181 lines
6.5 KiB
Groff
181 lines
6.5 KiB
Groff
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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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 = 0.038 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 = 0.003 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 # amat twostep
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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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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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2 neighbor lists, perpetual/occasional/extra = 2 0 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, perpetual, copy from (1)
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attributes: half, newton on
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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) = 23.16 | 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 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 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, 27.578 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 | 5.3666 | 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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Nghost: 5923.25 ave 5941 max 5906 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Neighs: 431582 ave 442090 max 419903 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 1726328
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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: 0:00:55
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