forked from lijiext/lammps
261 lines
12 KiB
Groff
261 lines
12 KiB
Groff
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LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for viscosity of 2d LJ liquid
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# Muller-Plathe via fix viscosity
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# settings
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variable x equal 20
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variable y equal 20
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variable rho equal 0.6
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variable t equal 1.0
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variable rc equal 2.5
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# problem setup
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units lj
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dimension 2
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atom_style atomic
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neigh_modify delay 0 every 1
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lattice sq2 ${rho}
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lattice sq2 0.6
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Lattice spacing in x,y,z = 1.82574 1.82574 1.82574
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region simbox block 0 $x 0 $y -0.1 0.1
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region simbox block 0 20 0 $y -0.1 0.1
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region simbox block 0 20 0 20 -0.1 0.1
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create_box 1 simbox
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Created orthogonal box = (0 0 -0.182574) to (36.5148 36.5148 0.182574)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 800 atoms
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pair_style lj/cut ${rc}
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pair_style lj/cut 2.5
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pair_coeff * * 1 1
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mass * 1.0
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velocity all create $t 97287
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velocity all create 1 97287
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fix 1 all nve
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fix 2 all langevin $t $t 0.1 498094
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fix 2 all langevin 1 $t 0.1 498094
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fix 2 all langevin 1 1 0.1 498094
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fix 3 all enforce2d
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# equilibration run
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thermo 1000
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run 5000
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Neighbor list info ...
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1 neighbor list requests
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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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4 -> bins = 27 27 1
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Memory usage per processor = 2.47956 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -1.56492 0 -0.56617 -1.535262
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1000 0.95906897 -1.571142 0 -0.61327189 0.82593948
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2000 1.0164992 -1.6006146 0 -0.58538603 0.88642098
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3000 1.0429232 -1.5801639 0 -0.53854441 1.157286
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4000 1.0955206 -1.6156387 0 -0.52148756 0.94410568
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5000 0.9411767 -1.6155061 0 -0.67550589 0.79353873
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Loop time of 0.860626 on 1 procs for 5000 steps with 800 atoms
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Performance: 2509801.057 tau/day, 5809.725 timesteps/s
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99.9% 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 | 0.48372 | 0.48372 | 0.48372 | 0.0 | 56.21
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Neigh | 0.11227 | 0.11227 | 0.11227 | 0.0 | 13.05
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Comm | 0.014462 | 0.014462 | 0.014462 | 0.0 | 1.68
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Output | 4.5061e-05 | 4.5061e-05 | 4.5061e-05 | 0.0 | 0.01
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Modify | 0.22682 | 0.22682 | 0.22682 | 0.0 | 26.35
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Other | | 0.02332 | | | 2.71
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Nlocal: 800 ave 800 max 800 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 256 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5583 ave 5583 max 5583 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5583
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Ave neighs/atom = 6.97875
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Neighbor list builds = 551
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Dangerous builds = 0
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unfix 2
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# turn on Muller-Plathe driving force and equilibrate some more
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velocity all scale $t
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velocity all scale 1
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fix 4 all viscosity 100 x y 20
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compute layers all chunk/atom bin/1d y center 0.05 units reduced
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fix 5 all ave/chunk 20 50 1000 layers vx file profile.mp.2d
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# equilibration run
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variable dVx equal f_5[11][3]-f_5[1][3]
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thermo 1000
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thermo_style custom step temp epair etotal press f_4 v_dVx
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run 20000
