mirror of https://github.com/lammps/lammps.git
replace logs for graph-il
This commit is contained in:
srtee
parent
a3f1c25537
commit
c7300f47b1
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@ -1,4 +1,4 @@
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LAMMPS (24 Mar 2022)
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LAMMPS (3 Nov 2022)
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# electrodes with constant potential
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# for graphene-ionic liquid supercapacitor
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@ -37,13 +37,20 @@ Finding 1-2 1-3 1-4 neighbors ...
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.036 seconds
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special bonds CPU = 0.004 seconds
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read_data CPU = 0.027 seconds
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group bot molecule 641
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416 atoms in group bot
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group top molecule 642
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# replicate 4 4 1 # test different sys sizes
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variable zpos atom "z > 0"
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group zpos variable zpos
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1891 atoms in group zpos
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group ele type 5
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832 atoms in group ele
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group top intersect ele zpos
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416 atoms in group top
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group bot subtract ele top
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416 atoms in group bot
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group bmi type 1 2 3
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960 atoms in group bmi
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@ -52,24 +59,54 @@ group electrolyte type 1 2 3 4
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fix nvt electrolyte nvt temp 500.0 500.0 100
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fix shake bmi shake 1e-4 20 0 b 1 2 a 1
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Finding SHAKE clusters ...
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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320 = # of frozen angles
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find clusters CPU = 0.001 seconds
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find clusters CPU = 0.005 seconds
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variable q atom q
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compute qtop top reduce sum v_q
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compute qbot bot reduce sum v_q
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compute ctemp electrolyte temp
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kspace_modify slab 3.0
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kspace_modify slab 3.0 # amat twostep
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fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
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fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
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832 atoms in group conp_group
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thermo 50
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thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
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run 500
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- kspace_style pppm/electrode command:
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@article{Ahrens2021,
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author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
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doi = {10.1063/5.0063381},
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title = {{Constant potential simulations on a mesh}},
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journal = {Journal of Chemical Physics},
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year = {2021}
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volume = {155},
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pages = {104104},
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}
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- fix electrode command:
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@article{Ahrens2022
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author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
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doi = {10.1063/5.0099239},
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title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
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journal = {The Journal of Chemical Physics},
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year = {2022}
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volume = {157},
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pages = {084801},
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM/electrode initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.20904498
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@ -79,9 +116,9 @@ PPPM/electrode initialization ...
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estimated relative force accuracy = 1.1149519e-07
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using double precision MKL FFT
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3d grid and FFT values/proc = 307242 204800
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generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
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Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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@ -97,35 +134,35 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 57.15 | 57.15 | 57.15 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 57.19 | 57.19 | 57.19 Mbytes
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Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
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0 0 0 25137191 25137191 0.0085142912 -0.0085142912
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0 0 0 25137190 25137190 0.0085142912 -0.0085142912
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50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
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100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
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150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
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200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
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250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
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300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
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350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
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400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
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450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
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500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
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Loop time of 103.439 on 1 procs for 500 steps with 3776 atoms
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100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
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150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
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200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
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250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
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300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
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350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799
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400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
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450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
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500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
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Loop time of 91.5523 on 1 procs for 500 steps with 3776 atoms
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Performance: 0.418 ns/day, 57.466 hours/ns, 4.834 timesteps/s
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393.6% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 0.472 ns/day, 50.862 hours/ns, 5.461 timesteps/s, 20.622 katom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 19.309 | 19.309 | 19.309 | 0.0 | 18.67
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Bond | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.00
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Kspace | 23.047 | 23.047 | 23.047 | 0.0 | 22.28
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Neigh | 0.25707 | 0.25707 | 0.25707 | 0.0 | 0.25
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Comm | 0.070734 | 0.070734 | 0.070734 | 0.0 | 0.07
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Output | 0.0023085 | 0.0023085 | 0.0023085 | 0.0 | 0.00
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Modify | 60.73 | 60.73 | 60.73 | 0.0 | 58.71
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Other | | 0.01994 | | | 0.02
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Pair | 18.906 | 18.906 | 18.906 | 0.0 | 20.65
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Bond | 0.0012922 | 0.0012922 | 0.0012922 | 0.0 | 0.00
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Kspace | 34.476 | 34.476 | 34.476 | 0.0 | 37.66
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Neigh | 0.26641 | 0.26641 | 0.26641 | 0.0 | 0.29
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Comm | 0.069067 | 0.069067 | 0.069067 | 0.0 | 0.08
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Output | 0.0021466 | 0.0021466 | 0.0021466 | 0.0 | 0.00
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Modify | 37.805 | 37.805 | 37.805 | 0.0 | 41.29
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Other | | 0.0271 | | | 0.03
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Nlocal: 3776 ave 3776 max 3776 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -139,4 +176,4 @@ Ave neighs/atom = 457.18432
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Ave special neighs/atom = 0.50847458
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Neighbor list builds = 7
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Dangerous builds = 0
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Total wall time: 0:03:10
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Total wall time: 0:01:48
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@ -1,4 +1,4 @@
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LAMMPS (24 Mar 2022)
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LAMMPS (3 Nov 2022)
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# electrodes with constant potential
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# for graphene-ionic liquid supercapacitor
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@ -38,13 +38,20 @@ Finding 1-2 1-3 1-4 neighbors ...
