 0.0 | 0.01
Kspace | 0.0014157 | 0.0015231 | 0.0016295 | 0.2 | 10.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0023552 | 0.0032209 | 0.0035502 | 0.9 | 10.92
Output | 0.0011969 | 0.0016057 | 0.002676 | 1.5 | 5.45
Modify | 0.018358 | 0.018553 | 0.018654 | 0.1 | 62.93
Other | | 0.0003563 | | | 1.21
Comm | 0.0019994 | 0.0020111 | 0.0020282 | 0.0 | 13.29
Output | 0.00072893 | 0.00095378 | 0.0015177 | 0.0 | 6.30
Modify | 0.0081934 | 0.0082729 | 0.0083794 | 0.1 | 54.67
Other | | 0.0008128 | | | 5.37
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0

63
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.1 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style pppm/electrode 1.0e-7
kspace_modify slab 3.0
@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
special bonds CPU = 0.001 seconds
read_data CPU = 0.004 seconds
group bot molecule 1
144 atoms in group bot
@ -67,6 +67,35 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 8.4221827e-08
using double precision MKL FFT
3d grid and FFT values/proc = 4563 1600
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -97,7 +126,7 @@ Neighbor list info ...
stencil: none
bin: none
WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314)
Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.942 | 7.942 | 7.942 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807
@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.93 | 7.93 | 7.93 Mbytes
8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807
9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807
10 2 -0.30912769 0.30912769 0.31376826 -1.4789807
Loop time of 0.0784857 on 1 procs for 10 steps with 288 atoms
Loop time of 0.0176221 on 1 procs for 10 steps with 288 atoms
Performance: 11.008 ns/day, 2.180 hours/ns, 127.412 timesteps/s
400.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 49.029 ns/day, 0.490 hours/ns, 567.471 timesteps/s, 163.432 katom-step/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 | 0.0075859 | 0.0075859 | 0.0075859 | 0.0 | 9.67
Bond | 2.817e-06 | 2.817e-06 | 2.817e-06 | 0.0 | 0.00
Kspace | 0.020841 | 0.020841 | 0.020841 | 0.0 | 26.55
Pair | 0.0051407 | 0.0051407 | 0.0051407 | 0.0 | 29.17
Bond | 9.92e-07 | 9.92e-07 | 9.92e-07 | 0.0 | 0.01
Kspace | 0.0029456 | 0.0029456 | 0.0029456 | 0.0 | 16.72
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00019415 | 0.00019415 | 0.00019415 | 0.0 | 0.25
Output | 0.0032534 | 0.0032534 | 0.0032534 | 0.0 | 4.15
Modify | 0.046545 | 0.046545 | 0.046545 | 0.0 | 59.30
Other | | 6.246e-05 | | | 0.08
Comm | 8.3497e-05 | 8.3497e-05 | 8.3497e-05 | 0.0 | 0.47
Output | 0.0012832 | 0.0012832 | 0.0012832 | 0.0 | 7.28
Modify | 0.0080737 | 0.0080737 | 0.0080737 | 0.0 | 45.82
Other | | 9.442e-05 | | | 0.54
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -140,4 +169,4 @@ Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:10
Total wall time: 0:00:01

63
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ew3dc.g++.4 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ew3dc.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p f
kspace_style pppm/electrode 1.0e-7
kspace_modify slab 3.0
@ -29,8 +29,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.014 seconds
special bonds CPU = 0.003 seconds
read_data CPU = 0.007 seconds
group bot molecule 1
144 atoms in group bot
@ -68,6 +68,35 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -79,9 +108,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 8.4221827e-08
using double precision MKL FFT
3d grid and FFT values/proc = 2691 672
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -98,7 +127,7 @@ Neighbor list info ...
