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replace au-aq logs

This commit is contained in:
srtee 2022-12-01 11:46:51 +10:00
parent c7300f47b1
commit a733e4ddf9
4 changed files with 244 additions and 124 deletions
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92
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.1 → examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field
# for z-periodic gold-saline electrochemical cell
@ -37,8 +37,8 @@ Finding 1-2 1-3 1-4 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 = 0.051 seconds
special bonds CPU = 0.006 seconds
read_data CPU = 0.097 seconds
group bot type 6
1620 atoms in group bot
@ -52,11 +52,12 @@ group electrolyte type 1 2 3 4 5
fix nvt electrolyte nvt temp 298.0 298.0 241
fix shake SPC 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
2160 = # of frozen angles
find clusters CPU = 0.002 seconds
find clusters CPU = 0.006 seconds
variable q atom q
variable qz atom q*(z-lz/2)
@ -67,12 +68,41 @@ compute qzbot bot reduce sum v_qz
compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
3240 atoms in group conp_group
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
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) = 0.24017705
@ -82,9 +112,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.093542e-07
using double precision MKL FFT
3d grid and FFT values/proc = 472567 349920
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
@ -105,35 +135,35 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372
50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255
100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573
150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855
200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925
250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185
300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905
350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.720202 138.28678
400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619396 138.11873
450 158.54164 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912674 133.55185
500 161.40138 280.33258 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464
Loop time of 246.197 on 1 procs for 500 steps with 9798 atoms
0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372
50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255
100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573
150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855
200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925
250 152.61146 265.06566 -39598.341 -36124.226 4.1835865 -4.1835865 79.56665 132.97185
300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905
350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720202 138.28678
400 156.26118 271.40474 -39490.412 -35933.213 4.344408 -4.344408 82.619398 138.11874
450 158.54163 275.36557 -39487.28 -35878.167 4.2020489 -4.2020489 79.912677 133.55186
500 161.40137 280.33257 -39485.763 -35811.55 4.3021927 -4.3021927 81.807532 136.74641
Loop time of 146.959 on 1 procs for 500 steps with 9798 atoms
Performance: 0.175 ns/day, 136.776 hours/ns, 2.031 timesteps/s
356.3% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.294 ns/day, 81.644 hours/ns, 3.402 timesteps/s, 33.336 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 | 105.64 | 105.64 | 105.64 | 0.0 | 42.91
Bond | 0.0010592 | 0.0010592 | 0.0010592 | 0.0 | 0.00
Kspace | 37.643 | 37.643 | 37.643 | 0.0 | 15.29
Neigh | 5.8827 | 5.8827 | 5.8827 | 0.0 | 2.39
Comm | 0.18181 | 0.18181 | 0.18181 | 0.0 | 0.07
Output | 0.0055762 | 0.0055762 | 0.0055762 | 0.0 | 0.00
Modify | 96.78 | 96.78 | 96.78 | 0.0 | 39.31
Other | | 0.06346 | | | 0.03
Pair | 69.832 | 69.832 | 69.832 | 0.0 | 47.52
Bond | 0.00091634 | 0.00091634 | 0.00091634 | 0.0 | 0.00