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.014 seconds
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special bonds CPU = 0.003 seconds
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read_data CPU = 0.038 seconds
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group bot molecule 641
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416 atoms in group bot
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group top molecule 642
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# replicate 4 4 1 # test different sys sizes
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variable zpos atom "z > 0"
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group zpos variable zpos
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1891 atoms in group zpos
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group ele type 5
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832 atoms in group ele
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group top intersect ele zpos
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416 atoms in group top
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group bot subtract ele top
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416 atoms in group bot
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group bmi type 1 2 3
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960 atoms in group bmi
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@ -53,24 +60,54 @@ group electrolyte type 1 2 3 4
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fix nvt electrolyte nvt temp 500.0 500.0 100
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fix shake bmi shake 1e-4 20 0 b 1 2 a 1
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Finding SHAKE clusters ...
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0 = # of size 2 clusters
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0 = # of size 3 clusters
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0 = # of size 4 clusters
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320 = # of frozen angles
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find clusters CPU = 0.001 seconds
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find clusters CPU = 0.003 seconds
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variable q atom q
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compute qtop top reduce sum v_q
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compute qbot bot reduce sum v_q
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compute ctemp electrolyte temp
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kspace_modify slab 3.0
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kspace_modify slab 3.0 # amat twostep
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fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on
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fix conp bot electrode/conp -1.0 1.979 couple top 1.0 symm on #algo mat_inv
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832 atoms in group conp_group
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thermo 50
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thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
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run 500
|
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|
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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},
|
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title = {{Constant potential simulations on a mesh}},
|
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journal = {Journal of Chemical Physics},
|
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year = {2021}
|
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volume = {155},
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pages = {104104},
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}
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- fix electrode command:
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@article{Ahrens2022
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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}},
|
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journal = {The Journal of Chemical Physics},
|
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year = {2022}
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volume = {157},
|
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pages = {084801},
|
||||
}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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PPPM/electrode initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.20904498
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@ -80,9 +117,9 @@ PPPM/electrode initialization ...
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estimated relative force accuracy = 1.1149519e-07
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using double precision MKL FFT
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3d grid and FFT values/proc = 151593 85504
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generated 10 of 10 mixed pair_coeff terms from geometric mixing rule
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Generated 15 of 15 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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update: every = 1 steps, delay = 0 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 18
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ghost atom cutoff = 18
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@ -98,35 +135,35 @@ Neighbor list info ...
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 23.13 | 26.96 | 30.79 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 23.16 | 26.99 | 30.82 Mbytes
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Step Temp c_ctemp E_pair TotEng c_qbot c_qtop
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0 0 0 25137191 25137191 0.0085142912 -0.0085142912
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0 0 0 25137190 25137190 0.0085142912 -0.0085142912
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50 17.83755 64.26354 25137031 25137214 0.0045923944 -0.0045923944
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100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
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150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
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200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
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250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
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300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
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350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
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400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
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450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
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500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
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Loop time of 49.6656 on 4 procs for 500 steps with 3776 atoms
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100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
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150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
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200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
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250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
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300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
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350 100.36017 361.56871 25136941 25137975 -0.15649799 0.15649799
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400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
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450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
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500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
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Loop time of 49.6413 on 4 procs for 500 steps with 3776 atoms
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Performance: 0.870 ns/day, 27.592 hours/ns, 10.067 timesteps/s
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95.1% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 0.870 ns/day, 27.578 hours/ns, 10.072 timesteps/s, 38.033 katom-step/s
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76.3% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 5.968 | 6.1677 | 6.382 | 6.5 | 12.42
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Bond | 0.00071151 | 0.00078617 | 0.00090387 | 0.0 | 0.00
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Kspace | 17.345 | 17.558 | 17.755 | 3.8 | 35.35
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Neigh | 0.10939 | 0.10945 | 0.10948 | 0.0 | 0.22
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Comm | 0.15295 | 0.15474 | 0.15699 | 0.4 | 0.31
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Output | 0.00074458 | 0.0010336 | 0.0018799 | 1.5 | 0.00
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Modify | 25.634 | 25.641 | 25.645 | 0.1 | 51.63
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Other | | 0.03276 | | | 0.07
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Pair | 5.3666 | 5.4998 | 5.6946 | 5.4 | 11.08
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Bond | 0.0011638 | 0.0012711 | 0.0014555 | 0.3 | 0.00
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Kspace | 24.047 | 24.241 | 24.374 | 2.6 | 48.83
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Neigh | 0.088235 | 0.088328 | 0.088432 | 0.0 | 0.18
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Comm | 0.30907 | 0.31913 | 0.32916 | 1.7 | 0.64
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Output | 0.0010669 | 0.0014463 | 0.0024232 | 1.5 | 0.00
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Modify | 19.435 | 19.445 | 19.454 | 0.2 | 39.17
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Other | | 0.04549 | | | 0.09
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Nlocal: 944 ave 951 max 941 min
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Histogram: 1 2 0 0 0 0 0 0 0 1
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@ -140,4 +177,4 @@ Ave neighs/atom = 457.18432
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Ave special neighs/atom = 0.50847458
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Neighbor list builds = 7
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Dangerous builds = 0
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Total wall time: 0:01:11
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Total wall time: 0:00:55
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@ -0,0 +1,186 @@
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LAMMPS (3 Nov 2022)
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# electrodes with constrained total charges
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# for graphene-ionic liquid supercapacitor
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boundary p p f # slab calculation
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include settings.mod # styles, groups, computes and fixes
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# set boundary in main script because ffield is periodic
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units real
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# distribute electrode atoms among all processors:
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if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
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atom_style full
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pair_style lj/cut/coul/long 16
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bond_style harmonic
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angle_style harmonic
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kspace_style pppm/electrode 1e-7
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# kspace_modify in main script because ffield is periodic
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read_data "data.graph-il"
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Reading data file ...