stencil: none
bin: none
WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314)
Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.725 | 7.774 | 7.823 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807
@ -111,22 +140,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.716 | 7.765 | 7.814 Mbytes
8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807
9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807
10 2 -0.30912769 0.30912769 0.31376826 -1.4789807
Loop time of 0.0296999 on 4 procs for 10 steps with 288 atoms
Loop time of 0.0162257 on 4 procs for 10 steps with 288 atoms
Performance: 29.091 ns/day, 0.825 hours/ns, 336.701 timesteps/s
91.5% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 53.249 ns/day, 0.451 hours/ns, 616.306 timesteps/s, 177.496 katom-step/s
50.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0021578 | 0.0022153 | 0.0022978 | 0.1 | 7.46
Bond | 1.161e-06 | 1.435e-06 | 1.943e-06 | 0.0 | 0.00
Kspace | 0.0054884 | 0.0057437 | 0.0059072 | 0.2 | 19.34
Pair | 0.0010955 | 0.0013022 | 0.0014351 | 0.3 | 8.03
Bond | 6.13e-07 | 7.795e-07 | 1.031e-06 | 0.0 | 0.00
Kspace | 0.0034606 | 0.003541 | 0.0036869 | 0.2 | 21.82
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015424 | 0.0025686 | 0.0031306 | 1.2 | 8.65
Output | 0.0019229 | 0.0023315 | 0.0033526 | 1.2 | 7.85
Modify | 0.016192 | 0.016494 | 0.016902 | 0.2 | 55.54
Other | | 0.0003449 | | | 1.16
Comm | 0.0015915 | 0.0017672 | 0.0019298 | 0.3 | 10.89
Output | 0.00071528 | 0.00095256 | 0.001506 | 0.0 | 5.87
Modify | 0.0080243 | 0.0080738 | 0.0081204 | 0.0 | 49.76
Other | | 0.0005881 | | | 3.62
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -141,4 +170,4 @@ Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:00

61
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.1 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p p # finite field, fully periodic
kspace_style pppm/electrode 1.0e-7
@ -28,7 +28,7 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.006 seconds
read_data CPU = 0.004 seconds
group bot molecule 1
144 atoms in group bot
@ -66,6 +66,35 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -77,9 +106,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 5.4638319e-08
using double precision MKL FFT
3d grid and FFT values/proc = 2873 768
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -96,7 +125,7 @@ Neighbor list info ...
stencil: none
bin: none
WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314)
Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.871 | 7.871 | 7.871 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030902 0.030902 0.031376826 -1.5133027
@ -109,22 +138,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.86 | 7.86 | 7.86 Mbytes
8 1.6 -0.247216 0.247216 0.25101461 -1.5133028
9 1.8 -0.278118 0.278118 0.28239144 -1.5133028
10 2 -0.30902 0.30902 0.31376826 -1.5133028
Loop time of 0.054016 on 1 procs for 10 steps with 288 atoms
Loop time of 0.0150845 on 1 procs for 10 steps with 288 atoms
Performance: 15.995 ns/day, 1.500 hours/ns, 185.130 timesteps/s
400.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 57.277 ns/day, 0.419 hours/ns, 662.933 timesteps/s, 190.925 katom-step/s
90.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0081119 | 0.0081119 | 0.0081119 | 0.0 | 15.02
Bond | 4.802e-06 | 4.802e-06 | 4.802e-06 | 0.0 | 0.01
Kspace | 0.0053539 | 0.0053539 | 0.0053539 | 0.0 | 9.91
Pair | 0.0052281 | 0.0052281 | 0.0052281 | 0.0 | 34.66
Bond | 9.72e-07 | 9.72e-07 | 9.72e-07 | 0.0 | 0.01
Kspace | 0.0017267 | 0.0017267 | 0.0017267 | 0.0 | 11.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00052577 | 0.00052577 | 0.00052577 | 0.0 | 0.97
Output | 0.0033476 | 0.0033476 | 0.0033476 | 0.0 | 6.20
Modify | 0.036562 | 0.036562 | 0.036562 | 0.0 | 67.69
Other | | 0.0001102 | | | 0.20
Comm | 0.00016423 | 0.00016423 | 0.00016423 | 0.0 | 1.09
Output | 0.0010211 | 0.0010211 | 0.0010211 | 0.0 | 6.77
Modify | 0.0068532 | 0.0068532 | 0.0068532 | 0.0 | 45.43
Other | | 9.022e-05 | | | 0.60
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -138,4 +167,4 @@ Ave neighs/atom = 92
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:09
Total wall time: 0:00:01

63
examples/PACKAGES/electrode/planar/log.26Apr2022.planar-pppm-ffield.g++.4 → examples/PACKAGES/electrode/planar/log.1Dec2022.planar-pppm-ffield.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
boundary p p p # finite field, fully periodic
kspace_style pppm/electrode 1.0e-7
@ -28,8 +28,8 @@ Finding 1-2 1-3 1-4 neighbors ...
