173 lines
6.5 KiB
Groff
173 lines
6.5 KiB
Groff
LAMMPS (3 Nov 2022)
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boundary p p f
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kspace_style pppm/electrode 1.0e-7
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kspace_modify slab 3.0
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include "settings.mod" # styles, computes, groups 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 14
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# kspace_style and _modify in main script to test different approaches
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read_data "data.au-vac"
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Reading data file ...
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orthogonal box = (0.285001 -0.368323 -1.043333) to (25.325067 24.671743 43.303354)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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288 atoms
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reading velocities ...
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288 velocities
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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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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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special bonds CPU = 0.001 seconds
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read_data CPU = 0.004 seconds
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group bot molecule 1
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144 atoms in group bot
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group top molecule 2
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144 atoms in group top
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# ramping potential difference
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variable v equal ramp(0,2)
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# get electrode charges
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variable q atom q
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compute qbot bot reduce sum v_q
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compute qtop top reduce sum v_q
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# get theoretical charges:
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# calculate distance dz between electrodes
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compute zbot bot reduce max z
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compute ztop top reduce min z
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variable dz equal c_ztop-c_zbot
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# calculate theoretical capacitance as eps0 * area / dz
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variable eps0 equal 55.26349406/10000 # epsilon zero
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variable capac equal "v_eps0 * lx * ly / v_dz"
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# calculate theoretical charges and deviation of constant potential charges from theory
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variable qtheory equal "v_capac * v_v"
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variable percdev equal "100 * (c_qtop - v_qtheory) / (v_qtheory + 1e-9)" # avoid divide-by-zero
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# constant potential electrodes with ramping potential difference
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fix conp bot electrode/conp 0 1.979 couple top v_v symm on
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288 atoms in group conp_group
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thermo 1
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# thermo: step, imposed potential, bottom charge, top charge, theory charge, percent deviation
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thermo_style custom step v_v c_qbot c_qtop v_qtheory v_percdev
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run 10
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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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WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
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PPPM/electrode initialization ...
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WARNING: System is not charge neutral, net charge = 0.000219 (src/kspace.cpp:327)
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.16696028
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grid = 8 8 25
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stencil order = 5
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estimated absolute RMS force accuracy = 2.7967012e-05
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estimated relative force accuracy = 8.4221827e-08
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using double precision MKL FFT
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3d grid and FFT values/proc = 4563 1600
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Generated 1 of 1 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 = 16
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ghost atom cutoff = 16
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binsize = 8, bins = 4 4 6
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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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WARNING: Using kspace solver on system with no charge (src/kspace.cpp:314)
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Per MPI rank memory allocation (min/avg/max) = 7.942 | 7.942 | 7.942 Mbytes
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Step v_v c_qbot c_qtop v_qtheory v_percdev
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0 0 0 0 0 0
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1 0.2 -0.030912769 0.030912769 0.031376826 -1.4789807
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2 0.4 -0.061825538 0.061825538 0.062753652 -1.4789807
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3 0.6 -0.092738307 0.092738307 0.094130479 -1.4789807
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4 0.8 -0.12365108 0.12365108 0.1255073 -1.4789807
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5 1 -0.15456384 0.15456384 0.15688413 -1.4789807
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6 1.2 -0.18547661 0.18547661 0.18826096 -1.4789807
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7 1.4 -0.21638938 0.21638938 0.21963778 -1.4789807
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8 1.6 -0.24730215 0.24730215 0.25101461 -1.4789807
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9 1.8 -0.27821492 0.27821492 0.28239144 -1.4789807
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10 2 -0.30912769 0.30912769 0.31376826 -1.4789807
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Loop time of 0.0176221 on 1 procs for 10 steps with 288 atoms
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Performance: 49.029 ns/day, 0.490 hours/ns, 567.471 timesteps/s, 163.432 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 | 0.0051407 | 0.0051407 | 0.0051407 | 0.0 | 29.17
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Bond | 9.92e-07 | 9.92e-07 | 9.92e-07 | 0.0 | 0.01
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Kspace | 0.0029456 | 0.0029456 | 0.0029456 | 0.0 | 16.72
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 8.3497e-05 | 8.3497e-05 | 8.3497e-05 | 0.0 | 0.47
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Output | 0.0012832 | 0.0012832 | 0.0012832 | 0.0 | 7.28
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Modify | 0.0080737 | 0.0080737 | 0.0080737 | 0.0 | 45.82
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Other | | 9.442e-05 | | | 0.54
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Nlocal: 288 ave 288 max 288 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1170 ave 1170 max 1170 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 26496 ave 26496 max 26496 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 26496
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Ave neighs/atom = 92
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Ave special neighs/atom = 0
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:01
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