143 lines
6.0 KiB
Groff
143 lines
6.0 KiB
Groff
LAMMPS (11 Aug 2017)
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### Heat conduction analog of periodic Poiseuille flow problem ###
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### using energy-conserving DPD (eDPD) 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 system setup follows Fig.12 in the publication: ###
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### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ###
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### "Energy-conserving dissipative particle dynamics with ###
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### temperature-dependent properties". J. Comput. Phys., ###
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### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ###
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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 edpd
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region edpd block -10 10 -10 10 -5 5 units box
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create_box 1 edpd
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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 * edpd/temp 1.0
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16000 settings made for edpd/temp
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set atom * edpd/cv 1.0E5
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16000 settings made for edpd/cv
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pair_style edpd 1.58 9872598
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#pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58
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pair_coeff 1 1 18.75 4.5 0.41 1.58 1.41E-5 2.0 1.58 power 10.54 -3.66 3.44 -4.10 kappa -0.44 -3.21 5.04 0.00
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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 432982 loop local dist gaussian
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fix mvv all mvv/edpd 0.5
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fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01
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fix lower all edpd/source 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 edpd, 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) = 4.969 | 4.979 | 4.985 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.948932 0 50.448838 199.51547
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100 1.0106415 43.744371 0 45.260239 196.39598
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200 1.0053215 43.714413 0 45.222301 195.35298
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300 0.99886399 43.713356 0 45.211559 196.74821
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400 1.0035264 43.699086 0 45.204282 195.47446
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500 1.0025285 43.698051 0 45.20175 197.27042
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Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms
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Performance: 20411.046 tau/day, 23.624 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 | 18.713 | 19.101 | 19.41 | 6.0 | 90.25
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Neigh | 1.2687 | 1.2925 | 1.3177 | 1.5 | 6.11
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Comm | 0.33013 | 0.66337 | 1.0747 | 34.3 | 3.13
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Output | 0.00023484 | 0.00028092 | 0.00036526 | 0.0 | 0.00
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Modify | 0.073931 | 0.075277 | 0.076306 | 0.3 | 0.36
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Other | | 0.03227 | | | 0.15
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Nlocal: 4000 ave 4067 max 3930 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Nghost: 5997.5 ave 6052 max 5943 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 187388 ave 193157 max 181221 min
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Histogram: 1 1 0 0 0 0 0 0 0 2
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Total # of neighbors = 749552
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Ave neighs/atom = 46.847
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Neighbor list builds = 181
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Dangerous builds = 0
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reset_timestep 0
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compute temp all edpd/temp/atom
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compute ccT all chunk/atom bin/1d y 0.0 1.0
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fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile
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run 500
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Per MPI rank memory allocation (min/avg/max) = 5.221 | 5.23 | 5.236 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.0025285 43.69801 0 45.201708 194.00452
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100 0.9885969 43.679927 0 45.16273 196.28442
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200 1.0028463 43.663067 0 45.167242 198.25592
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300 1.0027516 43.648817 0 45.152851 198.82226
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400 0.99695312 43.641469 0 45.136805 197.97499
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500 0.98202292 43.627163 0 45.100105 199.16319
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Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms
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Performance: 20022.203 tau/day, 23.174 timesteps/s
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99.8% 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 | 18.438 | 19.121 | 19.812 | 14.1 | 88.62
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Neigh | 1.2568 | 1.2885 | 1.325 | 2.5 | 5.97
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Comm | 0.29482 | 1.0219 | 1.7352 | 63.9 | 4.74
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Output | 0.00027728 | 0.00029719 | 0.0003531 | 0.0 | 0.00
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Modify | 0.11153 | 0.11265 | 0.1135 | 0.2 | 0.52
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Other | | 0.03194 | | | 0.15
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Nlocal: 4000 ave 4092 max 3899 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Nghost: 5974 ave 6019 max 5915 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Neighs: 187414 ave 196149 max 178418 min
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Histogram: 2 0 0 0 0 0 0 0 0 2
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Total # of neighbors = 749658
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Ave neighs/atom = 46.8536
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Neighbor list builds = 181
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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: 0:00:42
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