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replace logs for graph-il

This commit is contained in:
srtee 2022-12-01 11:17:49 +10:00
parent a3f1c25537
commit c7300f47b1
16 changed files with 1219 additions and 697 deletions
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105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.1
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@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential # electrodes with constant potential
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.004 seconds
read_data CPU = 0.036 seconds read_data CPU = 0.027 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,24 +59,54 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.005 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0 # amat twostep
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -79,9 +116,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800 3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -97,35 +134,35 @@ Neighbor list info ...
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes Per MPI rank memory allocation (min/avg/max) = 57.19 | 57.19 | 57.19 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 0 0 0 25137190 25137190 0.0085142912 -0.0085142912
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms Loop time of 91.5523 on 1 procs for 500 steps with 3776 atoms
Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s Performance: 0.472 ns/day, 50.862 hours/ns, 5.461 timesteps/s, 20.622 katom-step/s
393.6% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 19.309 | 19.309 | 19.309 | 0.0 | 18.67 Pair | 18.906 | 18.906 | 18.906 | 0.0 | 20.65
Bond | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.00 Bond | 0.0012922 | 0.0012922 | 0.0012922 | 0.0 | 0.00
Kspace | 23.047 | 23.047 | 23.047 | 0.0 | 22.28 Kspace | 34.476 | 34.476 | 34.476 | 0.0 | 37.66
Neigh | 0.25707 | 0.25707 | 0.25707 | 0.0 | 0.25 Neigh | 0.26641 | 0.26641 | 0.26641 | 0.0 | 0.29
Comm | 0.070734 | 0.070734 | 0.070734 | 0.0 | 0.07 Comm | 0.069067 | 0.069067 | 0.069067 | 0.0 | 0.08
Output | 0.0023085 | 0.0023085 | 0.0023085 | 0.0 | 0.00 Output | 0.0021466 | 0.0021466 | 0.0021466 | 0.0 | 0.00
Modify | 60.73 | 60.73 | 60.73 | 0.0 | 58.71 Modify | 37.805 | 37.805 | 37.805 | 0.0 | 41.29
Other | | 0.01994 | | | 0.02 Other | | 0.0271 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -139,4 +176,4 @@ Ave neighs/atom = 457.18432
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:03:10 Total wall time: 0:01:48

105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-conp.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conp.g++.4
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@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential # electrodes with constant potential
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.003 seconds
read_data CPU = 0.014 seconds read_data CPU = 0.038 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,24 +60,54 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.003 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0 # amat twostep
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -80,9 +117,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504 3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -98,35 +135,35 @@ Neighbor list info ...
pair build: copy pair build: copy
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes Per MPI rank memory allocation (min/avg/max) = 23.16 | 26.99 | 30.82 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 0 0 0 25137190 25137190 0.0085142912 -0.0085142912
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms Loop time of 49.6413 on 4 procs for 500 steps with 3776 atoms
Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s Performance: 0.870 ns/day, 27.578 hours/ns, 10.072 timesteps/s, 38.033 katom-step/s
95.1% CPU use with 4 MPI tasks x no OpenMP threads 76.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 5.968 | 6.1677 | 6.382 | 6.5 | 12.42 Pair | 5.3666 | 5.4998 | 5.6946 | 5.4 | 11.08
Bond | 0.00071151 | 0.00078617 | 0.00090387 | 0.0 | 0.00 Bond | 0.0011638 | 0.0012711 | 0.0014555 | 0.3 | 0.00
Kspace | 17.345 | 17.558 | 17.755 | 3.8 | 35.35 Kspace | 24.047 | 24.241 | 24.374 | 2.6 | 48.83
Neigh | 0.10939 | 0.10945 | 0.10948 | 0.0 | 0.22 Neigh | 0.088235 | 0.088328 | 0.088432 | 0.0 | 0.18
Comm | 0.15295 | 0.15474 | 0.15699 | 0.4 | 0.31 Comm | 0.30907 | 0.31913 | 0.32916 | 1.7 | 0.64
Output | 0.00074458 | 0.0010336 | 0.0018799 | 1.5 | 0.00 Output | 0.0010669 | 0.0014463 | 0.0024232 | 1.5 | 0.00
Modify | 25.634 | 25.641 | 25.645 | 0.1 | 51.63 Modify | 19.435 | 19.445 | 19.454 | 0.2 | 39.17
Other | | 0.03276 | | | 0.07 Other | | 0.04549 | | | 0.09
Nlocal: 944 ave 951 max 941 min Nlocal: 944 ave 951 max 941 min
Histogram: 1 2 0 0 0 0 0 0 0 1 Histogram: 1 2 0 0 0 0 0 0 0 1
@ -140,4 +177,4 @@ Ave neighs/atom = 457.18432
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:11 Total wall time: 0:00:55