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orthogonal box = (0 0 -68) to (32.2 34.4 68)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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3776 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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640 bonds
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reading angles ...
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320 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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read_data CPU = 0.023 seconds
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|
||||
# 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
|
||||
|
|
@ -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
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constrained total charges imposed from dynamically computed potentials
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.013 seconds
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.022 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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
|
||||
|
|
@ -64,7 +72,7 @@ compute qbot bot reduce sum v_q
|
|||
compute ctemp electrolyte temp
|
||||
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
|
||||
|
||||
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_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
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
|
||||
|
|
@ -88,9 +125,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -111,35 +148,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
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 44.4233 on 1 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137446 25137446 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261
|
||||
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
|
||||
394.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.505 ns/day, 47.538 hours/ns, 5.843 timesteps/s, 22.064 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 | 15.812 | 15.812 | 15.812 | 0.0 | 35.59
|
||||
Bond | 0.00085223 | 0.00085223 | 0.00085223 | 0.0 | 0.00
|
||||
Kspace | 17.03 | 17.03 | 17.03 | 0.0 | 38.33
|
||||
Neigh | 0.20513 | 0.20513 | 0.20513 | 0.0 | 0.46
|
||||
Comm | 0.04065 | 0.04065 | 0.04065 | 0.0 | 0.09
|
||||
Output | 0.0016819 | 0.0016819 | 0.0016819 | 0.0 | 0.00
|
||||
Modify | 11.32 | 11.32 | 11.32 | 0.0 | 25.48
|
||||
Other | | 0.01313 | | | 0.03
|
||||
Pair | 18.558 | 18.558 | 18.558 | 0.0 | 21.69
|
||||
Bond | 0.001404 | 0.001404 | 0.001404 | 0.0 | 0.00
|
||||
Kspace | 33.78 | 33.78 | 33.78 | 0.0 | 39.48
|
||||
Neigh | 0.27017 | 0.27017 | 0.27017 | 0.0 | 0.32
|
||||
Comm | 0.067438 | 0.067438 | 0.067438 | 0.0 | 0.08
|
||||
Output | 0.0026656 | 0.0026656 | 0.0026656 | 0.0 | 0.00
|
||||
Modify | 32.86 | 32.86 | 32.86 | 0.0 | 38.40
|
||||
Other | | 0.02916 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
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
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:37
|
||||
Total wall time: 0:01:42
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constrained total charges imposed from dynamically computed potentials
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.015 seconds
|
||||
special bonds CPU = 0.005 seconds
|
||||
read_data CPU = 0.044 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.001 seconds
|
||||
find clusters CPU = 0.002 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
|
|
@ -65,7 +73,7 @@ compute qbot bot reduce sum v_q
|
|||
compute ctemp electrolyte temp
|
||||
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
|
||||
|
||||
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_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_vbot v_vtop
|
||||
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
|
||||
|
|
@ -89,9 +126,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -112,35 +149,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
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 23.4081 on 4 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137446 25137446 -1 1 -9.931852 10.097344
|
||||
50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514
|
||||
100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787
|
||||
150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114
|
||||
200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694
|
||||
250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475
|
||||
300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115
|
||||
350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811
|
||||
400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657
|
||||
450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959
|
||||
500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261
|
||||
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
