mirror of https://github.com/lammps/lammps.git
add piston logs
This commit is contained in:
srtee
parent
793987e0c3
commit
ad68eb8a59
File diff suppressed because it is too large
Load Diff
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@ -61,5 +61,5 @@ fix fxprint all print 1000 "${s} ${top_wall}" file top_wall.csv screen no
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thermo_style custom step c_temp_mobile c_qwa c_qau v_top_wall
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thermo 5000
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run 100000
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write_data "data.pistoned"
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write_data "data.piston.final"
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@ -0,0 +1,223 @@
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LAMMPS (3 Nov 2022)
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# The intention is to find the average position of one wall at atmospheric
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# pressure. The output is the wall position over time which can be used to
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# find the average position for a run with fixed wall position.
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#
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# ----------------- Init Section -----------------
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atom_style full
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units real
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boundary p p f
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kspace_style pppm/electrode 1e-4
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kspace_modify slab 3.0
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pair_style lj/cut/coul/long 8 8
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bond_style harmonic
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angle_style harmonic
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if "$(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 = 0.001 seconds
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read_data CPU = 0.011 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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fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
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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 MKL FFT
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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 285.08828 -0.26105255 0.26105255 25.155629
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10000 323.19176 -0.26264003 0.26264003 24.541676
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15000 310.479 -0.27318148 0.27318148 23.141522
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20000 295.18544 -0.11313444 0.11313444 23.828735
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25000 295.38607 -0.25433086 0.25433086 23.673314
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30000 288.0613 -0.30099901 0.30099901 23.438086
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35000 278.5591 -0.15823576 0.15823576 24.311915
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40000 303.95751 -0.19941381 0.19941381 23.69594
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45000 279.026 -0.1659962 0.1659962 23.588604
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50000 298.79278 -0.28866703 0.28866703 23.372508
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55000 301.03353 -0.078370381 0.078370381 23.192985
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60000 306.77965 -0.12807205 0.12807205 23.968574
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65000 309.86008 -0.27162663 0.27162663 23.616704
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70000 287.31116 -0.029751882 0.029751882 23.667495
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75000 312.48654 -0.10759866 0.10759866 23.504105
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80000 309.94267 -0.2558548 0.2558548 23.810576
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85000 328.04389 -0.1575471 0.1575471 24.013437
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90000 302.9806 -0.032002164 0.032002164 24.264432
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95000 294.20804 -0.27797238 0.27797238 23.291758
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100000 307.63019 -0.19047448 0.19047448 23.632147
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Loop time of 530.844 on 1 procs for 100000 steps with 726 atoms
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Performance: 32.552 ns/day, 0.737 hours/ns, 188.379 timesteps/s, 136.763 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 | 190.47 | 190.47 | 190.47 | 0.0 | 35.88
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Bond | 0.10754 | 0.10754 | 0.10754 | 0.0 | 0.02
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Kspace | 73.179 | 73.179 | 73.179 | 0.0 | 13.79
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Neigh | 24.209 | 24.209 | 24.209 | 0.0 | 4.56
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Comm | 1.6857 | 1.6857 | 1.6857 | 0.0 | 0.32
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Output | 0.0016861 | 0.0016861 | 0.0016861 | 0.0 | 0.00
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Modify | 240.23 | 240.23 | 240.23 | 0.0 | 45.26
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Other | | 0.9595 | | | 0.18
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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: 2335 ave 2335 max 2335 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 120271 ave 120271 max 120271 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 120271
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Ave neighs/atom = 165.66253
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Ave special neighs/atom = 1.7355372
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Neighbor list builds = 7722
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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 = 0.029311365
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estimated relative force accuracy = 8.8270304e-05
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using double precision MKL FFT
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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: 0:08:50
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@ -0,0 +1,224 @@
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LAMMPS (3 Nov 2022)
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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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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 2 by 2 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 = 0.001 seconds
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read_data CPU = 0.017 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 = 0.002 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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fix fxpressure wall aveforce 0 0 -0.005246 # atomspheric pressure: area/force->nktv2p
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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
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- kspace_style pppm/electrode command:
|
||||
|
||||
@article{Ahrens2021,
|
||||
author = {Ahrens-Iwers, Ludwig J.V. and Mei{\ss}ner, Robert H.},
|
||||
doi = {10.1063/5.0063381},
|
||||
title = {{Constant potential simulations on a mesh}},
|
||||
journal = {Journal of Chemical Physics},
|
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year = {2021}
|
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volume = {155},
|
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pages = {104104},
|
||||
}
|
||||
- fix electrode command:
|
||||
|
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@article{Ahrens2022
|
||||
author = {Ahrens-Iwers, Ludwig J.V. and Janssen, Mahijs and Tee, Shern R. and Mei{\ss}ner, Robert H.},
|
||||
doi = {10.1063/5.0099239},
|
||||
title = {{ELECTRODE: An electrochemistry package for LAMMPS}},
|
||||
journal = {The Journal of Chemical Physics},
|
||||
year = {2022}
|
||||
volume = {157},
|
||||
pages = {084801},
|
||||
}
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
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|
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PPPM/electrode initialization ...