Kspace | 33.817 | 33.817 | 33.817 | 0.0 | 23.01
Neigh | 4.2067 | 4.2067 | 4.2067 | 0.0 | 2.86
Comm | 0.12212 | 0.12212 | 0.12212 | 0.0 | 0.08
Output | 0.0031896 | 0.0031896 | 0.0031896 | 0.0 | 0.00
Modify | 38.92 | 38.92 | 38.92 | 0.0 | 26.48
Other | | 0.05687 | | | 0.04
Nlocal: 9798 ave 9798 max 9798 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -147,4 +177,4 @@ Ave neighs/atom = 842.63544
Ave special neighs/atom = 1.3227189
Neighbor list builds = 22
Dangerous builds = 0
Total wall time: 0:19:39
Total wall time: 0:05:33

90
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-ffield.g++.4 → examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-ffield.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field
# for z-periodic gold-saline electrochemical cell
@ -39,7 +39,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.149 seconds
read_data CPU = 0.118 seconds
group bot type 6
1620 atoms in group bot
@ -53,11 +53,12 @@ group electrolyte type 1 2 3 4 5
fix nvt electrolyte nvt temp 298.0 298.0 241
fix shake SPC 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
2160 = # of frozen angles
find clusters CPU = 0.003 seconds
find clusters CPU = 0.002 seconds
variable q atom q
variable qz atom q*(z-lz/2)
@ -68,12 +69,41 @@ compute qzbot bot reduce sum v_qz
compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
3240 atoms in group conp_group
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
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) = 0.24017705
@ -83,9 +113,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.093542e-07
using double precision MKL FFT
3d grid and FFT values/proc = 138958 87480
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
@ -106,35 +136,35 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
0 171.61215 298.06731 -39212.819 -35306.164 4.1391573 -4.1391573 78.718381 131.56372
50 147.03139 255.37383 -39870.139 -36523.051 4.1312167 -4.1312167 78.563872 131.30255
100 149.89027 260.33932 -39878.859 -36466.689 4.0217834 -4.0217834 76.482548 127.82573
150 151.7382 263.54893 -39873.178 -36418.942 4.0469977 -4.0469977 76.967548 128.59855
200 151.7508 263.57081 -39827.015 -36372.492 4.1830375 -4.1830375 79.554159 132.93925
250 152.61146 265.06566 -39791.293 -36317.177 4.1835865 -4.1835865 79.56665 132.97185
300 153.51486 266.63475 -39751.841 -36257.16 4.1571861 -4.1571861 79.061431 132.12905
350 156.35115 271.561 -39754.955 -36195.708 4.3498059 -4.3498059 82.7202 138.28678
400 156.26118 271.40474 -39690.781 -36133.582 4.3444079 -4.3444079 82.619398 138.11873
450 158.54163 275.36558 -39681.083 -36071.97 4.2020488 -4.2020488 79.912675 133.55185
500 161.40138 280.33257 -39684.185 -36009.972 4.3021924 -4.3021924 81.807527 136.7464
Loop time of 111.902 on 4 procs for 500 steps with 9798 atoms
0 171.61215 298.06731 -39021.917 -35115.261 4.1391573 -4.1391573 78.718381 131.56372
50 147.03139 255.37383 -39679.603 -36332.515 4.1312167 -4.1312167 78.563872 131.30255
100 149.89027 260.33932 -39693.369 -36281.2 4.0217834 -4.0217834 76.482548 127.82573
150 151.7382 263.54893 -39686.526 -36232.29 4.0469977 -4.0469977 76.967548 128.59855
200 151.7508 263.57081 -39634.089 -36179.566 4.1830375 -4.1830375 79.554159 132.93925
250 152.61146 265.06566 -39598.341 -36124.226 4.1835864 -4.1835864 79.56665 132.97185
300 153.51486 266.63475 -39560.107 -36065.426 4.1571861 -4.1571861 79.06143 132.12905
350 156.35115 271.561 -39554.338 -35995.09 4.3498059 -4.3498059 82.720201 138.28678
400 156.26118 271.40474 -39490.412 -35933.213 4.3444079 -4.3444079 82.619397 138.11873
450 158.54163 275.36558 -39487.279 -35878.167 4.202049 -4.202049 79.912678 133.55186
500 161.40137 280.33256 -39485.763 -35811.55 4.3021925 -4.3021925 81.807529 136.7464