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Memory usage per processor = 2.72975 Mbytes
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Step Temp E_pair TotEng Press f_4 v_dVx
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5000 1 -1.6155061 -0.61675613 0.82878859 0 0
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6000 0.99205567 -1.6073706 -0.61655497 0.80256133 -40.441513 0.49442509
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7000 0.98076638 -1.5968401 -0.6172997 0.93482147 -74.701801 0.81873121
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8000 0.99350602 -1.6093282 -0.61706408 1.0032966 -108.00017 1.0369989
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9000 1.0130047 -1.6282491 -0.61651065 0.89200717 -133.06372 1.1272589
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10000 1.0016704 -1.6170906 -0.61667231 1.0115493 -164.86086 1.1885507
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11000 0.99991137 -1.6160496 -0.61738807 0.95811584 -190.62317 1.3389184
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12000 0.96344622 -1.5793561 -0.6171142 1.0416296 -221.40727 1.2111221
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13000 0.98692912 -1.6022586 -0.61656313 0.9183328 -250.6677 1.4028399
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14000 1.0007815 -1.6169097 -0.61737918 0.85210278 -280.3907 1.3446354
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15000 0.99742966 -1.6127263 -0.6165434 0.81573578 -308.44839 1.4070968
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16000 0.9955551 -1.6105533 -0.61624268 0.88385735 -336.00553 1.3867041
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17000 0.98598927 -1.6016934 -0.61693666 1.0601453 -363.09101 1.3716356
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18000 0.9827155 -1.5988654 -0.61737831 0.97685532 -391.14488 1.2259196
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19000 0.96881647 -1.5839283 -0.6163228 0.9709967 -418.82566 1.2683115
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20000 1.0265924 -1.6430234 -0.61771432 0.66156099 -448.12442 1.0964927
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21000 1.0001781 -1.6169267 -0.61799878 0.94637366 -477.11852 1.3532793
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22000 1.0014617 -1.6170345 -0.61682461 0.89064741 -503.16769 1.2348173
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23000 0.98723824 -1.6033256 -0.61732136 0.95636024 -533.04118 1.309259
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24000 0.97802015 -1.5945708 -0.61777318 1.1331272 -560.01862 1.3396892
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25000 0.98672719 -1.6025172 -0.61702339 1.0225572 -585.97779 1.5256433
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Loop time of 2.83606 on 1 procs for 20000 steps with 800 atoms
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Performance: 3046484.279 tau/day, 7052.047 timesteps/s
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99.9% 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 | 1.9431 | 1.9431 | 1.9431 | 0.0 | 68.52
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Neigh | 0.48329 | 0.48329 | 0.48329 | 0.0 | 17.04
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Comm | 0.061027 | 0.061027 | 0.061027 | 0.0 | 2.15
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Output | 0.00022459 | 0.00022459 | 0.00022459 | 0.0 | 0.01
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Modify | 0.25409 | 0.25409 | 0.25409 | 0.0 | 8.96
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Other | | 0.09429 | | | 3.32
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Nlocal: 800 ave 800 max 800 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 258 ave 258 max 258 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5583 ave 5583 max 5583 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5583
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Ave neighs/atom = 6.97875
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Neighbor list builds = 2363
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Dangerous builds = 0
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# data gathering run
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# reset fix viscosity to zero flux accumulation
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unfix 4
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fix 4 all viscosity 100 x y 20
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variable visc equal -(f_4/(2*(step*0.005-125)*lx+1.0e-10))/(v_dVx/(ly/2))
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fix vave all ave/time 1000 1 1000 v_visc ave running start 26000
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thermo_style custom step temp f_4 v_dVx v_visc f_vave
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# only need to run for 10000 steps to make a good 100-frame movie
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#dump 1 all custom 100 dump.mp.2d id type x y z vx
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#dump 2 all image 100 image.*.jpg vx type zoom 1.6 adiam 1.2
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#dump_modify 2 pad 5 amap -0.7 0.7 ca 0.0 2 min blue max red
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run 50000
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Memory usage per processor = 2.73047 Mbytes
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Step Temp f_4 v_dVx v_visc f_vave
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25000 0.98672719 0 1.5256433 -0 0
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26000 0.98401533 -25.559065 1.3332094 0.95855405 0.47927702
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27000 0.99050741 -53.17367 1.3419843 0.99057919 0.64971108
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28000 0.98153807 -83.114662 1.1794868 1.1744467 0.78089498
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29000 1.0204966 -110.22215 1.3360187 1.0312556 0.83096712
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30000 0.99625662 -133.82368 1.5944344 0.83931757 0.83235886
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31000 1.0151551 -158.7453 1.5031209 0.88008718 0.83917719
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32000 0.98303358 -184.40723 1.4652847 0.89893417 0.84664681