|
||||
93.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.799 ns/day, 30.019 hours/ns, 9.253 timesteps/s, 34.940 katom-step/s
|
||||
75.8% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.1792 | 4.3002 | 4.4836 | 5.7 | 18.37
|
||||
Bond | 0.00045023 | 0.00053483 | 0.00058432 | 0.0 | 0.00
|
||||
Kspace | 12.016 | 12.199 | 12.32 | 3.4 | 52.11
|
||||
Neigh | 0.062683 | 0.062707 | 0.062734 | 0.0 | 0.27
|
||||
Comm | 0.086385 | 0.08861 | 0.090874 | 0.7 | 0.38
|
||||
Output | 0.00082773 | 0.0010401 | 0.0016576 | 1.1 | 0.00
|
||||
Modify | 6.7386 | 6.7413 | 6.7443 | 0.1 | 28.80
|
||||
Other | | 0.0151 | | | 0.06
|
||||
Pair | 6.5878 | 6.8799 | 7.1455 | 8.0 | 12.73
|
||||
Bond | 0.0011081 | 0.0014187 | 0.0018792 | 0.8 | 0.00
|
||||
Kspace | 25.907 | 26.173 | 26.464 | 4.1 | 48.44
|
||||
Neigh | 0.16417 | 0.16425 | 0.16438 | 0.0 | 0.30
|
||||
Comm | 0.34948 | 0.36296 | 0.37524 | 1.9 | 0.67
|
||||
Output | 0.0017398 | 0.0021707 | 0.0033966 | 1.5 | 0.00
|
||||
Modify | 20.392 | 20.403 | 20.416 | 0.2 | 37.76
|
||||
Other | | 0.04783 | | | 0.09
|
||||
|
||||
Nlocal: 944 ave 948 max 940 min
|
||||
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
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:45
|
||||
Total wall time: 0:01:00
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constant potential and smart neighborlists
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.024 seconds
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.021 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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
|
||||
|
|
@ -64,12 +72,41 @@ compute qbot bot reduce sum v_q
|
|||
compute ctemp electrolyte temp
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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
|
||||
|
|
@ -79,9 +116,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -102,35 +139,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
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
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 63.497 on 1 procs for 500 steps with 3776 atoms
|
||||
100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
|
||||
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
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.496 ns/day, 48.373 hours/ns, 5.742 timesteps/s, 21.683 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 | 20.628 | 20.628 | 20.628 | 0.0 | 32.49
|
||||
Bond | 0.0019309 | 0.0019309 | 0.0019309 | 0.0 | 0.00
|
||||
Kspace | 23.61 | 23.61 | 23.61 | 0.0 | 37.18
|
||||
Neigh | 0.28156 | 0.28156 | 0.28156 | 0.0 | 0.44
|
||||
Comm | 0.061191 | 0.061191 | 0.061191 | 0.0 | 0.10
|
||||
Output | 0.0022666 | 0.0022666 | 0.0022666 | 0.0 | 0.00
|
||||
Modify | 18.891 | 18.891 | 18.891 | 0.0 | 29.75
|
||||
Other | | 0.02047 | | | 0.03
|
||||
Pair | 18.617 | 18.617 | 18.617 | 0.0 | 21.38
|
||||
Bond | 0.0014056 | 0.0014056 | 0.0014056 | 0.0 | 0.00
|
||||
Kspace | 34.856 | 34.856 | 34.856 | 0.0 | 40.03
|
||||
Neigh | 0.30015 | 0.30015 | 0.30015 | 0.0 | 0.34
|
||||
Comm | 0.065303 | 0.065303 | 0.065303 | 0.0 | 0.08
|
||||
Output | 0.0021663 | 0.0021663 | 0.0021663 | 0.0 | 0.00
|
||||
Modify | 33.201 | 33.201 | 33.201 | 0.0 | 38.13
|
||||
Other | | 0.0282 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:02:24
|
||||
Total wall time: 0:01:43
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constant potential and smart neighborlists
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.016 seconds
|
||||
special bonds CPU = 0.004 seconds
|
||||
read_data CPU = 0.047 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.001 seconds
|
||||
find clusters CPU = 0.005 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
|
|
@ -65,12 +73,41 @@ compute qbot bot reduce sum v_q
|
|||
compute ctemp electrolyte temp
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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
|
||||
|
|
@ -80,9 +117,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -103,35 +140,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
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
|
||||
100 48.393682 174.34846 25136774 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136655 25137380 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136667 25137514 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136757 25137659 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136865 25137810 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136934 25137968 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136986 25138133 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137043 25138298 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137145 25138453 -0.21037535 0.21037535
|
||||
Loop time of 30.7883 on 4 procs for 500 steps with 3776 atoms
|
||||
