187 lines
7.3 KiB
Groff
187 lines
7.3 KiB
Groff
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
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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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group electrolyte type 1 2 3 4
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1280 atoms in group electrolyte
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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 = 0.002 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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fix conq bot electrode/conq -1.0 1.979 couple top 1.0 etypes on # symm on
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832 atoms in group conp_group
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variable dv equal f_conq[2]-f_conq[1]
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# symm on and off give different electrode potentials, but identical potential difference
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thermo 50
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thermo_style custom step temp c_ctemp epair etotal c_qbot c_qtop f_conq[1] f_conq[2] v_dv
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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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grid = 32 32 200
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stencil order = 5
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estimated absolute RMS force accuracy = 3.7023506e-05
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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 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 = 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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binsize = 9, bins = 4 4 16
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3 neighbor lists, perpetual/occasional/extra = 2 1 0
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(1) pair lj/cut/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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(2) fix electrode/conq, occasional, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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(3) fix electrode/conq, perpetual, skip from (1)
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attributes: half, newton on
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pair build: skip
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 54.25 | 54.25 | 54.25 Mbytes
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Step Temp c_ctemp E_pair TotEng c_qbot c_qtop f_conq[1] f_conq[2] v_dv
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0 0 0 25137446 25137446 -1 1 -9.931852 10.097344 20.029196
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50 20.206425 72.797911 25137263 25137472 -1 1 -9.4359366 9.5964514 19.032388
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100 55.931663 201.50563 25136961 25137537 -1 1 -8.0440112 8.1861787 16.23019
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150 81.389273 293.22204 25136818 25137656 -1 1 -6.1113109 6.2267114 12.338022
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200 92.867946 334.57639 25136841 25137798 -1 1 -4.1857807 4.2740694 8.4598501
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250 97.518304 351.33028 25136942 25137946 -1 1 -2.8383703 2.9101475 5.7485179
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300 102.36577 368.79431 25137045 25138099 -1 1 -2.3831643 2.4461115 4.8292759
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350 113.66597 409.50566 25137086 25138256 -1 1 -2.7083563 2.7457811 5.4541374
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400 122.8443 442.57252 25137148 25138413 -1 1 -3.4311003 3.3941657 6.825266
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450 128.63713 463.44243 25137235 25138560 -1 1 -4.132871 3.9852959 8.1181669
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500 131.18361 472.61665 25137344 25138695 -1 1 -4.5104095 4.2567261 8.7671355
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Loop time of 89.4461 on 1 procs for 500 steps with 3776 atoms
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Performance: 0.483 ns/day, 49.692 hours/ns, 5.590 timesteps/s, 21.108 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 | 19.404 | 19.404 | 19.404 | 0.0 | 21.69
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Bond | 0.0014902 | 0.0014902 | 0.0014902 | 0.0 | 0.00
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Kspace | 35.449 | 35.449 | 35.449 | 0.0 | 39.63
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Neigh | 0.26499 | 0.26499 | 0.26499 | 0.0 | 0.30
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Comm | 0.068497 | 0.068497 | 0.068497 | 0.0 | 0.08
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Output | 0.0023974 | 0.0023974 | 0.0023974 | 0.0 | 0.00
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Modify | 34.225 | 34.225 | 34.225 | 0.0 | 38.26
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Other | | 0.03044 | | | 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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Nghost: 12510 ave 12510 max 12510 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 1.72559e+06 ave 1.72559e+06 max 1.72559e+06 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 1725588
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Ave neighs/atom = 456.98835
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Ave special neighs/atom = 0.50847458
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Neighbor list builds = 6
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Dangerous builds = 0
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Total wall time: 0:01:48
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