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33000 0.99939957 -210.86096 1.3135851 1.0032703 0.86404943
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34000 0.96853185 -235.91032 1.3291636 0.98604334 0.87624882
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35000 1.0054026 -267.07311 1.4280769 0.93507957 0.88159707
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36000 0.97047213 -290.05846 1.4030844 0.93967798 0.88643714
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37000 0.99339602 -317.88469 1.3395274 0.98879613 0.89431091
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38000 1.0095839 -339.72956 1.5081424 0.86639838 0.89231716
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39000 1.033396 -365.46114 1.4202859 0.91898285 0.89409487
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40000 1.0069829 -391.35939 1.4315171 0.91129289 0.89516975
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41000 1.0145044 -417.94062 1.5126265 0.86344149 0.89330338
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42000 0.99701243 -442.43582 1.3830081 0.94090688 0.89594802
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43000 1.011832 -466.04588 1.514607 0.8547246 0.89377837
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44000 1.016323 -494.28239 1.4459083 0.89960277 0.89406959
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45000 1.0048565 -518.02843 1.4397428 0.89951556 0.89432892
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46000 0.99726082 -546.29139 1.2399161 1.0490176 0.90136022
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47000 0.9817128 -579.0368 1.2816209 1.026819 0.90681495
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48000 0.99883406 -606.89944 1.3508577 0.97667325 0.90972571
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49000 1.0327324 -639.80418 1.227321 1.0860446 0.91677847
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50000 0.99442217 -668.69881 1.1824503 1.1310391 0.92501927
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51000 0.99412485 -695.56436 1.3288051 1.0066366 0.92804213
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52000 1.0368955 -724.06214 1.2921091 1.0377265 0.93195943
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53000 1.02122 -749.03672 1.5201682 0.87988 0.93016359
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54000 1.0304794 -772.90678 1.3994802 0.9522092 0.93089844
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55000 1.0150735 -800.69744 1.2226831 1.0914486 0.93607748
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56000 1.0066993 -830.92913 1.4581021 0.91914572 0.93554836
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57000 0.99054006 -858.94251 1.3736656 0.97701919 0.93680505
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58000 1.0300499 -881.47715 1.5995216 0.83498179 0.93381025
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59000 0.99187983 -909.58612 1.4692824 0.91039454 0.93314123
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60000 1.0116153 -936.80603 1.372993 0.9747277 0.93429641
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61000 0.98778111 -966.36841 1.3911445 0.9648015 0.93512087
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62000 0.97796351 -996.15306 1.2818309 1.0501797 0.93814874
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63000 1.0241007 -1026.5146 1.3364909 1.0106145 0.94000683
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64000 1.0447876 -1051.1752 1.4339955 0.93979412 0.94000152
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65000 1.013822 -1078.5189 1.5730359 0.85703609 0.93797797
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66000 1.0003625 -1104.7839 1.4374578 0.93727789 0.9379613
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67000 1.0411074 -1132.5569 1.4426372 0.93459539 0.93788302
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68000 1.0005746 -1162.5849 1.2729721 1.061958 0.94070291
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69000 1.0032978 -1189.5061 1.4109135 0.95803997 0.94108818
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70000 1.003145 -1215.7498 1.4255228 0.94760543 0.94122986
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71000 1.0216551 -1244.4852 1.1329731 1.1939394 0.94660666
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72000 0.96169183 -1272.9346 1.1024076 1.2283893 0.95247713
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73000 0.96956712 -1298.3657 1.3689638 0.98794738 0.95320101
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74000 1.0081417 -1327.5255 1.3483851 1.0046224 0.95422944
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75000 1.0315254 -1357.3275 1.4937254 0.9086861 0.95333643
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Loop time of 7.08146 on 1 procs for 50000 steps with 800 atoms
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Performance: 3050218.869 tau/day, 7060.692 timesteps/s
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99.9% 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 | 4.8558 | 4.8558 | 4.8558 | 0.0 | 68.57
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Neigh | 1.2027 | 1.2027 | 1.2027 | 0.0 | 16.98
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Comm | 0.15117 | 0.15117 | 0.15117 | 0.0 | 2.13
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Output | 0.00069261 | 0.00069261 | 0.00069261 | 0.0 | 0.01
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Modify | 0.63608 | 0.63608 | 0.63608 | 0.0 | 8.98
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Other | | 0.235 | | | 3.32
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Nlocal: 800 ave 800 max 800 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 273 ave 273 max 273 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5612 ave 5612 max 5612 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5612
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Ave neighs/atom = 7.015
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Neighbor list builds = 5873
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Dangerous builds = 0
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Total wall time: 0:00:10
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