100 48.393682 174.34846 25136775 25137273 -0.009514517 0.009514517
|
||||
150 70.421272 253.7075 25136657 25137382 -0.033017005 0.033017005
|
||||
200 82.204844 296.16031 25136670 25137517 -0.063668175 0.063668175
|
||||
250 87.54223 315.38937 25136762 25137663 -0.096776257 0.096776257
|
||||
300 91.704746 330.38571 25136871 25137816 -0.1283784 0.1283784
|
||||
350 100.36017 361.56871 25136942 25137975 -0.15649799 0.15649799
|
||||
400 111.37575 401.25467 25136994 25138141 -0.18065435 0.18065435
|
||||
450 121.79848 438.80476 25137052 25138307 -0.19979365 0.19979365
|
||||
500 126.95916 457.39718 25137155 25138463 -0.21037535 0.21037535
|
||||
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
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.892 ns/day, 26.893 hours/ns, 10.329 timesteps/s, 39.002 katom-step/s
|
||||
75.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.5102 | 6.7303 | 6.9362 | 7.6 | 21.86
|
||||
Bond | 0.00064504 | 0.00071061 | 0.000779 | 0.0 | 0.00
|
||||
Kspace | 14.081 | 14.287 | 14.507 | 5.2 | 46.40
|
||||
Neigh | 0.11831 | 0.11841 | 0.11851 | 0.0 | 0.38
|
||||
Comm | 0.12216 | 0.12434 | 0.12651 | 0.6 | 0.40
|
||||
Output | 0.00083347 | 0.0010533 | 0.0017069 | 1.2 | 0.00
|
||||
Modify | 9.5052 | 9.5071 | 9.5093 | 0.1 | 30.88
|
||||
Other | | 0.01927 | | | 0.06
|
||||
Pair | 5.3095 | 5.5504 | 5.7923 | 8.2 | 11.47
|
||||
Bond | 0.0011128 | 0.0012414 | 0.0014028 | 0.3 | 0.00
|
||||
Kspace | 24.084 | 24.322 | 24.559 | 3.9 | 50.24
|
||||
Neigh | 0.093557 | 0.09408 | 0.094377 | 0.1 | 0.19
|
||||
Comm | 0.30394 | 0.31319 | 0.3225 | 1.6 | 0.65
|
||||
Output | 0.0012719 | 0.0015908 | 0.0024592 | 1.3 | 0.00
|
||||
Modify | 18.066 | 18.079 | 18.091 | 0.2 | 37.35
|
||||
Other | | 0.04692 | | | 0.10
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:56
|
||||
Total wall time: 0:00:54
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.022 seconds
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.021 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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
|
||||
|
|
@ -63,12 +71,41 @@ compute qtop top reduce sum v_q
|
|||
compute qbot bot reduce sum v_q
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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) = 0.20949995
|
||||
|
|
@ -78,9 +115,9 @@ PPPM/electrode initialization ...
|
|||
estimated relative force accuracy = 1.0544465e-07
|
||||
using double precision MKL FFT
|
||||
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 ...
|
||||
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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -101,35 +138,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137187 25137187 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221
|
||||
Loop time of 36.7618 on 1 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137186 25137186 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221
|
||||
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
|
||||
393.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.802 ns/day, 29.912 hours/ns, 9.287 timesteps/s, 35.066 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 | 19.737 | 19.737 | 19.737 | 0.0 | 53.69
|
||||
Bond | 0.00092668 | 0.00092668 | 0.00092668 | 0.0 | 0.00
|
||||
Kspace | 6.5854 | 6.5854 | 6.5854 | 0.0 | 17.91
|
||||
Neigh | 0.33914 | 0.33914 | 0.33914 | 0.0 | 0.92
|
||||
Comm | 0.090124 | 0.090124 | 0.090124 | 0.0 | 0.25
|
||||
Output | 0.0013975 | 0.0013975 | 0.0013975 | 0.0 | 0.00
|
||||
Modify | 9.9834 | 9.9834 | 9.9834 | 0.0 | 27.16
|
||||
Other | | 0.02455 | | | 0.07
|
||||
Pair | 19.843 | 19.843 | 19.843 | 0.0 | 36.85
|
||||
Bond | 0.0016963 | 0.0016963 | 0.0016963 | 0.0 | 0.00
|
||||
Kspace | 11.232 | 11.232 | 11.232 | 0.0 | 20.86
|
||||
Neigh | 0.39189 | 0.39189 | 0.39189 | 0.0 | 0.73
|
||||
Comm | 0.12348 | 0.12348 | 0.12348 | 0.0 | 0.23
|
||||
Output | 0.0017904 | 0.0017904 | 0.0017904 | 0.0 | 0.00
|
||||
Modify | 22.207 | 22.207 | 22.207 | 0.0 | 41.25
|
||||
Other | | 0.04008 | | | 0.07
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:39
|
||||
Total wall time: 0:01:10
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with constant potential using finite field
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.016 seconds
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.033 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -53,23 +60,53 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.001 seconds
|
||||
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
|
||||
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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) = 0.20949995
|
||||
|
|
@ -79,9 +116,9 @@ PPPM/electrode initialization ...
|
|||
estimated relative force accuracy = 1.0544465e-07
|
||||
using double precision MKL FFT
|
||||
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 ...
