187 lines
6.9 KiB
Groff
187 lines
6.9 KiB
Groff
LAMMPS (3 Nov 2022)
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# electrodes with equal-style ramped (electrode-)constant potential
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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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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 2 by 2 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 = 0.003 seconds
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read_data CPU = 0.034 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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variable v equal ramp(2,4)
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fix conp bot electrode/conp 0.0 1.979 couple top v_v symm on etypes on
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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 v_v
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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 = 151593 85504
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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/conp, 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/conp, 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) = 22.9 | 26.72 | 30.55 Mbytes
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Step Temp c_ctemp E_pair TotEng c_qbot c_qtop v_v
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0 0 0 25137190 25137190 0.0085142912 -0.0085142912 2
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50 17.839699 64.271283 25137031 25137215 -0.0067894391 0.0067894391 2.2
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100 48.411618 174.41308 25136776 25137275 -0.033422174 0.033422174 2.4
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150 70.478909 253.91515 25136658 25137384 -0.071583953 0.071583953 2.6
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200 82.322716 296.58497 25136673 25137521 -0.11962095 0.11962095 2.8
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250 87.739905 316.10153 25136766 25137670 -0.17281469 0.17281469 3
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300 91.974584 331.35786 25136877 25137825 -0.22657123 0.22657123 3.2
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350 100.73048 362.90284 25136949 25137987 -0.27817429 0.27817429 3.4
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400 111.78597 402.73256 25137004 25138156 -0.32659395 0.32659395 3.6
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450 122.14181 440.04167 25137066 25138324 -0.37054363 0.37054363 3.8
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500 127.32331 458.70912 25137171 25138482 -0.40653009 0.40653009 4
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Loop time of 49.2075 on 4 procs for 500 steps with 3776 atoms
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Performance: 0.878 ns/day, 27.337 hours/ns, 10.161 timesteps/s, 38.368 katom-step/s
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75.7% 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 | 5.7517 | 5.9151 | 6.0961 | 6.6 | 12.02
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Bond | 0.0011959 | 0.0013362 | 0.0014512 | 0.2 | 0.00
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Kspace | 24.223 | 24.404 | 24.566 | 3.2 | 49.59
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Neigh | 0.10283 | 0.10288 | 0.10301 | 0.0 | 0.21
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Comm | 0.30801 | 0.31944 | 0.33141 | 2.0 | 0.65
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Output | 0.0010416 | 0.0014127 | 0.0024086 | 1.5 | 0.00
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Modify | 18.405 | 18.418 | 18.432 | 0.3 | 37.43
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Other | | 0.04459 | | | 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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Nghost: 5924.75 ave 5941 max 5910 min
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Histogram: 1 0 0 1 0 1 0 0 0 1
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Neighs: 431570 ave 442073 max 419253 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 1726280
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Ave neighs/atom = 457.17161
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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: 0:00:55
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