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.022 seconds
special bonds CPU = 0.002 seconds
read_data CPU = 0.006 seconds
group bot molecule 1
144 atoms in group bot
@ -67,6 +67,35 @@ thermo 1
thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
run 10
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- kspace_style pppm/electrode command:
@article{Ahrens2021,
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0063381},
title = {{Constant potential simulations on a mesh}},
journal = {Journal of Chemical Physics},
year = {2021}
volume = {155},
pages = {104104},
}
- fix electrode command:
@article{Ahrens2022
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
doi = {10.1063/5.0099239},
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
journal = {The Journal of Chemical Physics},
year = {2022}
volume = {157},
pages = {084801},
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
PPPM/electrode initialization ...
WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
@ -78,9 +107,9 @@ WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327
estimated relative force accuracy = 5.4638319e-08
using double precision MKL FFT
3d grid and FFT values/proc = 1287 192
generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 16
ghost atom cutoff = 16
@ -97,7 +126,7 @@ Neighbor list info ...
stencil: none
bin: none
WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314)
Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes
Per MPI rank memory allocation (min/avg/max) = 7.721 | 7.721 | 7.721 Mbytes
Step v_v c_qbot c_qtop v_qtheory v_percdev
0 0 0 0 0 0
1 0.2 -0.030902 0.030902 0.031376826 -1.5133027
@ -110,22 +139,22 @@ Per MPI rank memory allocation (min/avg/max) = 7.712 | 7.712 | 7.712 Mbytes
8 1.6 -0.247216 0.247216 0.25101461 -1.5133028
9 1.8 -0.278118 0.278118 0.28239144 -1.5133028
10 2 -0.30902 0.30902 0.31376826 -1.5133028
Loop time of 0.0301351 on 4 procs for 10 steps with 288 atoms
Loop time of 0.0169132 on 4 procs for 10 steps with 288 atoms
Performance: 28.671 ns/day, 0.837 hours/ns, 331.839 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 51.084 ns/day, 0.470 hours/ns, 591.252 timesteps/s, 170.281 katom-step/s
49.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0020768 | 0.0022701 | 0.0024074 | 0.3 | 7.53
Bond | 1.271e-06 | 2.2107e-06 | 4.237e-06 | 0.0 | 0.01
Kspace | 0.0039171 | 0.0040631 | 0.0042468 | 0.2 | 13.48
Pair | 0.00098343 | 0.0013515 | 0.0015461 | 0.6 | 7.99
Bond | 6.21e-07 | 6.81e-07 | 7.3e-07 | 0.0 | 0.00
Kspace | 0.0036673 | 0.0038144 | 0.004106 | 0.3 | 22.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0020711 | 0.0032953 | 0.0038884 | 1.3 | 10.93
Output | 0.0013425 | 0.001877 | 0.0031692 | 1.7 | 6.23
Modify | 0.018076 | 0.018252 | 0.018479 | 0.1 | 60.57
Other | | 0.0003755 | | | 1.25
Comm | 0.0015601 | 0.0016528 | 0.0017294 | 0.2 | 9.77
Output | 0.00072013 | 0.00087465 | 0.0012429 | 0.0 | 5.17
Modify | 0.0086712 | 0.0087641 | 0.0089049 | 0.1 | 51.82
Other | | 0.0004551 | | | 2.69
Nlocal: 72 ave 72 max 72 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -139,4 +168,4 @@ Ave neighs/atom = 92
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:00