186
examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.1 Normal file
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@ -0,0 +1,186 @@
LAMMPS (3 Nov 2022)
# electrodes with constrained total charges
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic
read_data "data.graph-il"
Reading data file ...
orthogonal box = (0 0 -68) to (32.2 34.4 68)
1 by 1 by 1 MPI processor grid
reading atoms ...
3776 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
640 bonds
reading angles ...
320 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.023 seconds
# replicate 4 4 1 # test different sys sizes
variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte
fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
320 = # of frozen angles
find clusters CPU = 0.002 seconds
variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
832 atoms in group conp_group
variable dv equal f_conq[2]-f_conq[1]
# symm on and off give different electrode potentials, but identical potential difference
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
run 500
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
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498
grid = 32 32 200
stencil order = 5
estimated absolute RMS force accuracy = 3.7023506e-05
estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800
Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 4 4 16
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conq, occasional, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) fix electrode/conq, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv
0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196
50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388
100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019
150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022
200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501
250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179
300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759
350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374
400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266
450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669
500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355
Loop time of 89.4461 on 1 procs for 500 steps with 3776 atoms
Performance: 0.483 ns/day, 49.692 hours/ns, 5.590 timesteps/s, 21.108 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 | 19.404 | 19.404 | 19.404 | 0.0 | 21.69
Bond | 0.0014902 | 0.0014902 | 0.0014902 | 0.0 | 0.00
Kspace | 35.449 | 35.449 | 35.449 | 0.0 | 39.63
Neigh | 0.26499 | 0.26499 | 0.26499 | 0.0 | 0.30
Comm | 0.068497 | 0.068497 | 0.068497 | 0.0 | 0.08
Output | 0.0023974 | 0.0023974 | 0.0023974 | 0.0 | 0.00
Modify | 34.225 | 34.225 | 34.225 | 0.0 | 38.26
Other | | 0.03044 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12510 ave 12510 max 12510 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1725588
Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:01:48

187
examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq.g++.4 Normal file
View File

@ -0,0 +1,187 @@
LAMMPS (3 Nov 2022)
# electrodes with constrained total charges
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
processors * * 2
atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic
read_data "data.graph-il"
Reading data file ...
orthogonal box = (0 0 -68) to (32.2 34.4 68)
1 by 2 by 2 MPI processor grid
reading atoms ...
3776 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
640 bonds
reading angles ...
320 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.034 seconds
# replicate 4 4 1 # test different sys sizes
variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte
fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
320 = # of frozen angles
find clusters CPU = 0.002 seconds
variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
832 atoms in group conp_group
variable dv equal f_conq[2]-f_conq[1]
# symm on and off give different electrode potentials, but identical potential difference
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
run 500
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
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498
grid = 32 32 200
stencil order = 5
estimated absolute RMS force accuracy = 3.7023506e-05
estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504
Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 4 4 16
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conq, occasional, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) fix electrode/conq, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv
0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196
50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388
100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019
150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022
200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501
250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179
300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759
350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374
400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266
450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669
500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355
Loop time of 53.4299 on 4 procs for 500 steps with 3776 atoms
Performance: 0.809 ns/day, 29.683 hours/ns, 9.358 timesteps/s, 35.336 katom-step/s
74.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.5806 | 5.8872 | 6.1547 | 8.8 | 11.02
Bond | 0.0011404 | 0.0012245 | 0.0012898 | 0.2 | 0.00
Kspace | 26.55 | 26.822 | 27.129 | 4.1 | 50.20
Neigh | 0.098647 | 0.099673 | 0.10083 | 0.3 | 0.19
Comm | 0.35493 | 0.37282 | 0.3909 | 2.1 | 0.70
Output | 0.0012274 | 0.001617 | 0.0026374 | 1.5 | 0.00
Modify | 20.172 | 20.188 | 20.203 | 0.3 | 37.78
Other | | 0.05647 | | | 0.11
Nlocal: 944 ave 948 max 940 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 5920.5 ave 5941 max 5899 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 431397 ave 442329 max 421103 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 1725588
Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:59

103
examples/PACKAGES/electrode/graph-il/log.27May2022.graph-il-conq2.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constrained total charges imposed from dynamically computed potentials # electrodes with constrained total charges imposed from dynamically computed potentials
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.013 seconds read_data CPU = 0.022 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
@ -64,7 +72,7 @@ compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
832 atoms in group conp_group 832 atoms in group conp_group
variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
@ -79,6 +87,35 @@ variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -88,9 +125,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800 3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -111,35 +148,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261
Loop time of 44.4233 on 1 procs for 500 steps with 3776 atoms Loop time of 85.5691 on 1 procs for 500 steps with 3776 atoms
Performance: 0.972 ns/day, 24.680 hours/ns, 11.255 timesteps/s Performance: 0.505 ns/day, 47.538 hours/ns, 5.843 timesteps/s, 22.064 katom-step/s
394.3% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 15.812 | 15.812 | 15.812 | 0.0 | 35.59 Pair | 18.558 | 18.558 | 18.558 | 0.0 | 21.69
Bond | 0.00085223 | 0.00085223 | 0.00085223 | 0.0 | 0.00 Bond | 0.001404 | 0.001404 | 0.001404 | 0.0 | 0.00
Kspace | 17.03 | 17.03 | 17.03 | 0.0 | 38.33 Kspace | 33.78 | 33.78 | 33.78 | 0.0 | 39.48
Neigh | 0.20513 | 0.20513 | 0.20513 | 0.0 | 0.46 Neigh | 0.27017 | 0.27017 | 0.27017 | 0.0 | 0.32
Comm | 0.04065 | 0.04065 | 0.04065 | 0.0 | 0.09 Comm | 0.067438 | 0.067438 | 0.067438 | 0.0 | 0.08
Output | 0.0016819 | 0.0016819 | 0.0016819 | 0.0 | 0.00 Output | 0.0026656 | 0.0026656 | 0.0026656 | 0.0 | 0.00
Modify | 11.32 | 11.32 | 11.32 | 0.0 | 25.48 Modify | 32.86 | 32.86 | 32.86 | 0.0 | 38.40
Other | | 0.01313 | | | 0.03 Other | | 0.02916 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -153,4 +190,4 @@ Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 6 Neighbor list builds = 6
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:37 Total wall time: 0:01:42