Loop time of 97.2399 on 4 procs for 500 steps with 9798 atoms
Performance: 0.386 ns/day, 62.168 hours/ns, 4.468 timesteps/s
97.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.444 ns/day, 54.022 hours/ns, 5.142 timesteps/s, 50.381 katom-step/s
87.0% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.816 | 31.136 | 40.866 | 166.5 | 27.82
Bond | 0.00073413 | 0.00080346 | 0.00084203 | 0.0 | 0.00
Kspace | 29.546 | 39.137 | 48.326 | 146.4 | 34.97
Neigh | 2.5867 | 2.5872 | 2.5877 | 0.0 | 2.31
Comm | 0.33289 | 0.33603 | 0.33791 | 0.3 | 0.30
Output | 0.0022537 | 0.0030028 | 0.005192 | 2.3 | 0.00
Modify | 38.498 | 38.635 | 38.77 | 2.2 | 34.53
Other | | 0.06679 | | | 0.06
Pair | 19.363 | 28.08 | 37.126 | 160.3 | 28.88
Bond | 0.00094043 | 0.00096516 | 0.00098016 | 0.0 | 0.00
Kspace | 31.655 | 40.554 | 49.143 | 131.3 | 41.71
Neigh | 2.2289 | 2.2294 | 2.2297 | 0.0 | 2.29
Comm | 0.5341 | 0.54079 | 0.5478 | 0.9 | 0.56
Output | 0.0024141 | 0.0026943 | 0.0034176 | 0.8 | 0.00
Modify | 25.6 | 25.755 | 25.908 | 2.8 | 26.49
Other | | 0.07733 | | | 0.08
Nlocal: 2449.5 ave 2908 max 2012 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -148,4 +178,4 @@ Ave neighs/atom = 842.63544
Ave special neighs/atom = 1.3227189
Neighbor list builds = 22
Dangerous builds = 0
Total wall time: 0:07:48
Total wall time: 0:03:03

92
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.1 → examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.1
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field
# for z-periodic gold-saline electrochemical cell
# using Thomas-Fermi metallicity model: electrode q and qz will be
@ -39,8 +39,8 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.010 seconds
read_data CPU = 0.115 seconds
special bonds CPU = 0.003 seconds
read_data CPU = 0.065 seconds
group bot type 6
1620 atoms in group bot
@ -54,11 +54,12 @@ group electrolyte type 1 2 3 4 5
fix nvt electrolyte nvt temp 298.0 298.0 241
fix shake SPC 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
2160 = # of frozen angles
find clusters CPU = 0.010 seconds
find clusters CPU = 0.002 seconds
variable q atom q
variable qz atom q*(z-lz/2)
@ -69,7 +70,7 @@ compute qzbot bot reduce sum v_qz
compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
3240 atoms in group conp_group
fix_modify conp tf 6 1.0 18.1715745
fix_modify conp tf 7 1.0 18.1715745
@ -77,6 +78,35 @@ fix_modify conp tf 7 1.0 18.1715745
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
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) = 0.24017705
@ -86,9 +116,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.093542e-07
using double precision MKL FFT
3d grid and FFT values/proc = 472567 349920
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
@ -109,35 +139,35 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 194.6 | 194.6 | 194.6 Mbytes
Per MPI rank memory allocation (min/avg/max) = 194.8 | 194.8 | 194.8 Mbytes
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697
50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759
100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315
150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201
200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496
250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226
300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395
350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394
400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599
450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713484 125.59216
500 161.63639 280.74075 -39669.412 -35989.849 3.9261656 -3.9261656 76.0806 126.22255
Loop time of 280.183 on 1 procs for 500 steps with 9798 atoms
0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697
50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759
