forked from lijiext/lammps
247 lines
10 KiB
Groff
247 lines
10 KiB
Groff
LAMMPS (13 Oct 2016)
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# sample LAMMPS input script for viscosity of 2d LJ liquid
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# use shearing wall, thermostat via fix langevin
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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 ylo equal -2.5
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variable yhi equal 23
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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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variable srate equal 2.7
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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 ${ylo} ${yhi} -0.1 0.1
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region simbox block 0 20 ${ylo} ${yhi} -0.1 0.1
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region simbox block 0 20 -2.5 ${yhi} -0.1 0.1
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region simbox block 0 20 -2.5 23 -0.1 0.1
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create_box 3 simbox
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Created orthogonal box = (0 -4.56435 -0.182574) to (36.5148 41.9921 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 1020 atoms
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mass * 1.0
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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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region lower block INF INF INF 0.0 INF INF
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region upper block INF INF $y INF INF INF
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region upper block INF INF 20 INF INF INF
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group lower region lower
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120 atoms in group lower
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group upper region upper
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120 atoms in group upper
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set group lower type 2
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120 settings made for type
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set group upper type 3
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120 settings made for type
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group wall union lower upper
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240 atoms in group wall
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group flow subtract all wall
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780 atoms in group flow
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velocity flow create $t 97287
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velocity flow create 1 97287
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velocity upper set ${srate} 0.0 0.0 units box
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velocity upper set 2.7 0.0 0.0 units box
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compute thermal flow temp/partial 0 1 0
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compute flow flow temp
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fix 1 all nve
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fix 2 flow langevin $t $t 0.1 498094
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fix 2 flow langevin 1 $t 0.1 498094
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fix 2 flow langevin 1 1 0.1 498094
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fix_modify 2 temp thermal
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fix 3 wall setforce 0.0 0.0 0.0
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compute layers all chunk/atom bin/1d y center 0.05 units reduced
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fix 4 all ave/chunk 20 500 10000 layers vx file profile.wall.2d
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fix 5 all enforce2d
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# equilibration run
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variable ybox equal $y*ylat
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variable ybox equal 20*ylat
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compute tilt flow temp/ramp vx 0 ${srate} y 0 ${ybox} units box
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compute tilt flow temp/ramp vx 0 2.7 y 0 ${ybox} units box
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compute tilt flow temp/ramp vx 0 2.7 y 0 36.5148371670111 units box
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thermo 1000
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thermo_style custom step temp c_tilt epair etotal press pxy
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run 20000
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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 34 1
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Memory usage per processor = 2.7306 Mbytes
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Step Temp c_tilt E_pair TotEng Press Pxy
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0 1.1937193 2.1893943 -1.4419854 -0.24943634 -0.78936698 0.014349737
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1000 1.3454512 1.9300306 -1.5968842 -0.25275207 0.66766599 -0.14162185
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2000 1.4039195 1.7346977 -1.5342235 -0.13168039 1.0083734 0.018811845
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3000 1.3945539 1.6038724 -1.5472166 -0.15402987 0.89714673 -0.21459294
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4000 1.4507445 1.5640577 -1.5682837 -0.11896142 0.80780492 -0.11602642
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5000 1.5081166 1.5260484 -1.4466585 0.059979546 1.5213379 0.15651364
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6000 1.471403 1.3275791 -1.5730732 -0.10311276 0.76780953 -0.028043991
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7000 1.5811576 1.3851463 -1.5518076 0.027799848 1.0149281 0.004725238
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8000 1.5298095 1.3333038 -1.536974 -0.0086643578 1.2325979 -0.11754624
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9000 1.5269137 1.253444 -1.5995915 -0.074174772 0.72678912 0.068344793
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10000 1.6201621 1.2415469 -1.4659459 0.15262788 1.4780324 0.12762214
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11000 1.6422795 1.2595346 -1.5659612 0.074708257 1.0471534 -0.039697954
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12000 1.7111306 1.1978075 -1.5685671 0.14088596 0.97371007 0.099889098
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13000 1.6871075 1.1495076 -1.4967158 0.18873768 1.3445558 -0.058891196
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14000 1.7237433 1.1976445 -1.5857394 0.13631394 0.96603231 0.082195882
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15000 1.7080799 1.1550766 -1.4962561 0.21014912 1.3733324 0.062008565
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16000 1.7030363 1.1186642 -1.5735945 0.12777215 1.0071474 -0.12038271
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17000 1.7442786 1.1134856 -1.5544631 0.18810536 0.98640596 -0.10793154
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18000 1.7433517 1.0565945 -1.4702226 0.27141996 1.5983127 -0.1847178
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19000 1.7909641 1.071494 -1.5628363 0.22637195 1.0487763 -0.16215298
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20000 1.8291721 1.1152277 -1.4955372 0.33184161 1.4404718 0.13157652
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Loop time of 4.60977 on 1 procs for 20000 steps with 1020 atoms
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Performance: 1874278.390 tau/day, 4338.607 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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Pair | 2.2771 | 2.2771 | 2.2771 | 0.0 | 49.40
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Neigh | 0.77127 | 0.77127 | 0.77127 | 0.0 | 16.73
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Comm | 0.08461 | 0.08461 | 0.08461 | 0.0 | 1.84
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Output | 0.00045896 | 0.00045896 | 0.00045896 | 0.0 | 0.01
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Modify | 1.3487 | 1.3487 | 1.3487 | 0.0 | 29.26
