193 lines
7.0 KiB
Groff
193 lines
7.0 KiB
Groff
LAMMPS (3 Nov 2022)
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# electrodes with thermopotentiostat
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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 = 0.002 seconds
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read_data CPU = 0.036 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 = 0.005 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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unfix nvt # remove NVT thermostat included from "settings.mod"
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fix conpthermo bot electrode/thermo -1.0 1.979 couple top 1.0 etypes on temp 500 100 7 symm on # temp tau rng
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832 atoms in group conp_group
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# to compare to regular constant potential, switch previous line to this:
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#fix conp bot electrode/conp -1.0 1.979 couple top 1.0 etypes on symm on
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fix nve electrolyte nve
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# note ionic liquid does not reach 500K immediately
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# because its thermal response time is finite
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# run this about 10k steps (10ps) to reach preset temperature
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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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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/thermo, 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/thermo, 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
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0 0 0 25137188 25137188 0.12767608 -0.12767608
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50 16.63971 59.94807 25137031 25137202 0.11714711 -0.11714711
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100 40.785523 146.93846 25136782 25137202 0.12783578 -0.12783578
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150 53.394067 192.3634 25136653 25137203 0.080257127 -0.080257127
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200 56.419019 203.26143 25136623 25137204 0.024756474 -0.024756474
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250 54.922935 197.87147 25136641 25137206 -0.024533734 0.024533734
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300 52.884861 190.52888 25136664 25137209 -0.066341109 0.066341109
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350 52.41676 188.84244 25136670 25137210 -0.089546266 0.089546266
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400 54.366979 195.86852 25136651 25137211 -0.10239755 0.10239755
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450 54.906542 197.81241 25136645 25137210 -0.099987411 0.099987411
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500 54.33841 195.7656 25136656 25137216 -0.21295943 0.21295943
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Loop time of 49.2564 on 4 procs for 500 steps with 3776 atoms
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Performance: 0.877 ns/day, 27.365 hours/ns, 10.151 timesteps/s, 38.330 katom-step/s
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76.1% 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 | 5.6984 | 5.9083 | 6.1177 | 6.4 | 12.00
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Bond | 0.0011785 | 0.0012201 | 0.0013055 | 0.1 | 0.00
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Kspace | 24.311 | 24.519 | 24.729 | 3.1 | 49.78
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Neigh | 0.075406 | 0.075487 | 0.07556 | 0.0 | 0.15
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Comm | 0.29972 | 0.30943 | 0.31881 | 1.7 | 0.63
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Output | 0.0012474 | 0.001684 | 0.0027062 | 1.5 | 0.00
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Modify | 18.377 | 18.384 | 18.391 | 0.2 | 37.32
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Other | | 0.05679 | | | 0.12
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Nlocal: 944 ave 951 max 940 min
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Histogram: 1 1 1 0 0 0 0 0 0 1
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Nghost: 5918.5 ave 5940 max 5899 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 431492 ave 442132 max 419533 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 1725966
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Ave neighs/atom = 457.08845
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Ave special neighs/atom = 0.50847458
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Neighbor list builds = 5
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Dangerous builds = 0
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Total wall time: 0:00:55
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