105
examples/PACKAGES/electrode/graph-il/log.27May2022.graph-il-conq2.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-conq2.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constrained total charges imposed from dynamically computed potentials # electrodes with constrained total charges imposed from dynamically computed potentials
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.005 seconds
read_data CPU = 0.015 seconds read_data CPU = 0.044 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.002 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
@ -65,7 +73,7 @@ compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes 5 fix conp bot electrode/conp v_vbot 1.979 couple top v_vtop etypes on
832 atoms in group conp_group 832 atoms in group conp_group
variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge variable qex_bot equal -1.0-f_conp[1][1] # difference between desired and 0V charge
@ -80,6 +88,35 @@ variable vtop equal f_conp[2][4]*v_qex_bot+f_conp[2][5]*v_qex_top
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -89,9 +126,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504 3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -112,35 +149,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_vbot v_vtop
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344 0 0 0 25137446 25137446 -1 1 -9.931852 10.097344
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514 50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787 100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114 150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694 200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475 250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115 300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811 350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657 400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959 450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261 500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261
Loop time of 23.4081 on 4 procs for 500 steps with 3776 atoms Loop time of 54.0351 on 4 procs for 500 steps with 3776 atoms
Performance: 1.846 ns/day, 13.005 hours/ns, 21.360 timesteps/s Performance: 0.799 ns/day, 30.019 hours/ns, 9.253 timesteps/s, 34.940 katom-step/s
93.5% CPU use with 4 MPI tasks x no OpenMP threads 75.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.1792 | 4.3002 | 4.4836 | 5.7 | 18.37 Pair | 6.5878 | 6.8799 | 7.1455 | 8.0 | 12.73
Bond | 0.00045023 | 0.00053483 | 0.00058432 | 0.0 | 0.00 Bond | 0.0011081 | 0.0014187 | 0.0018792 | 0.8 | 0.00
Kspace | 12.016 | 12.199 | 12.32 | 3.4 | 52.11 Kspace | 25.907 | 26.173 | 26.464 | 4.1 | 48.44
Neigh | 0.062683 | 0.062707 | 0.062734 | 0.0 | 0.27 Neigh | 0.16417 | 0.16425 | 0.16438 | 0.0 | 0.30
Comm | 0.086385 | 0.08861 | 0.090874 | 0.7 | 0.38 Comm | 0.34948 | 0.36296 | 0.37524 | 1.9 | 0.67
Output | 0.00082773 | 0.0010401 | 0.0016576 | 1.1 | 0.00 Output | 0.0017398 | 0.0021707 | 0.0033966 | 1.5 | 0.00
Modify | 6.7386 | 6.7413 | 6.7443 | 0.1 | 28.80 Modify | 20.392 | 20.403 | 20.416 | 0.2 | 37.76
Other | | 0.0151 | | | 0.06 Other | | 0.04783 | | | 0.09
Nlocal: 944 ave 948 max 940 min Nlocal: 944 ave 948 max 940 min
Histogram: 1 0 0 1 0 0 1 0 0 1 Histogram: 1 0 0 1 0 0 1 0 0 1
@ -154,4 +191,4 @@ Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 6 Neighbor list builds = 6
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:45 Total wall time: 0:01:00

101
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential and smart neighborlists # electrodes with constant potential and smart neighborlists
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.024 seconds read_data CPU = 0.021 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
@ -64,12 +72,41 @@ compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -79,9 +116,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800 3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -102,35 +139,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 0 0 0 25137190 25137190 0.0085142912 -0.0085142912
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms Loop time of 87.0709 on 1 procs for 500 steps with 3776 atoms
Performance: 0.680 ns/day, 35.276 hours/ns, 7.874 timesteps/s Performance: 0.496 ns/day, 48.373 hours/ns, 5.742 timesteps/s, 21.683 katom-step/s
393.9% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 20.628 | 20.628 | 20.628 | 0.0 | 32.49 Pair | 18.617 | 18.617 | 18.617 | 0.0 | 21.38
Bond | 0.0019309 | 0.0019309 | 0.0019309 | 0.0 | 0.00 Bond | 0.0014056 | 0.0014056 | 0.0014056 | 0.0 | 0.00
Kspace | 23.61 | 23.61 | 23.61 | 0.0 | 37.18 Kspace | 34.856 | 34.856 | 34.856 | 0.0 | 40.03
Neigh | 0.28156 | 0.28156 | 0.28156 | 0.0 | 0.44 Neigh | 0.30015 | 0.30015 | 0.30015 | 0.0 | 0.34
Comm | 0.061191 | 0.061191 | 0.061191 | 0.0 | 0.10 Comm | 0.065303 | 0.065303 | 0.065303 | 0.0 | 0.08
Output | 0.0022666 | 0.0022666 | 0.0022666 | 0.0 | 0.00 Output | 0.0021663 | 0.0021663 | 0.0021663 | 0.0 | 0.00
Modify | 18.891 | 18.891 | 18.891 | 0.0 | 29.75 Modify | 33.201 | 33.201 | 33.201 | 0.0 | 38.13
Other | | 0.02047 | | | 0.03 Other | | 0.0282 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -144,4 +181,4 @@ Ave neighs/atom = 457.18432
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:02:24 Total wall time: 0:01:43

