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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1 by 1 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) = 11.64 | 11.64 | 11.64 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1 48.948932 0 50.448838 201.73366
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100 1.0069712 43.754293 0 45.264656 199.5369
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200 0.98667561 43.716052 0 45.195973 196.72854
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300 1.0036944 43.706299 0 45.211746 195.35714
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400 1.0024228 43.697014 0 45.200554 197.0062
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500 0.99968161 43.687445 0 45.186873 193.80596
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Loop time of 80.7995 on 1 procs for 500 steps with 16000 atoms
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Performance: 5346.567 tau/day, 6.188 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 | 75.106 | 75.106 | 75.106 | 0.0 | 92.95
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Neigh | 4.9836 | 4.9836 | 4.9836 | 0.0 | 6.17
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Comm | 0.31199 | 0.31199 | 0.31199 | 0.0 | 0.39
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Output | 0.00048232 | 0.00048232 | 0.00048232 | 0.0 | 0.00
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Modify | 0.29985 | 0.29985 | 0.29985 | 0.0 | 0.37
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Other | | 0.09751 | | | 0.12
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14091 ave 14091 max 14091 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 749111 ave 749111 max 749111 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 749111
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Ave neighs/atom = 46.8194
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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) = 12.14 | 12.14 | 12.14 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0.99968161 43.687397 0 45.186825 196.38426
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100 1.0041443 43.668196 0 45.174318 195.38066
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200 0.99628392 43.666173 0 45.160505 197.84675
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300 1.0029116 43.66224 0 45.166513 199.67414
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400 0.99922193 43.64406 0 45.142799 196.94404
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500 0.99355431 43.623266 0 45.113505 195.94136
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Loop time of 80.7742 on 1 procs for 500 steps with 16000 atoms
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Performance: 5348.242 tau/day, 6.190 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 | 75.073 | 75.073 | 75.073 | 0.0 | 92.94
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Neigh | 4.8786 | 4.8786 | 4.8786 | 0.0 | 6.04
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Comm | 0.31086 | 0.31086 | 0.31086 | 0.0 | 0.38
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Output | 0.00045919 | 0.00045919 | 0.00045919 | 0.0 | 0.00
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Modify | 0.4139 | 0.4139 | 0.4139 | 0.0 | 0.51
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Other | | 0.09731 | | | 0.12
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Nlocal: 16000 ave 16000 max 16000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 14091 ave 14091 max 14091 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 749667 ave 749667 max 749667 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 749667
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Ave neighs/atom = 46.8542
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Neighbor list builds = 178
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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: 0:02:41
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