|
||||
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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -102,35 +139,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137187 25137187 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137211 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137269 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136651 25137377 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136664 25137510 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136754 25137655 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136862 25137806 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136930 25137964 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136982 25138129 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137039 25138294 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137142 25138449 -0.21305221 0.21305221
|
||||
Loop time of 19.3932 on 4 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137186 25137186 0.0085209384 -0.0085209384
|
||||
50 17.837642 64.263873 25137027 25137210 0.0045513522 -0.0045513522
|
||||
100 48.393984 174.34955 25136771 25137270 -0.0097291786 0.0097291786
|
||||
150 70.421823 253.70949 25136653 25137378 -0.033522793 0.033522793
|
||||
200 82.205535 296.1628 25136667 25137513 -0.064555648 0.064555648
|
||||
250 87.542843 315.39158 25136758 25137660 -0.098075546 0.098075546
|
||||
300 91.705733 330.38927 25136868 25137812 -0.13006751 0.13006751
|
||||
350 100.36128 361.5727 25136938 25137971 -0.15852814 0.15852814
|
||||
400 111.37586 401.25505 25136990 25138137 -0.18297207 0.18297207
|
||||
450 121.79814 438.80351 25137049 25138303 -0.2023394 0.2023394
|
||||
500 126.95882 457.39597 25137151 25138459 -0.21305221 0.21305221
|
||||
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
|
||||
96.3% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 1.644 ns/day, 14.600 hours/ns, 19.025 timesteps/s, 71.840 katom-step/s
|
||||
83.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.1247 | 7.6399 | 8.1323 | 13.3 | 39.39
|
||||
Bond | 0.00072445 | 0.00077581 | 0.00085933 | 0.0 | 0.00
|
||||
Kspace | 5.098 | 5.5905 | 6.1036 | 15.6 | 28.83
|
||||
Neigh | 0.145 | 0.14517 | 0.14532 | 0.0 | 0.75
|
||||
Comm | 0.24683 | 0.25127 | 0.25907 | 1.0 | 1.30
|
||||
Output | 0.00084146 | 0.0011298 | 0.0019741 | 1.5 | 0.01
|
||||
Modify | 5.6957 | 5.7129 | 5.729 | 0.6 | 29.46
|
||||
Other | | 0.05153 | | | 0.27
|
||||
Pair | 5.8233 | 6.1941 | 6.6294 | 12.1 | 23.57
|
||||
Bond | 0.0010807 | 0.0011705 | 0.0013494 | 0.3 | 0.00
|
||||
Kspace | 8.0325 | 8.4703 | 8.8457 | 10.4 | 32.23
|
||||
Neigh | 0.14184 | 0.1421 | 0.14238 | 0.1 | 0.54
|
||||
Comm | 0.52248 | 0.54323 | 0.56352 | 2.7 | 2.07
|
||||
Output | 0.00079782 | 0.0011547 | 0.0021987 | 1.8 | 0.00
|
||||
Modify | 10.831 | 10.856 | 10.881 | 0.7 | 41.31
|
||||
Other | | 0.07293 | | | 0.28
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:44
|
||||
Total wall time: 0:00:32
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with equal-style ramped (electrode-)constant potential
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.014 seconds
|
||||
special bonds CPU = 0.002 seconds
|
||||
read_data CPU = 0.021 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -52,6 +59,7 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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
|
||||
|
|
@ -65,12 +73,41 @@ compute ctemp electrolyte temp
|
|||
kspace_modify slab 3.0
|
||||
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
|
||||
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
|
||||
|
|
@ -80,9 +117,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -103,35 +140,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4
|
||||
Loop time of 50.8569 on 1 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4
|
||||
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
|
||||
393.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.493 ns/day, 48.689 hours/ns, 5.705 timesteps/s, 21.543 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 | 18.166 | 18.166 | 18.166 | 0.0 | 35.72
|
||||
Bond | 0.00091918 | 0.00091918 | 0.00091918 | 0.0 | 0.00
|
||||
Kspace | 17.267 | 17.267 | 17.267 | 0.0 | 33.95
|
||||
Neigh | 0.27635 | 0.27635 | 0.27635 | 0.0 | 0.54
|
||||
Comm | 0.044714 | 0.044714 | 0.044714 | 0.0 | 0.09
|
||||
Output | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.00
|
||||
Modify | 15.086 | 15.086 | 15.086 | 0.0 | 29.66
|
||||
Other | | 0.01409 | | | 0.03
|
||||
Pair | 18.484 | 18.484 | 18.484 | 0.0 | 21.09
|
||||
Bond | 0.0016824 | 0.0016824 | 0.0016824 | 0.0 | 0.00
|
||||
Kspace | 35.426 | 35.426 | 35.426 | 0.0 | 40.42
|
||||
Neigh | 0.30201 | 0.30201 | 0.30201 | 0.0 | 0.34
|
||||
Comm | 0.066546 | 0.066546 | 0.066546 | 0.0 | 0.08
|
||||
Output | 0.0022768 | 0.0022768 | 0.0022768 | 0.0 | 0.00
|
||||
Modify | 33.33 | 33.33 | 33.33 | 0.0 | 38.03
|
||||
Other | | 0.0286 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:50
|
||||
Total wall time: 0:01:44
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with equal-style ramped (electrode-)constant potential
|
||||
# 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 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.024 seconds
|
||||
special bonds CPU = 0.003 seconds
|
||||
read_data CPU = 0.034 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.001 seconds
|
||||
find clusters CPU = 0.002 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
|
|
@ -66,12 +74,41 @@ compute ctemp electrolyte temp
|
|||
kspace_modify slab 3.0
|
||||
|
||||
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
|
||||
|
||||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop v_v
|
||||
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
|
||||
|
|
@ -81,9 +118,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -104,35 +141,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137191 25137191 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137214 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136774 25137273 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136654 25137380 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136666 25137513 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136754 25137658 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136861 25137808 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136928 25137965 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25136977 25138129 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137033 25138291 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137133 25138444 -0.40653009 0.40653009 4
|
||||
Loop time of 31.7642 on 4 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2
|
||||
50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2
|
||||
100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4
|
||||
150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6