100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315
150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201
200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496
250 152.36874 264.64408 -39579.164 -36110.574 3.9925863 -3.9925863 77.379445 128.37226
300 153.83916 267.19802 -39554.899 -36052.836 3.94995 -3.94995 76.553896 127.00395
350 155.88897 270.75827 -39535.02 -35986.294 4.0598524 -4.0598524 78.679643 130.5394
400 156.51993 271.85415 -39484.219 -35921.13 4.1312898 -4.1312898 80.060368 132.83598
450 160.21339 278.26919 -39517.776 -35870.607 3.9068098 -3.9068098 75.713484 125.59216
500 161.63639 280.74075 -39488.333 -35808.771 3.9261656 -3.9261656 76.080599 126.22255
Loop time of 185.804 on 1 procs for 500 steps with 9798 atoms
Performance: 0.154 ns/day, 155.657 hours/ns, 1.785 timesteps/s
341.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 0.233 ns/day, 103.225 hours/ns, 2.691 timesteps/s, 26.366 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 | 119.69 | 119.69 | 119.69 | 0.0 | 42.72
Bond | 0.0010952 | 0.0010952 | 0.0010952 | 0.0 | 0.00
Kspace | 42.137 | 42.137 | 42.137 | 0.0 | 15.04
Neigh | 6.5403 | 6.5403 | 6.5403 | 0.0 | 2.33
Comm | 0.19411 | 0.19411 | 0.19411 | 0.0 | 0.07
Output | 0.0053644 | 0.0053644 | 0.0053644 | 0.0 | 0.00
Modify | 111.54 | 111.54 | 111.54 | 0.0 | 39.81
Other | | 0.07244 | | | 0.03
Pair | 91 | 91 | 91 | 0.0 | 48.98
Bond | 0.0010315 | 0.0010315 | 0.0010315 | 0.0 | 0.00
Kspace | 40.32 | 40.32 | 40.32 | 0.0 | 21.70
Neigh | 5.6505 | 5.6505 | 5.6505 | 0.0 | 3.04
Comm | 0.15304 | 0.15304 | 0.15304 | 0.0 | 0.08
Output | 0.0041829 | 0.0041829 | 0.0041829 | 0.0 | 0.00
Modify | 48.607 | 48.607 | 48.607 | 0.0 | 26.16
Other | | 0.06807 | | | 0.04
Nlocal: 9798 ave 9798 max 9798 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -151,4 +181,4 @@ Ave neighs/atom = 842.7079
Ave special neighs/atom = 1.3227189
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:21:11
Total wall time: 0:06:18

94
examples/PACKAGES/electrode/au-aq/log.26Apr2022.au-aq-tf.g++.4 → examples/PACKAGES/electrode/au-aq/log.1Dec2022.au-aq-tf.g++.4
View File

@ -1,4 +1,4 @@
LAMMPS (24 Mar 2022)
LAMMPS (3 Nov 2022)
# electrodes with constant potential using finite field
# for z-periodic gold-saline electrochemical cell
# using Thomas-Fermi metallicity model: electrode q and qz will be
@ -41,7 +41,7 @@ Finding 1-2 1-3 1-4 neighbors ...
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_data CPU = 0.091 seconds
read_data CPU = 0.114 seconds
group bot type 6
1620 atoms in group bot
@ -55,11 +55,12 @@ group electrolyte type 1 2 3 4 5
fix nvt electrolyte nvt temp 298.0 298.0 241
fix shake SPC 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
2160 = # of frozen angles
find clusters CPU = 0.001 seconds
find clusters CPU = 0.002 seconds
variable q atom q
variable qz atom q*(z-lz/2)
@ -70,7 +71,7 @@ compute qzbot bot reduce sum v_qz
compute ctemp electrolyte temp
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes 6*7
fix conp bot electrode/conp -1.0 1.805132 couple top 1.0 symm on ffield yes etypes on
3240 atoms in group conp_group
fix_modify conp tf 6 1.0 18.1715745
fix_modify conp tf 7 1.0 18.1715745
@ -78,6 +79,35 @@ fix_modify conp tf 7 1.0 18.1715745
thermo 50
thermo_style custom step temp c_ctemp epair etotal c_qtop c_qbot c_qztop c_qzbot
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) = 0.24017705
@ -87,9 +117,9 @@ PPPM/electrode initialization ...
estimated relative force accuracy = 1.093542e-07
using double precision MKL FFT
3d grid and FFT values/proc = 138958 87480
generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Generated 21 of 21 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 17
ghost atom cutoff = 17
@ -110,35 +140,35 @@ Neighbor list info ...