103
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-etypes.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-etypes.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential and smart neighborlists # electrodes with constant potential and smart neighborlists
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.004 seconds
read_data CPU = 0.016 seconds read_data CPU = 0.047 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.005 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
@ -65,12 +73,41 @@ compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -80,9 +117,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504 3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -103,35 +140,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 0 0 0 25137190 25137190 0.0085142912 -0.0085142912
50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944 50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517 100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005 150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175 200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257 250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784 300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799 350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435 400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365 450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535 500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms Loop time of 48.4075 on 4 procs for 500 steps with 3776 atoms
Performance: 1.403 ns/day, 17.105 hours/ns, 16.240 timesteps/s Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s
94.1% CPU use with 4 MPI tasks x no OpenMP threads 75.3% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 6.5102 | 6.7303 | 6.9362 | 7.6 | 21.86 Pair | 5.3095 | 5.5504 | 5.7923 | 8.2 | 11.47
Bond | 0.00064504 | 0.00071061 | 0.000779 | 0.0 | 0.00 Bond | 0.0011128 | 0.0012414 | 0.0014028 | 0.3 | 0.00
Kspace | 14.081 | 14.287 | 14.507 | 5.2 | 46.40 Kspace | 24.084 | 24.322 | 24.559 | 3.9 | 50.24
Neigh | 0.11831 | 0.11841 | 0.11851 | 0.0 | 0.38 Neigh | 0.093557 | 0.09408 | 0.094377 | 0.1 | 0.19
Comm | 0.12216 | 0.12434 | 0.12651 | 0.6 | 0.40 Comm | 0.30394 | 0.31319 | 0.3225 | 1.6 | 0.65
Output | 0.00083347 | 0.0010533 | 0.0017069 | 1.2 | 0.00 Output | 0.0012719 | 0.0015908 | 0.0024592 | 1.3 | 0.00
Modify | 9.5052 | 9.5071 | 9.5093 | 0.1 | 30.88 Modify | 18.066 | 18.079 | 18.091 | 0.2 | 37.35
Other | | 0.01927 | | | 0.06 Other | | 0.04692 | | | 0.10
Nlocal: 944 ave 951 max 941 min Nlocal: 944 ave 951 max 941 min
Histogram: 1 2 0 0 0 0 0 0 0 1 Histogram: 1 2 0 0 0 0 0 0 0 1
@ -145,4 +182,4 @@ Ave neighs/atom = 457.18432
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:56 Total wall time: 0:00:54

103
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field # electrodes with constant potential using finite field
# for z-periodic graphene-ionic liquid supercapacitor # for z-periodic graphene-ionic liquid supercapacitor
@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.022 seconds read_data CPU = 0.021 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
@ -63,12 +71,41 @@ compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20949995 G vector (1/distance) = 0.20949995
@ -78,9 +115,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.0544465e-07 estimated relative force accuracy = 1.0544465e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 147537 92160 3d grid and FFT values/proc = 147537 92160
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -101,35 +138,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 49.5 | 49.5 | 49.5 Mbytes Per MPI rank memory allocation (min/avg/max) = 46.1 | 46.1 | 46.1 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137187 25137187 0.0085209384 -0.0085209384 0 0 0 25137186 25137186 0.0085209384 -0.0085209384
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221
Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms Loop time of 53.8411 on 1 procs for 500 steps with 3776 atoms
Performance: 1.175 ns/day, 20.423 hours/ns, 13.601 timesteps/s Performance: 0.802 ns/day, 29.912 hours/ns, 9.287 timesteps/s, 35.066 katom-step/s
393.9% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 19.737 | 19.737 | 19.737 | 0.0 | 53.69 Pair | 19.843 | 19.843 | 19.843 | 0.0 | 36.85
Bond | 0.00092668 | 0.00092668 | 0.00092668 | 0.0 | 0.00 Bond | 0.0016963 | 0.0016963 | 0.0016963 | 0.0 | 0.00
Kspace | 6.5854 | 6.5854 | 6.5854 | 0.0 | 17.91 Kspace | 11.232 | 11.232 | 11.232 | 0.0 | 20.86
Neigh | 0.33914 | 0.33914 | 0.33914 | 0.0 | 0.92 Neigh | 0.39189 | 0.39189 | 0.39189 | 0.0 | 0.73
Comm | 0.090124 | 0.090124 | 0.090124 | 0.0 | 0.25 Comm | 0.12348 | 0.12348 | 0.12348 | 0.0 | 0.23
Output | 0.0013975 | 0.0013975 | 0.0013975 | 0.0 | 0.00 Output | 0.0017904 | 0.0017904 | 0.0017904 | 0.0 | 0.00
Modify | 9.9834 | 9.9834 | 9.9834 | 0.0 | 27.16 Modify | 22.207 | 22.207 | 22.207 | 0.0 | 41.25
Other | | 0.02455 | | | 0.07 Other | | 0.04008 | | | 0.07
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -143,4 +180,4 @@ Ave neighs/atom = 493.56224
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:39 Total wall time: 0:01:10