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Other | | 0.1277 | | | 2.77
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Nlocal: 1020 ave 1020 max 1020 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 319 ave 319 max 319 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 6977 ave 6977 max 6977 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 6977
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Ave neighs/atom = 6.8402
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Neighbor list builds = 3091
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Dangerous builds = 0
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# data gathering run
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variable visc equal -pxy/(v_srate/ly)
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fix vave all ave/time 1000 1 1000 v_visc ave running
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thermo_style custom step temp pxy v_visc f_vave
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thermo_modify temp tilt
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WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474)
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# only need to run for 5000 steps to make a good 100-frame movie
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#dump 1 all custom 50 dump.wall.2d id type x y z vx
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#dump 2 all image 50 image.*.jpg vx type zoom 1.6 adiam 1.2
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#dump_modify 2 pad 5 amap 0.0 ${srate} ca 0.0 2 min blue max red
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run 50000
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Memory usage per processor = 2.73133 Mbytes
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Step Temp Pxy v_visc f_vave
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20000 1.1152277 0.14873839 -2.5647136 -2.5647136
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21000 1.0675243 -0.064336523 1.1093622 -0.72767568
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22000 1.1044647 -0.092189802 1.5896396 0.044762746
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23000 1.0278193 -0.16030404 2.7641414 0.72460741
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24000 1.032998 -0.025162118 0.43387337 0.6664606
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25000 1.012257 0.15289388 -2.6363671 0.11598931
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26000 1.0678095 -0.15317374 2.6411929 0.47673268
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27000 0.99951185 -0.013635884 0.23512515 0.44653174
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28000 1.0663423 -0.061009474 1.0519935 0.51380527
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29000 1.0753719 -0.037018843 0.63832026 0.52625677
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30000 1.0749259 -0.0092916614 0.16021721 0.49298044
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31000 1.0171594 -0.14103555 2.4318926 0.65455646
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32000 1.0811717 -0.22037237 3.7999068 0.89650648
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33000 1.0123567 -0.076368085 1.3168239 0.92652915
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34000 1.0923478 -0.017551868 0.30264892 0.88493714
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35000 1.0252013 0.0042522796 -0.073322558 0.82504591
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36000 1.0205412 -0.17942577 3.0938596 0.95850554
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37000 1.016861 -0.15185242 2.6184092 1.0507224
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38000 1.0156825 -0.058057333 1.0010894 1.0481101
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39000 1.0299458 -0.028138186 0.48519005 1.0199641
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40000 1.0109947 0.069370747 -1.1961679 0.91443404
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41000 0.99255941 -0.20057649 3.4585639 1.0300763
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42000 0.93280953 -0.20797609 3.5861562 1.1412102
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43000 0.98040039 0.070643632 -1.2181165 1.0429049
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44000 1.001795 -0.06620924 1.1416537 1.0468549
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45000 0.96231963 0.028026245 -0.48325983 0.98800432
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46000 1.0193639 -0.15553891 2.6819757 1.050744
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47000 1.0241202 0.0053565438 -0.092363514 1.0099187
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48000 0.9736932 0.12643935 -2.1802085 0.89991435
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49000 0.96326617 -0.14719163 2.5380426 0.95451862
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50000 0.99008772 0.03563038 -0.61437884 0.90390903
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51000 1.0689018 -0.11122259 1.9178243 0.93559388
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52000 1.0123467 0.021882959 -0.37733044 0.89580829
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53000 1.0075671 0.20840798 -3.5936033 0.76376678
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54000 0.97454265 -0.027528034 0.47466913 0.75550684
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55000 1.0072632 -0.02991098 0.51575854 0.74884717
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56000 0.94706748 -0.29624115 5.108121 0.86666538
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57000 1.0411989 -0.043160809 0.74422691 0.86344332
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58000 1.0040809 0.10858868 -1.8724074 0.7932933
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59000 1.0101096 -0.17512944 3.0197775 0.8489554
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60000 0.97394086 0.025630293 -0.44194616 0.81747
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61000 0.97631407 -0.21776922 3.7550203 0.88741167
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62000 0.9650689 -0.036733674 0.63340305 0.88150449
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63000 1.0401136 0.11852825 -2.0437965 0.81502038
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64000 0.99261276 -0.20362786 3.5111792 0.87493502
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65000 1.0397086 -0.056685607 0.97743658 0.87716332
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66000 1.0115793 -0.20411863 3.5196415 0.93338626
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67000 1.1243059 -0.086897372 1.4983816 0.94515699
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68000 1.0005962 0.081847197 -1.4113008 0.89706602
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69000 1.0412065 -0.21375629 3.6858249 0.95284119
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70000 0.97952466 -0.060208765 1.0381868 0.95451464
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Loop time of 11.6259 on 1 procs for 50000 steps with 1020 atoms
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Performance: 1857923.682 tau/day, 4300.749 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 | 5.6901 | 5.6901 | 5.6901 | 0.0 | 48.94
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Neigh | 2.0175 | 2.0175 | 2.0175 | 0.0 | 17.35
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Comm | 0.21634 | 0.21634 | 0.21634 | 0.0 | 1.86
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Output | 0.00069594 | 0.00069594 | 0.00069594 | 0.0 | 0.01
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Modify | 3.3775 | 3.3775 | 3.3775 | 0.0 | 29.05
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Other | | 0.3236 | | | 2.78
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Nlocal: 1020 ave 1020 max 1020 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 332 ave 332 max 332 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 6969 ave 6969 max 6969 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 6969
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Ave neighs/atom = 6.83235
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Neighbor list builds = 8088
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Dangerous builds = 0
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Total wall time: 0:00:16
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