pair build: skip
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 118.1 | 120.6 | 123.1 Mbytes
Per MPI rank memory allocation (min/avg/max) = 118.2 | 120.7 | 123.2 Mbytes
Step Temp c_ctemp E_pair TotEng c_qtop c_qbot c_qztop c_qzbot
0 171.61215 298.06731 -39190.106 -35283.45 4.0804484 -4.0804484 79.075127 131.20697
50 147.14308 255.56782 -39849.964 -36500.334 3.9990346 -3.9990346 77.497181 128.57759
100 149.94935 260.44194 -39857.533 -36444.019 3.8613914 -3.8613914 74.82985 124.15315
150 151.95924 263.93285 -39855.567 -36396.299 3.8677064 -3.8677064 74.957279 124.33201
200 151.66737 263.42591 -39802.585 -36349.961 3.99842 -3.99842 77.491015 128.54496
250 152.36874 264.64408 -39763.306 -36294.716 3.9925863 -3.9925863 77.379445 128.37226
300 153.83916 267.19802 -39737.075 -36235.012 3.94995 -3.94995 76.553896 127.00395
350 155.88897 270.75827 -39722.265 -36173.539 4.0598524 -4.0598524 78.679643 130.5394
400 156.51993 271.85415 -39674.759 -36111.669 4.1312899 -4.1312899 80.060369 132.83599
450 160.21339 278.26919 -39697.962 -36050.793 3.9068098 -3.9068098 75.713485 125.59216
500 161.63639 280.74075 -39669.412 -35989.849 3.9261654 -3.9261654 76.080597 126.22255
Loop time of 110.716 on 4 procs for 500 steps with 9798 atoms
0 171.61215 298.06731 -39001.911 -35095.255 4.0804484 -4.0804484 79.075127 131.20697
50 147.14308 255.56782 -39665.525 -36315.894 3.9990346 -3.9990346 77.497181 128.57759
100 149.94935 260.44194 -39679.441 -36265.927 3.8613914 -3.8613914 74.82985 124.15315
150 151.95924 263.93285 -39677.184 -36217.916 3.8677064 -3.8677064 74.957279 124.33201
200 151.66737 263.42591 -39618.173 -36165.549 3.99842 -3.99842 77.491015 128.54496
250 152.36874 264.64408 -39579.163 -36110.574 3.9925863 -3.9925863 77.379445 128.37226
300 153.83916 267.19802 -39554.899 -36052.835 3.94995 -3.94995 76.553896 127.00395
350 155.88897 270.75826 -39535.02 -35986.294 4.0598523 -4.0598523 78.679642 130.5394
400 156.51993 271.85415 -39484.219 -35921.13 4.1312897 -4.1312897 80.060366 132.83598
450 160.21339 278.26919 -39517.776 -35870.607 3.9068099 -3.9068099 75.713486 125.59216
500 161.63639 280.74075 -39488.333 -35808.771 3.9261657 -3.9261657 76.080602 126.22256
Loop time of 104.099 on 4 procs for 500 steps with 9798 atoms
Performance: 0.390 ns/day, 61.509 hours/ns, 4.516 timesteps/s
97.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 0.415 ns/day, 57.833 hours/ns, 4.803 timesteps/s, 47.061 katom-step/s
87.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 21.17 | 30.449 | 39.65 | 164.9 | 27.50
Bond | 0.0007313 | 0.00077537 | 0.00081477 | 0.0 | 0.00
Kspace | 29.854 | 38.911 | 48.058 | 143.8 | 35.14
Neigh | 2.7206 | 2.7213 | 2.722 | 0.0 | 2.46
Comm | 0.33023 | 0.33225 | 0.33384 | 0.2 | 0.30
Output | 0.0024528 | 0.0027565 | 0.0035754 | 0.9 | 0.00
Modify | 38.091 | 38.233 | 38.365 | 2.1 | 34.53
Other | | 0.06636 | | | 0.06
Pair | 20.951 | 30.326 | 40.07 | 166.7 | 29.13
Bond | 0.00098259 | 0.0010706 | 0.0011926 | 0.3 | 0.00
Kspace | 33.465 | 43.037 | 52.268 | 137.5 | 41.34
Neigh | 2.6007 | 2.6014 | 2.6021 | 0.0 | 2.50
Comm | 0.57766 | 0.58318 | 0.58875 | 0.7 | 0.56
Output | 0.0022277 | 0.0024765 | 0.0031841 | 0.8 | 0.00
Modify | 27.292 | 27.47 | 27.647 | 3.1 | 26.39
Other | | 0.0787 | | | 0.08
Nlocal: 2449.5 ave 2908 max 2017 min
Histogram: 2 0 0 0 0 0 0 0 0 2
@ -147,9 +177,9 @@ Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 2.06421e+06 ave 2.7551e+06 max 1.40237e+06 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 8256853
Ave neighs/atom = 842.708
Total # of neighbors = 8256852
Ave neighs/atom = 842.7079
Ave special neighs/atom = 1.3227189
Neighbor list builds = 23
Dangerous builds = 0
Total wall time: 0:08:22
Total wall time: 0:03:12