105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ffield.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ffield.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field # electrodes with constant potential using finite field
# for z-periodic graphene-ionic liquid supercapacitor # for z-periodic graphene-ionic liquid supercapacitor
@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.016 seconds read_data CPU = 0.033 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,23 +60,53 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.002 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q compute qbot bot reduce sum v_q
compute ctemp electrolyte temp compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes 5 ffield yes fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on etypes on ffield yes
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20949995 G vector (1/distance) = 0.20949995
@ -79,9 +116,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.0544465e-07 estimated relative force accuracy = 1.0544465e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 46644 23552 3d grid and FFT values/proc = 46644 23552
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -102,35 +139,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 21.96 | 22.27 | 22.77 Mbytes Per MPI rank memory allocation (min/avg/max) = 21.23 | 21.34 | 21.65 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137187 25137187 0.0085209384 -0.0085209384 0 0 0 25137186 25137186 0.0085209384 -0.0085209384
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522 50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786 100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793 150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648 200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546 250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751 300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814 350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207 400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394 450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221 500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221
Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms Loop time of 26.2807 on 4 procs for 500 steps with 3776 atoms
Performance: 2.228 ns/day, 10.774 hours/ns, 25.782 timesteps/s Performance: 1.644 ns/day, 14.600 hours/ns, 19.025 timesteps/s, 71.840 katom-step/s
96.3% CPU use with 4 MPI tasks x no OpenMP threads 83.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 7.1247 | 7.6399 | 8.1323 | 13.3 | 39.39 Pair | 5.8233 | 6.1941 | 6.6294 | 12.1 | 23.57
Bond | 0.00072445 | 0.00077581 | 0.00085933 | 0.0 | 0.00 Bond | 0.0010807 | 0.0011705 | 0.0013494 | 0.3 | 0.00
Kspace | 5.098 | 5.5905 | 6.1036 | 15.6 | 28.83 Kspace | 8.0325 | 8.4703 | 8.8457 | 10.4 | 32.23
Neigh | 0.145 | 0.14517 | 0.14532 | 0.0 | 0.75 Neigh | 0.14184 | 0.1421 | 0.14238 | 0.1 | 0.54
Comm | 0.24683 | 0.25127 | 0.25907 | 1.0 | 1.30 Comm | 0.52248 | 0.54323 | 0.56352 | 2.7 | 2.07
Output | 0.00084146 | 0.0011298 | 0.0019741 | 1.5 | 0.01 Output | 0.00079782 | 0.0011547 | 0.0021987 | 1.8 | 0.00
Modify | 5.6957 | 5.7129 | 5.729 | 0.6 | 29.46 Modify | 10.831 | 10.856 | 10.881 | 0.7 | 41.31
Other | | 0.05153 | | | 0.27 Other | | 0.07293 | | | 0.28
Nlocal: 944 ave 951 max 941 min Nlocal: 944 ave 951 max 941 min
Histogram: 1 2 0 0 0 0 0 0 0 1 Histogram: 1 2 0 0 0 0 0 0 0 1
@ -144,4 +181,4 @@ Ave neighs/atom = 493.56224
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:44 Total wall time: 0:00:32

103
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with equal-style ramped (electrode-)constant potential # electrodes with equal-style ramped (electrode-)constant potential
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.014 seconds read_data CPU = 0.021 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
@ -65,12 +73,41 @@ compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
variable v equal ramp(2,4) variable v equal ramp(2,4)
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -80,9 +117,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800 3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -103,35 +140,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4
Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms Loop time of 87.6405 on 1 procs for 500 steps with 3776 atoms
Performance: 0.849 ns/day, 28.254 hours/ns, 9.831 timesteps/s Performance: 0.493 ns/day, 48.689 hours/ns, 5.705 timesteps/s, 21.543 katom-step/s
393.5% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 18.166 | 18.166 | 18.166 | 0.0 | 35.72 Pair | 18.484 | 18.484 | 18.484 | 0.0 | 21.09
Bond | 0.00091918 | 0.00091918 | 0.00091918 | 0.0 | 0.00 Bond | 0.0016824 | 0.0016824 | 0.0016824 | 0.0 | 0.00
Kspace | 17.267 | 17.267 | 17.267 | 0.0 | 33.95 Kspace | 35.426 | 35.426 | 35.426 | 0.0 | 40.42
Neigh | 0.27635 | 0.27635 | 0.27635 | 0.0 | 0.54 Neigh | 0.30201 | 0.30201 | 0.30201 | 0.0 | 0.34
Comm | 0.044714 | 0.044714 | 0.044714 | 0.0 | 0.09 Comm | 0.066546 | 0.066546 | 0.066546 | 0.0 | 0.08
Output | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.00 Output | 0.0022768 | 0.0022768 | 0.0022768 | 0.0 | 0.00
Modify | 15.086 | 15.086 | 15.086 | 0.0 | 29.66 Modify | 33.33 | 33.33 | 33.33 | 0.0 | 38.03
Other | | 0.01409 | | | 0.03 Other | | 0.0286 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -145,4 +182,4 @@ Ave neighs/atom = 457.17161
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:50 Total wall time: 0:01:44