|
||||
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
|
||||
estimated absolute RMS force accuracy = 0.02930901
|
||||
estimated relative force accuracy = 8.8263214e-05
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 8512 2880
|
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Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
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max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 10
|
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ghost atom cutoff = 10
|
||||
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) = 10.06 | 10.22 | 10.41 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 292.03027 -0.19040435 0.19040435 24.581338
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10000 309.52764 -0.48308301 0.48308301 23.776985
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15000 295.00243 -0.16591109 0.16591109 23.672038
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20000 293.5536 -0.086669084 0.086669084 23.426455
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25000 303.0079 -0.16488112 0.16488112 23.862966
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30000 306.31463 -0.23192653 0.23192653 23.819882
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35000 303.66268 -0.2317907 0.2317907 23.495344
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40000 301.39435 -0.34661329 0.34661329 23.657835
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45000 291.61205 -0.30539427 0.30539427 23.437303
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50000 298.65319 -0.096107034 0.096107034 23.57809
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55000 282.65069 -0.14943539 0.14943539 23.823728
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60000 310.64182 -0.17418813 0.17418813 23.286959
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65000 308.47141 -0.02075662 0.02075662 23.91313
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70000 292.5186 -0.080163162 0.080163162 23.96283
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75000 270.13928 -0.029528648 0.029528648 23.488972
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80000 322.10914 0.030761045 -0.030761045 23.47592
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85000 310.60347 -0.24069996 0.24069996 23.987091
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90000 294.35695 -0.070458235 0.070458235 23.397929
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95000 308.69043 -0.2652581 0.2652581 23.473813
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100000 318.71883 0.024035956 -0.024035956 23.449863
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Loop time of 590.232 on 4 procs for 100000 steps with 726 atoms
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Performance: 29.277 ns/day, 0.820 hours/ns, 169.425 timesteps/s, 123.003 katom-step/s
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72.5% CPU use with 4 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 57.391 | 75.867 | 96.292 | 212.1 | 12.85
|
||||
Bond | 0.10177 | 0.11042 | 0.12415 | 2.7 | 0.02
|
||||
Kspace | 102.79 | 123.16 | 141.5 | 165.7 | 20.87
|
||||
Neigh | 12.808 | 12.895 | 12.982 | 2.3 | 2.18
|
||||
Comm | 18.885 | 19.973 | 21.064 | 24.0 | 3.38
|
||||
Output | 0.0022573 | 0.0022749 | 0.0023225 | 0.1 | 0.00
|
||||
Modify | 355.89 | 356.74 | 357.61 | 4.2 | 60.44
|
||||
Other | | 1.478 | | | 0.25
|
||||
|
||||
Nlocal: 181.5 ave 207 max 169 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 1961.5 ave 1984 max 1926 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 30051 ave 41646 max 20775 min
|
||||
Histogram: 1 1 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 120204
|
||||
Ave neighs/atom = 165.57025
|
||||
Ave special neighs/atom = 1.7355372
|
||||
Neighbor list builds = 7663
|
||||
Dangerous builds = 0
|
||||
write_data "data.piston.final"
|
||||
System init for write_data ...
|
||||
PPPM/electrode initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 0.32814871
|
||||
grid = 12 15 36
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.029311028
|
||||
estimated relative force accuracy = 8.8269289e-05
|
||||
using double precision MKL FFT
|
||||
3d grid and FFT values/proc = 8512 2880
|
||||
Generated 6 of 6 mixed pair_coeff terms from arithmetic mixing rule
|
||||
|
||||
Average conjugate gradient steps: 1.982
|
||||
Total wall time: 0:09:50
|
||||
Loading…
Reference in New Issue