|
||||
200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8
|
||||
250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3
|
||||
300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2
|
||||
350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4
|
||||
400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6
|
||||
450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8
|
||||
500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4
|
||||
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
|
||||
94.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s
|
||||
75.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 6.7949 | 7.0359 | 7.3092 | 7.9 | 22.15
|
||||
Bond | 0.00069874 | 0.00073747 | 0.00077928 | 0.0 | 0.00
|
||||
Kspace | 14.375 | 14.648 | 14.89 | 5.5 | 46.12
|
||||
Neigh | 0.12057 | 0.1206 | 0.12062 | 0.0 | 0.38
|
||||
Comm | 0.13412 | 0.13439 | 0.13483 | 0.1 | 0.42
|
||||
Output | 0.0010019 | 0.0013088 | 0.0020937 | 1.3 | 0.00
|
||||
Modify | 9.8017 | 9.8025 | 9.8031 | 0.0 | 30.86
|
||||
Other | | 0.02036 | | | 0.06
|
||||
Pair | 5.7517 | 5.9151 | 6.0961 | 6.6 | 12.02
|
||||
Bond | 0.0011959 | 0.0013362 | 0.0014512 | 0.2 | 0.00
|
||||
Kspace | 24.223 | 24.404 | 24.566 | 3.2 | 49.59
|
||||
Neigh | 0.10283 | 0.10288 | 0.10301 | 0.0 | 0.21
|
||||
Comm | 0.30801 | 0.31944 | 0.33141 | 2.0 | 0.65
|
||||
Output | 0.0010416 | 0.0014127 | 0.0024086 | 1.5 | 0.00
|
||||
Modify | 18.405 | 18.418 | 18.432 | 0.3 | 37.43
|
||||
Other | | 0.04459 | | | 0.09
|
||||
|
||||
Nlocal: 944 ave 951 max 941 min
|
||||
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
|
||||
Neighbor list builds = 7
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:58
|
||||
Total wall time: 0:00:55
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with thermopotentiostat
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
|
|
@ -38,12 +38,19 @@ 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 = 0.024 seconds
|
||||
read_data CPU = 0.021 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -52,11 +59,12 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.000 seconds
|
||||
find clusters CPU = 0.001 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
|
|
@ -65,10 +73,10 @@ compute ctemp electrolyte temp
|
|||
kspace_modify slab 3.0
|
||||
|
||||
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
|
||||
# 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
|
||||
|
||||
# note ionic liquid does not reach 500K immediately
|
||||
|
|
@ -77,6 +85,35 @@ fix nve electrolyte nve
|
|||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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
|
||||
|
|
@ -86,9 +123,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -109,35 +146,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137187 25137187 0.12767613 -0.12767613
|
||||
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714
|
||||
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358
|
||||
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143
|
||||
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489
|
||||
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719
|
||||
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094
|
||||
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252
|
||||
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753
|
||||
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401
|
||||
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942
|
||||
Loop time of 49.9831 on 1 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137188 25137188 0.12767608 -0.12767608
|
||||
50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711
|
||||
100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578
|
||||
150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127
|
||||
200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474
|
||||
250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734
|
||||
300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109
|
||||
350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266
|
||||
400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755
|
||||
450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411
|
||||
500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943
|
||||
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
|
||||
393.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 0.494 ns/day, 48.627 hours/ns, 5.712 timesteps/s, 21.570 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 | 17.01 | 17.01 | 17.01 | 0.0 | 34.03
|
||||
Bond | 0.0010374 | 0.0010374 | 0.0010374 | 0.0 | 0.00
|
||||
Kspace | 18.096 | 18.096 | 18.096 | 0.0 | 36.20
|
||||
Neigh | 0.1828 | 0.1828 | 0.1828 | 0.0 | 0.37
|
||||
Comm | 0.043856 | 0.043856 | 0.043856 | 0.0 | 0.09
|
||||
Output | 0.0018373 | 0.0018373 | 0.0018373 | 0.0 | 0.00
|
||||
Modify | 14.632 | 14.632 | 14.632 | 0.0 | 29.27
|
||||
Other | | 0.01548 | | | 0.03
|
||||
Pair | 18.819 | 18.819 | 18.819 | 0.0 | 21.50
|
||||
Bond | 0.0014336 | 0.0014336 | 0.0014336 | 0.0 | 0.00
|
||||
Kspace | 34.891 | 34.891 | 34.891 | 0.0 | 39.86
|
||||
Neigh | 0.21542 | 0.21542 | 0.21542 | 0.0 | 0.25
|
||||
Comm | 0.063383 | 0.063383 | 0.063383 | 0.0 | 0.07
|
||||
Output | 0.0020476 | 0.0020476 | 0.0020476 | 0.0 | 0.00
|
||||
Modify | 33.507 | 33.507 | 33.507 | 0.0 | 38.28
|
||||
Other | | 0.0281 | | | 0.03
|
||||
|
||||
Nlocal: 3776 ave 3776 max 3776 min
|
||||
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
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:50
|
||||
Total wall time: 0:01:44
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
LAMMPS (24 Mar 2022)
|
||||
LAMMPS (3 Nov 2022)
|
||||
# electrodes with thermopotentiostat
|
||||
# for graphene-ionic liquid supercapacitor
|
||||
|
||||
|
|
@ -39,12 +39,19 @@ 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 = 0.025 seconds
|
||||
read_data CPU = 0.036 seconds
|
||||
|
||||
group bot molecule 641
|
||||
416 atoms in group bot
|
||||
group top molecule 642
|
||||
# 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
|
||||
|
|
@ -53,11 +60,12 @@ group electrolyte type 1 2 3 4
|
|||
|
||||
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 = 0.001 seconds
|
||||
find clusters CPU = 0.005 seconds
|
||||
|
||||
variable q atom q
|
||||
compute qtop top reduce sum v_q
|
||||
|
|
@ -66,10 +74,10 @@ compute ctemp electrolyte temp
|
|||
kspace_modify slab 3.0
|
||||
|
||||
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
|
||||
# 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
|
||||
|
||||
# note ionic liquid does not reach 500K immediately
|
||||
|
|
@ -78,6 +86,35 @@ fix nve electrolyte nve
|
|||
thermo 50
|
||||
thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop
|
||||
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
|
||||
|
|
@ -87,9 +124,9 @@ PPPM/electrode initialization ...