105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-ramp.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-ramp.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with equal-style ramped (electrode-)constant potential # electrodes with equal-style ramped (electrode-)constant potential
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors 1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.001 seconds special bonds CPU = 0.003 seconds
read_data CPU = 0.024 seconds read_data CPU = 0.034 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.002 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
@ -66,12 +74,41 @@ compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
variable v equal ramp(2,4) variable v equal ramp(2,4)
fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes 5 fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
832 atoms in group conp_group 832 atoms in group conp_group
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -81,9 +118,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504 3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -104,35 +141,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2 0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2 50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4 100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6 150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8 200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3 250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2 300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4 350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6 400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8 450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4 500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4
Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms Loop time of 49.2075 on 4 procs for 500 steps with 3776 atoms
Performance: 1.360 ns/day, 17.647 hours/ns, 15.741 timesteps/s Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s
94.1% CPU use with 4 MPI tasks x no OpenMP threads 75.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 6.7949 | 7.0359 | 7.3092 | 7.9 | 22.15 Pair | 5.7517 | 5.9151 | 6.0961 | 6.6 | 12.02
Bond | 0.00069874 | 0.00073747 | 0.00077928 | 0.0 | 0.00 Bond | 0.0011959 | 0.0013362 | 0.0014512 | 0.2 | 0.00
Kspace | 14.375 | 14.648 | 14.89 | 5.5 | 46.12 Kspace | 24.223 | 24.404 | 24.566 | 3.2 | 49.59
Neigh | 0.12057 | 0.1206 | 0.12062 | 0.0 | 0.38 Neigh | 0.10283 | 0.10288 | 0.10301 | 0.0 | 0.21
Comm | 0.13412 | 0.13439 | 0.13483 | 0.1 | 0.42 Comm | 0.30801 | 0.31944 | 0.33141 | 2.0 | 0.65
Output | 0.0010019 | 0.0013088 | 0.0020937 | 1.3 | 0.00 Output | 0.0010416 | 0.0014127 | 0.0024086 | 1.5 | 0.00
Modify | 9.8017 | 9.8025 | 9.8031 | 0.0 | 30.86 Modify | 18.405 | 18.418 | 18.432 | 0.3 | 37.43
Other | | 0.02036 | | | 0.06 Other | | 0.04459 | | | 0.09
Nlocal: 944 ave 951 max 941 min Nlocal: 944 ave 951 max 941 min
Histogram: 1 2 0 0 0 0 0 0 0 1 Histogram: 1 2 0 0 0 0 0 0 0 1
@ -146,4 +183,4 @@ Ave neighs/atom = 457.17161
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 7 Neighbor list builds = 7
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:58 Total wall time: 0:00:55

105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.1 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with thermopotentiostat # electrodes with thermopotentiostat
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -38,12 +38,19 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.002 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.024 seconds read_data CPU = 0.021 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -52,11 +59,12 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.000 seconds find clusters CPU = 0.001 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
@ -65,10 +73,10 @@ compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
unfix nvt # remove NVT thermostat included from "settings.mod" unfix nvt # remove NVT thermostat included from "settings.mod"
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
832 atoms in group conp_group 832 atoms in group conp_group
# to compare to regular constant potential, switch previous line to this: # to compare to regular constant potential, switch previous line to this:
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on #fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
fix nve electrolyte nve fix nve electrolyte nve
# note ionic liquid does not reach 500K immediately # note ionic liquid does not reach 500K immediately
@ -77,6 +85,35 @@ fix nve electrolyte nve
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -86,9 +123,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800 3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -109,35 +146,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137187 25137187 0.12767613 -0.12767613 0 0 0 25137188 25137188 0.12767608 -0.12767608
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943
Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms Loop time of 87.5281 on 1 procs for 500 steps with 3776 atoms
Performance: 0.864 ns/day, 27.768 hours/ns, 10.003 timesteps/s Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 katom-step/s
393.3% CPU use with 1 MPI tasks x no OpenMP threads 100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 17.01 | 17.01 | 17.01 | 0.0 | 34.03 Pair | 18.819 | 18.819 | 18.819 | 0.0 | 21.50
Bond | 0.0010374 | 0.0010374 | 0.0010374 | 0.0 | 0.00 Bond | 0.0014336 | 0.0014336 | 0.0014336 | 0.0 | 0.00
Kspace | 18.096 | 18.096 | 18.096 | 0.0 | 36.20 Kspace | 34.891 | 34.891 | 34.891 | 0.0 | 39.86
Neigh | 0.1828 | 0.1828 | 0.1828 | 0.0 | 0.37 Neigh | 0.21542 | 0.21542 | 0.21542 | 0.0 | 0.25
Comm | 0.043856 | 0.043856 | 0.043856 | 0.0 | 0.09 Comm | 0.063383 | 0.063383 | 0.063383 | 0.0 | 0.07
Output | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.00 Output | 0.0020476 | 0.0020476 | 0.0020476 | 0.0 | 0.00
Modify | 14.632 | 14.632 | 14.632 | 0.0 | 29.27 Modify | 33.507 | 33.507 | 33.507 | 0.0 | 38.28
Other | | 0.01548 | | | 0.03 Other | | 0.0281 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,4 +188,4 @@ Ave neighs/atom = 457.08845
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 5 Neighbor list builds = 5
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:01:50 Total wall time: 0:01:44

