231 lines
8.5 KiB
Groff
231 lines
8.5 KiB
Groff
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-217-g1909233c69-modified)
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using 1 OpenMP thread(s) per MPI task
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# The intention is to find the average position of one wall at atmospheric
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# pressure. The output is the wall position over time which can be used to
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# find the average position for a run with fixed wall position.
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#
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# ----------------- Init Section -----------------
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atom_style full
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units real
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boundary p p f
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kspace_style pppm/electrode 1e-4
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kspace_modify slab 3.0
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pair_style lj/cut/coul/long 8 8
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bond_style harmonic
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angle_style harmonic
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if "$(extract_setting(world_size) % 2) == 0" then "processors * * 2"
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# ----------------- Atom Definition Section -----------------
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read_data "data.piston"
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Reading data file ...
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orthogonal box = (0 0 0) to (17.6494 20.3798 26)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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726 atoms
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reading velocities ...
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726 velocities
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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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420 bonds
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reading angles ...
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210 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 = 0.000 seconds
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read_data CPU = 0.012 seconds
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# ----------------- Settings Section -----------------
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pair_coeff 1 1 0.069 2.78
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pair_coeff 2 2 5.29 2.951
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pair_coeff 3 3 0.1553 3.166
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pair_coeff 4 4 0.0 0.0
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bond_coeff 1 600.0 1.0
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angle_coeff 1 75.0 109.47
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group wall type 1
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48 atoms in group wall
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group gold type 2
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48 atoms in group gold
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group spce type 3:4
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630 atoms in group spce
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group ele union wall gold
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96 atoms in group ele
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fix fRattleSPCE spce shake 0.0001 10 0 b 1 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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210 = # of frozen angles
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find clusters CPU = 0.000 seconds
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pair_modify mix arithmetic
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# ----------------- Run Section -----------------
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neigh_modify every 1 delay 0
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timestep 2
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fix fxnvt spce nvt temp 300 300 500
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fix fxforce_au gold setforce 0.0 0.0 0.0
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# equilibrate z-coordinate of upper electrode while keeping the electrode rigid
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fix fxforce_wa wall setforce 0.0 0.0 NULL
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variable atm equal 1/68568.415 # 1/force->nktv2p
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variable area equal (xhi-xlo)*(yhi-ylo)
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variable wall_force equal -v_atm*v_area/count(wall)
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print "Wall force per atom: ${wall_force}"
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Wall force per atom: -0.000109285996244287
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fix fxpressure wall aveforce 0 0 ${wall_force} # atomspheric pressure: area/force->nktv2p
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fix fxpressure wall aveforce 0 0 -0.000109285996244287
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fix fxdrag wall viscous 100
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fix fxrigid wall rigid/nve single
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1 rigid bodies with 48 atoms
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# maintain constant potential during equilibration
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# 'algo cg' allows for moving electrodes
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fix fxele ele electrode/conp 0.0 1.805 symm on algo cg 1e-4
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96 atoms in group conp_group
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# setup output and run
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variable q atom q
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compute qwa wall reduce sum v_q
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compute qau gold reduce sum v_q
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variable top_wall equal (bound(wall,zmin))
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compute temp_mobile spce temp
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variable s equal step
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fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no
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thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall
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thermo 5000
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run 100000
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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) = 0.32814871
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grid = 12 15 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.02930901
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estimated relative force accuracy = 8.8263214e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 15884 6480
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Generated 6 of 6 mixed pair_coeff terms from arithmetic 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 = 10
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ghost atom cutoff = 10
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binsize = 5, bins = 4 5 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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Per MPI rank memory allocation (min/avg/max) = 11.7 | 11.7 | 11.7 Mbytes
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Step c_temp_mobile c_qwa c_qau v_top_wall
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0 303.38967 -0.042963484 0.042963484 21.4018
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5000 311.85363 0.03543775 -0.03543775 24.79665
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10000 285.91321 -0.16873703 0.16873703 23.103088
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15000 295.39476 -0.44424612 0.44424612 23.767107
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20000 296.12969 -0.14120993 0.14120993 23.96361
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25000 306.59629 -0.29333182 0.29333182 23.884488
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30000 297.98559 -0.10749684 0.10749684 23.73316
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35000 297.98503 -0.11809975 0.11809975 23.984669
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40000 300.26292 -0.32784184 0.32784184 23.462748
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45000 295.68441 -0.25940165 0.25940165 23.516403
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50000 315.12883 -0.36037614 0.36037614 23.627879
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55000 290.55151 -0.0032838106 0.0032838106 23.684931
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60000 316.4625 -0.17245368 0.17245368 24.126883
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65000 296.79343 -0.054061851 0.054061851 23.695094
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70000 305.99923 -0.11363801 0.11363801 23.55476
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75000 297.40131 -0.27054153 0.27054153 23.928994
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80000 306.54811 -0.25409719 0.25409719 23.869448
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85000 303.95231 -0.17895561 0.17895561 23.658833
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90000 313.43739 -0.059036514 0.059036514 23.36056
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95000 290.3077 -0.31394478 0.31394478 23.885538
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100000 297.5156 -0.30730083 0.30730083 23.511674
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Loop time of 1586.06 on 1 procs for 100000 steps with 726 atoms
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Performance: 10.895 ns/day, 2.203 hours/ns, 63.049 timesteps/s, 45.774 katom-step/s
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99.6% CPU use with 1 MPI tasks x 1 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 | 460.91 | 460.91 | 460.91 | 0.0 | 29.06
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Bond | 0.047873 | 0.047873 | 0.047873 | 0.0 | 0.00
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Kspace | 341.4 | 341.4 | 341.4 | 0.0 | 21.53
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Neigh | 52.868 | 52.868 | 52.868 | 0.0 | 3.33
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Comm | 5.2321 | 5.2321 | 5.2321 | 0.0 | 0.33
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Output | 0.00099102 | 0.00099102 | 0.00099102 | 0.0 | 0.00
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Modify | 724.63 | 724.63 | 724.63 | 0.0 | 45.69
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Other | | 0.9741 | | | 0.06
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Nlocal: 726 ave 726 max 726 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 2336 ave 2336 max 2336 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 120321 ave 120321 max 120321 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 120321
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Ave neighs/atom = 165.7314
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Ave special neighs/atom = 1.7355372
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Neighbor list builds = 7670
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Dangerous builds = 0
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write_data "data.piston.final"
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System init for write_data ...
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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) = 0.32814871
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grid = 12 15 36
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stencil order = 5
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estimated absolute RMS force accuracy = 0.029311329
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estimated relative force accuracy = 8.8270197e-05
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using double precision FFTW3
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3d grid and FFT values/proc = 15884 6480
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Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
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Average conjugate gradient steps: 1.981
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Total wall time: 0:26:26
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