|
|||
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
|
||||
Generated 15 of 15 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 = 18
|
||||
ghost atom cutoff = 18
|
||||
|
|
@ -110,35 +147,35 @@ Neighbor list info ...
|
|||
pair build: skip
|
||||
stencil: 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
|
||||
0 0 0 25137187 25137187 0.12767613 -0.12767613
|
||||
50 16.63971 59.94807 25137031 25137203 0.11714714 -0.11714714
|
||||
100 40.785523 146.93846 25136782 25137202 0.1278358 -0.1278358
|
||||
150 53.394067 192.3634 25136654 25137204 0.080257143 -0.080257143
|
||||
200 56.419019 203.26143 25136624 25137205 0.024756489 -0.024756489
|
||||
250 54.922935 197.87147 25136640 25137205 -0.024533719 0.024533719
|
||||
300 52.884861 190.52888 25136660 25137205 -0.066341094 0.066341094
|
||||
350 52.41676 188.84244 25136666 25137206 -0.089546252 0.089546252
|
||||
400 54.366979 195.86852 25136646 25137206 -0.10239753 0.10239753
|
||||
450 54.906542 197.81241 25136642 25137208 -0.099987401 0.099987401
|
||||
500 54.33841 195.7656 25136642 25137201 -0.21295942 0.21295942
|
||||
Loop time of 27.6772 on 4 procs for 500 steps with 3776 atoms
|
||||
0 0 0 25137188 25137188 0.12767608 -0.12767608
|
||||
50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711
|
||||
100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578
|
||||
150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127
|
||||
200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474
|
||||
250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734
|
||||
300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109
|
||||
350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266
|
||||
400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755
|
||||
450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411
|
||||
500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943
|
||||
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
|
||||
91.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s
|
||||
76.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.6214 | 4.8032 | 4.9546 | 6.5 | 17.35
|
||||
Bond | 0.0005324 | 0.00060509 | 0.00069468 | 0.0 | 0.00
|
||||
Kspace | 13.883 | 14.034 | 14.216 | 3.8 | 50.71
|
||||
Neigh | 0.061704 | 0.061727 | 0.06176 | 0.0 | 0.22
|
||||
Comm | 0.10101 | 0.10374 | 0.10645 | 0.8 | 0.37
|
||||
Output | 0.00086818 | 0.0010909 | 0.001715 | 1.1 | 0.00
|
||||
Modify | 8.65 | 8.6524 | 8.6545 | 0.1 | 31.26
|
||||
Other | | 0.02055 | | | 0.07
|
||||
Pair | 5.6984 | 5.9083 | 6.1177 | 6.4 | 12.00
|
||||
Bond | 0.0011785 | 0.0012201 | 0.0013055 | 0.1 | 0.00
|
||||
Kspace | 24.311 | 24.519 | 24.729 | 3.1 | 49.78
|
||||
Neigh | 0.075406 | 0.075487 | 0.07556 | 0.0 | 0.15
|
||||
Comm | 0.29972 | 0.30943 | 0.31881 | 1.7 | 0.63
|
||||
Output | 0.0012474 | 0.001684 | 0.0027062 | 1.5 | 0.00
|
||||
Modify | 18.377 | 18.384 | 18.391 | 0.2 | 37.32
|
||||
Other | | 0.05679 | | | 0.12
|
||||
|
||||
Nlocal: 944 ave 951 max 940 min
|
||||
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
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:50
|
||||
Total wall time: 0:00:55
|
||||
|
|
@ -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
|
||||
|
|
@ -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
|
||||
Loading…
Reference in New Issue