105
examples/PACKAGES/electrode/graph-il/log.26Apr2022.graph-il-thermo.g++.4 → examples/PACKAGES/electrode/graph-il/log.1Dec2022.graph-il-thermo.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022) LAMMPS (3 Nov 2022)
# electrodes with thermopotentiostat # electrodes with thermopotentiostat
# for graphene-ionic liquid supercapacitor # for graphene-ionic liquid supercapacitor
@ -39,12 +39,19 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors 1 = max # of 1-4 neighbors
2 = max # of special neighbors 2 = max # of special neighbors
special bonds CPU = 0.002 seconds special bonds CPU = 0.002 seconds
read_data CPU = 0.025 seconds read_data CPU = 0.036 seconds
group bot molecule 641 # replicate 4 4 1 # test different sys sizes
416 atoms in group bot
group top molecule 642 variable zpos atom "z > 0"
group zpos variable zpos
1891 atoms in group zpos
group ele type 5
832 atoms in group ele
group top intersect ele zpos
416 atoms in group top 416 atoms in group top
group bot subtract ele top
416 atoms in group bot
group bmi type 1 2 3 group bmi type 1 2 3
960 atoms in group bmi 960 atoms in group bmi
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
fix nvt electrolyte nvt temp 500.0 500.0 100 fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1 fix shake bmi shake 1e-4 20 0 b 1 2 a 1
Finding SHAKE clusters ...
0 = # of size 2 clusters 0 = # of size 2 clusters
0 = # of size 3 clusters 0 = # of size 3 clusters
0 = # of size 4 clusters 0 = # of size 4 clusters
320 = # of frozen angles 320 = # of frozen angles
find clusters CPU = 0.001 seconds find clusters CPU = 0.005 seconds
variable q atom q variable q atom q
compute qtop top reduce sum v_q compute qtop top reduce sum v_q
@ -66,10 +74,10 @@ compute ctemp electrolyte temp
kspace_modify slab 3.0 kspace_modify slab 3.0
unfix nvt # remove NVT thermostat included from "settings.mod" unfix nvt # remove NVT thermostat included from "settings.mod"
fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes 5 temp 500 100 7 # temp tau rng fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
832 atoms in group conp_group 832 atoms in group conp_group
# to compare to regular constant potential, switch previous line to this: # to compare to regular constant potential, switch previous line to this:
#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes 5 symm on #fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
fix nve electrolyte nve fix nve electrolyte nve
# note ionic liquid does not reach 500K immediately # note ionic liquid does not reach 500K immediately
@ -78,6 +86,35 @@ fix nve electrolyte nve
thermo 50 thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
run 500 run 500
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
PPPM/electrode initialization ... PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342) using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498 G vector (1/distance) = 0.20904498
@ -87,9 +124,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.1149519e-07 estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504 3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ... 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 max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18 master list distance cutoff = 18
ghost atom cutoff = 18 ghost atom cutoff = 18
@ -110,35 +147,35 @@ Neighbor list info ...
pair build: skip pair build: skip
stencil: none stencil: none
bin: none bin: none
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes Per MPI rank memory allocation (min/avg/max) = 22.9 | 26.72 | 30.55 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
0 0 0 25137187 25137187 0.12767613 -0.12767613 0 0 0 25137188 25137188 0.12767608 -0.12767608
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714 50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358 100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143 150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489 200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719 250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094 300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252 350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753 400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401 450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942 500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943
Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms Loop time of 49.2564 on 4 procs for 500 steps with 3776 atoms
Performance: 1.561 ns/day, 15.376 hours/ns, 18.065 timesteps/s Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s
91.7% CPU use with 4 MPI tasks x no OpenMP threads 76.1% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.6214 | 4.8032 | 4.9546 | 6.5 | 17.35 Pair | 5.6984 | 5.9083 | 6.1177 | 6.4 | 12.00
Bond | 0.0005324 | 0.00060509 | 0.00069468 | 0.0 | 0.00 Bond | 0.0011785 | 0.0012201 | 0.0013055 | 0.1 | 0.00
Kspace | 13.883 | 14.034 | 14.216 | 3.8 | 50.71 Kspace | 24.311 | 24.519 | 24.729 | 3.1 | 49.78
Neigh | 0.061704 | 0.061727 | 0.06176 | 0.0 | 0.22 Neigh | 0.075406 | 0.075487 | 0.07556 | 0.0 | 0.15
Comm | 0.10101 | 0.10374 | 0.10645 | 0.8 | 0.37 Comm | 0.29972 | 0.30943 | 0.31881 | 1.7 | 0.63
Output | 0.00086818 | 0.0010909 | 0.001715 | 1.1 | 0.00 Output | 0.0012474 | 0.001684 | 0.0027062 | 1.5 | 0.00
Modify | 8.65 | 8.6524 | 8.6545 | 0.1 | 31.26 Modify | 18.377 | 18.384 | 18.391 | 0.2 | 37.32
Other | | 0.02055 | | | 0.07 Other | | 0.05679 | | | 0.12
Nlocal: 944 ave 951 max 940 min Nlocal: 944 ave 951 max 940 min
Histogram: 1 1 1 0 0 0 0 0 0 1 Histogram: 1 1 1 0 0 0 0 0 0 1
@ -152,4 +189,4 @@ Ave neighs/atom = 457.08845
Ave special neighs/atom = 0.50847458 Ave special neighs/atom = 0.50847458
Neighbor list builds = 5 Neighbor list builds = 5
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:50 Total wall time: 0:00:55

