147 lines
6.2 KiB
Groff
147 lines
6.2 KiB
Groff
LAMMPS (11 Aug 2017)
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### Pure diffusion with a reaction source term analog of a periodic ###
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### Poiseuille flow problem using transport DPD (tDPD) 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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### tDPD system setup follows Fig.1 in the publication: ###
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### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ###
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### "Transport dissipative particle dynamics model for mesoscopic ###
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### advection-diffusion-reaction problems. J. Chem. Phys., ###
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### 2015, 143: 014101. DOI: 10.1063/1.4923254 ###
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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 0.2 bin
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neigh_modify every 1 delay 0 check yes
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atom_style tdpd 2
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region tdpd block -10 10 -10 10 -5 5 units box
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create_box 1 tdpd
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Created orthogonal box = (-10 -10 -5) to (10 10 5)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 random 16000 276438 NULL
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Created 16000 atoms
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mass 1 1.0
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set atom * cc 1 1.0
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16000 settings made for cc index 1
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set atom * cc 2 1.0
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16000 settings made for cc index 2
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pair_style tdpd 1.0 1.58 9872598
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pair_coeff 1 1 18.75 4.5 0.41 1.58 1.58 1.0 1.0E-5 2.0 3.0 1.0E-5 2.0
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compute mythermo all temp
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thermo 50
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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 432982 loop local dist gaussian
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fix mvv all mvv/tdpd 0.5
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fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
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fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01
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fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01
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fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01
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timestep 0.01
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run 500
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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 = 1.78
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ghost atom cutoff = 1.78
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binsize = 0.89, bins = 23 23 12
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair tdpd, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 4.814 | 4.823 | 4.829 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.948932 0 50.448838 199.65978
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50 1.0153476 43.948796 0 45.471722 198.3346
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100 1.0064284 43.754875 0 45.264424 197.5308
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150 0.99609985 43.726751 0 45.220807 197.50623
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200 1.0016604 43.720283 0 45.22268 197.81129
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250 1.0054979 43.718568 0 45.22672 195.79405
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300 0.9997618 43.716617 0 45.216166 197.84788
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350 0.99170101 43.72093 0 45.208389 196.07711
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400 1.0043692 43.71648 0 45.22294 199.55247
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450 1.0086263 43.709988 0 45.222833 198.20516
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500 1.0029076 43.717879 0 45.222146 197.26281
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Loop time of 24.5533 on 4 procs for 500 steps with 16000 atoms
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Performance: 17594.412 tau/day, 20.364 timesteps/s
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99.9% 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 | 22.236 | 22.418 | 22.736 | 4.0 | 91.30
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Neigh | 1.2759 | 1.2883 | 1.3077 | 1.1 | 5.25
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Comm | 0.35749 | 0.69526 | 0.88462 | 24.1 | 2.83
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Output | 0.00043321 | 0.00050318 | 0.00070691 | 0.0 | 0.00
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Modify | 0.11555 | 0.11648 | 0.11888 | 0.4 | 0.47
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Other | | 0.03473 | | | 0.14
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Nlocal: 4000 ave 4012 max 3982 min
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Histogram: 1 0 0 0 0 1 0 0 0 2
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Nghost: 5986.25 ave 6016 max 5956 min
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Histogram: 1 0 0 0 1 0 1 0 0 1
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Neighs: 187309 ave 188264 max 186087 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Total # of neighbors = 749235
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Ave neighs/atom = 46.8272
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Neighbor list builds = 180
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Dangerous builds = 0
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reset_timestep 0
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compute cc1 all tdpd/cc/atom 1
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compute cc2 all tdpd/cc/atom 2
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compute bin all chunk/atom bin/1d y 0.0 1.0
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fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile
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run 100
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Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.074 | 5.082 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.0029076 43.717879 0 45.222146 198.45789
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50 1.0077982 43.713264 0 45.224867 196.56183
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100 1.0036823 43.708022 0 45.213451 196.00815
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Loop time of 4.79577 on 4 procs for 100 steps with 16000 atoms
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Performance: 18015.870 tau/day, 20.852 timesteps/s
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99.9% 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 | 4.3481 | 4.39 | 4.4398 | 1.7 | 91.54
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Neigh | 0.25477 | 0.25675 | 0.25963 | 0.4 | 5.35
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Comm | 0.059327 | 0.11194 | 0.15608 | 11.0 | 2.33
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Output | 0.00011206 | 0.00011748 | 0.00011992 | 0.0 | 0.00
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Modify | 0.030417 | 0.030622 | 0.030739 | 0.1 | 0.64
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Other | | 0.006301 | | | 0.13
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Nlocal: 4000 ave 4010 max 3987 min
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Histogram: 1 0 0 0 0 1 1 0 0 1
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Nghost: 5985.25 ave 6025 max 5959 min
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Histogram: 2 0 0 0 0 1 0 0 0 1
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Neighs: 187304 ave 188092 max 186449 min
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Histogram: 1 0 0 0 0 2 0 0 0 1
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Total # of neighbors = 749216
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Ave neighs/atom = 46.826
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Neighbor list builds = 38
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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: 0:00:29
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