148 lines
7.0 KiB
Groff
148 lines
7.0 KiB
Groff
LAMMPS (11 Aug 2017)
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########################################################################
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#### 3D droplet oscilation using many-body DPD simulation ###
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#### ###
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#### Created : Zhen Li (zhen_li@brown.edu) ###
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#### Division of Applied Mathematics, Brown University. ###
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#### ###
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#### mDPD parameters follow the choice of the publication: ###
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#### Z. Li et al. "Three dimensional flow structures in a moving ###
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#### droplet on substrate: a dissipative particle dynamics study" ###
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#### Physics of Fluids, 2013, 25: 072103. DOI: 10.1063/1.4812366 ###
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########################################################################
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units lj
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dimension 3
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boundary p p p
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neighbor 0.3 bin
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neigh_modify every 1 delay 0 check yes
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atom_style mdpd
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region mdpd block -25 25 -10 10 -10 10 units box
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create_box 1 mdpd
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Created orthogonal box = (-25 -10 -10) to (25 10 10)
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4 by 1 by 1 MPI processor grid
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lattice fcc 6
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Lattice spacing in x,y,z = 0.87358 0.87358 0.87358
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region film block -20 20 -7.5 7.5 -2.0 2.0 units box
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create_atoms 1 region film
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Created 14333 atoms
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pair_style hybrid/overlay mdpd/rhosum mdpd 1.0 1.0 9872598
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pair_coeff 1 1 mdpd/rhosum 0.75
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pair_coeff 1 1 mdpd -40 25 18.0 1.0 0.75
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mass 1 1.0
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compute mythermo all temp
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thermo 100
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thermo_modify temp mythermo
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thermo_modify flush yes
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velocity all create 1.0 38497 loop local dist gaussian
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fix mvv all mvv/dpd
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dump mydump all atom 100 atom.lammpstrj
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#dump jpg all image 200 image.*.jpg type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
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#dump_modify jpg pad 4
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#dump avi all movie 200 movie.avi type type zoom 5 adiam 0.5 # view 90 90 box no 0 size 600 200
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#dump_modify avi pad 4
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timestep 0.01
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run 4000
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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 = 1.3
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ghost atom cutoff = 1.3
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binsize = 0.65, bins = 77 31 31
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair mdpd/rhosum, perpetual
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attributes: full, newton on
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pair build: full/bin/atomonly
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stencil: full/bin/3d
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bin: standard
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(2) pair mdpd, perpetual, half/full from (1)
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attributes: half, newton on
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pair build: halffull/newton
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 6.265 | 6.655 | 7.045 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 -13.346542 0 -11.846647 -6.9757225
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100 1.0406108 -7.2500697 0 -5.6892624 -0.80306477
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200 1.0535506 -6.9452928 0 -5.3650772 -0.39911584
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300 1.0644295 -6.8599907 0 -5.2634577 -0.2997968
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400 1.0780123 -6.9471342 0 -5.3302286 -0.06274869
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500 1.0672153 -6.8269984 0 -5.2262872 0.021251762
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600 1.0634304 -6.8366569 0 -5.2416226 -0.021863333
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700 1.0544807 -6.8272074 0 -5.2455967 -0.0064688066
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800 1.0556172 -6.8859788 0 -5.3026634 0.023983333
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900 1.0436201 -6.9246523 0 -5.3593313 -0.12409618
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1000 1.0617016 -6.8632331 0 -5.2707919 -0.1145505
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1100 1.0323831 -6.951554 0 -5.4030874 -0.030031884
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1200 1.0407785 -6.931048 0 -5.3699892 -0.018362136
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1300 1.0380953 -6.8785296 0 -5.3214953 -0.099308737
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1400 1.0418898 -6.8998 0 -5.3370743 -0.14199421
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1500 1.0487254 -6.9671212 0 -5.3941429 -0.12132644
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1600 1.0561042 -6.8948881 0 -5.3108424 -0.09627292
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1700 1.0524479 -6.9531441 0 -5.3745823 -0.11959782
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1800 1.0541197 -6.9219819 0 -5.3409126 0.032964029
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1900 1.0531221 -6.8805815 0 -5.3010085 0.030124685
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2000 1.0531819 -6.8612868 0 -5.2816242 -0.076876781
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2100 1.0757791 -6.919875 0 -5.3063189 -0.04060439
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2200 1.069423 -6.9005754 0 -5.2965527 0.015347467
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2300 1.0403109 -6.9015402 0 -5.3411827 0.0034687897
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2400 1.0547448 -6.9325539 0 -5.3505471 -0.021202325
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2500 1.0404195 -6.8494675 0 -5.2889472 0.086947847
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2600 1.0499828 -6.9861392 0 -5.4112749 -0.018079308
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2700 1.0294278 -6.8525151 0 -5.3084811 0.16911472
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2800 1.0220652 -6.8993978 0 -5.366407 0.064820531
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2900 1.0347904 -6.9322703 0 -5.3801929 -0.11384964
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3000 1.0391372 -6.9519088 0 -5.3933117 0.003050577
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3100 1.0335828 -7.0090074 0 -5.4587413 -0.17366664
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3200 1.0211896 -6.9421289 0 -5.4104513 0.025299853
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3300 1.0019232 -6.9426488 0 -5.4398688 -0.098334724
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3400 1.0203541 -6.9310981 0 -5.4006737 -0.0015544982
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3500 1.0076794 -6.9519932 0 -5.4405796 -0.056956902
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3600 1.0086525 -6.9620979 0 -5.4492247 0.020014884
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3700 1.0046112 -7.0011625 0 -5.4943508 -0.083936527
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3800 1.0096867 -6.9470382 0 -5.4326138 -0.089521759
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3900 1.0074482 -6.9959414 0 -5.4848745 -0.11873698
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4000 1.01222 -6.9535694 0 -5.4353454 0.042191466
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Loop time of 63.0327 on 4 procs for 4000 steps with 14333 atoms
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Performance: 54828.695 tau/day, 63.459 timesteps/s
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98.8% CPU use with 4 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 | 16.591 | 29.795 | 42.814 | 236.6 | 47.27
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Neigh | 2.0347 | 10.239 | 18.555 | 255.6 | 16.24
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Comm | 0.70099 | 6.0601 | 11.386 | 207.4 | 9.61
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Output | 0.20713 | 0.40902 | 0.61087 | 31.5 | 0.65
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Modify | 0.058089 | 0.27033 | 0.4851 | 40.7 | 0.43
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Other | | 16.26 | | | 25.79
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Nlocal: 3583.25 ave 7207 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 1055.75 ave 2131 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Neighs: 100549 ave 202192 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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FullNghs: 201098 ave 404372 max 0 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 804390
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Ave neighs/atom = 56.1215
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Neighbor list builds = 1049
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:01:03
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