147
examples/PACKAGES/electrode/graph-il/log.27May2022.graph-il-conq.g++.1
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@ -1,147 +0,0 @@
LAMMPS (24 Mar 2022)
# electrodes with constrained total charges
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic
read_data "data.graph-il"
Reading data file ...
orthogonal box = (0 0 -68) to (32.2 34.4 68)
1 by 1 by 1 MPI processor grid
reading atoms ...
3776 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
640 bonds
reading angles ...
320 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.014 seconds
group bot molecule 641
416 atoms in group bot
group top molecule 642
416 atoms in group top
group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte
fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
320 = # of frozen angles
find clusters CPU = 0.001 seconds
variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
832 atoms in group conp_group
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2]
run 500
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498
grid = 32 32 200
stencil order = 5
estimated absolute RMS force accuracy = 3.7023506e-05
estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT
3d grid and FFT values/proc = 307242 204800
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 4 4 16
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conq, occasional, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) fix electrode/conq, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 56.89 | 56.89 | 56.89 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2]
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
Loop time of 43.3117 on 1 procs for 500 steps with 3776 atoms
Performance: 0.997 ns/day, 24.062 hours/ns, 11.544 timesteps/s
394.5% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.554 | 15.554 | 15.554 | 0.0 | 35.91
Bond | 0.00094737 | 0.00094737 | 0.00094737 | 0.0 | 0.00
Kspace | 16.502 | 16.502 | 16.502 | 0.0 | 38.10
Neigh | 0.20285 | 0.20285 | 0.20285 | 0.0 | 0.47
Comm | 0.039776 | 0.039776 | 0.039776 | 0.0 | 0.09
Output | 0.0014342 | 0.0014342 | 0.0014342 | 0.0 | 0.00
Modify | 10.998 | 10.998 | 10.998 | 0.0 | 25.39
Other | | 0.01261 | | | 0.03
Nlocal: 3776 ave 3776 max 3776 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12510 ave 12510 max 12510 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1725588
Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:01:38

148
examples/PACKAGES/electrode/graph-il/log.27May2022.graph-il-conq.g++.4
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@ -1,148 +0,0 @@
LAMMPS (24 Mar 2022)
# electrodes with constrained total charges
# for graphene-ionic liquid supercapacitor
boundary p p f # slab calculation
include settings.mod # styles, groups, computes and fixes
# set boundary in main script because ffield is periodic
units real
# distribute electrode atoms among all processors:
if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
processors * * 2
atom_style full
pair_style lj/cut/coul/long 16
bond_style harmonic
angle_style harmonic
kspace_style pppm/electrode 1e-7
# kspace_modify in main script because ffield is periodic
read_data "data.graph-il"
Reading data file ...
orthogonal box = (0 0 -68) to (32.2 34.4 68)
1 by 2 by 2 MPI processor grid
reading atoms ...
3776 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
640 bonds
reading angles ...
320 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.015 seconds
group bot molecule 641
416 atoms in group bot
group top molecule 642
416 atoms in group top
group bmi type 1 2 3
960 atoms in group bmi
group electrolyte type 1 2 3 4
1280 atoms in group electrolyte
fix nvt electrolyte nvt temp 500.0 500.0 100
fix shake bmi shake 1e-4 20 0 b 1 2 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
320 = # of frozen angles
find clusters CPU = 0.001 seconds
variable q atom q
compute qtop top reduce sum v_q
compute qbot bot reduce sum v_q
compute ctemp electrolyte temp
kspace_modify slab 3.0
fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes 5 # conq doesn't take symm option
832 atoms in group conp_group
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2]
run 500
PPPM/electrode initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.20904498
grid = 32 32 200
stencil order = 5
estimated absolute RMS force accuracy = 3.7023506e-05
estimated relative force accuracy = 1.1149519e-07
using double precision MKL FFT
3d grid and FFT values/proc = 151593 85504
generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 18
ghost atom cutoff = 18
binsize = 9, bins = 4 4 16
3 neighbor lists, perpetual/occasional/extra = 2 1 0
(1) pair lj/cut/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
(2) fix electrode/conq, occasional, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
(3) fix electrode/conq, perpetual, skip from (1)
attributes: half, newton on
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 23.63 | 27.46 | 31.29 Mbytes
Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2]
0 0 0 25136984 25136984 -1 1 -9.931852 10.097344
50 20.206425 72.797911 25136825 25137033 -1 1 -9.4359366 9.5964514
100 55.931663 201.50563 25136587 25137163 -1 1 -8.0440112 8.1861787
150 81.389273 293.22204 25136533 25137371 -1 1 -6.1113109 6.2267114
200 92.867946 334.57639 25136646 25137603 -1 1 -4.1857807 4.2740694
250 97.518304 351.33028 25136809 25137814 -1 1 -2.8383703 2.9101475
300 102.36577 368.79431 25136933 25137987 -1 1 -2.3831643 2.4461115
350 113.66597 409.50566 25136960 25138131 -1 1 -2.7083563 2.7457811
400 122.8443 442.57252 25136991 25138256 -1 1 -3.4311003 3.3941657
450 128.63713 463.44243 25137048 25138373 -1 1 -4.132871 3.9852959
500 131.18361 472.61665 25137142 25138493 -1 1 -4.5104095 4.2567261
Loop time of 23.8659 on 4 procs for 500 steps with 3776 atoms
Performance: 1.810 ns/day, 13.259 hours/ns, 20.950 timesteps/s
93.5% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2231 | 4.3451 | 4.5145 | 5.6 | 18.21
Bond | 0.00048756 | 0.00052807 | 0.00058913 | 0.0 | 0.00
Kspace | 12.239 | 12.408 | 12.53 | 3.3 | 51.99
Neigh | 0.062108 | 0.062136 | 0.062173 | 0.0 | 0.26
Comm | 0.092261 | 0.096857 | 0.10111 | 1.1 | 0.41
Output | 0.00063911 | 0.00082467 | 0.0013664 | 0.0 | 0.00
Modify | 6.9315 | 6.9362 | 6.9417 | 0.2 | 29.06
Other | | 0.01626 | | | 0.07
Nlocal: 944 ave 948 max 940 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 5920.5 ave 5941 max 5899 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 431397 ave 442329 max 421103 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 1725588
Ave neighs/atom = 456.98835
Ave special neighs/atom = 0.50847458
Neighbor list builds = 6
Dangerous builds = 0
Total wall time: 0:00:44