LAMMPS (11 Aug 2017) ######################################################################## ### Heat conduction analog of periodic Poiseuille flow problem ### ### using energy-conserving DPD (eDPD) simulation ### ### ### ### Created : Zhen Li (zhen_li@brown.edu) ### ### Division of Applied Mathematics, Brown University. ### ### ### ### mDPD system setup follows Fig.12 in the publication: ### ### Z. Li, Y.-H. Tang, H. Lei, B. Caswell and G.E. Karniadakis. ### ### "Energy-conserving dissipative particle dynamics with ### ### temperature-dependent properties". J. Comput. Phys., ### ### 2014, 265: 113-127. DOI: 10.1016/j.jcp.2014.02.003 ### ######################################################################## units lj dimension 3 boundary p p p neighbor 0.2 bin neigh_modify every 1 delay 0 check yes atom_style edpd region edpd block -10 10 -10 10 -5 5 units box create_box 1 edpd Created orthogonal box = (-10 -10 -5) to (10 10 5) 2 by 2 by 1 MPI processor grid create_atoms 1 random 16000 276438 NULL Created 16000 atoms mass 1 1.0 set atom * edpd/temp 1.0 16000 settings made for edpd/temp set atom * edpd/cv 1.0E5 16000 settings made for edpd/cv pair_style edpd 1.58 9872598 #pair_coeff 1 1 18.75 4.5 0.41 1.58 1.45E-5 2.0 1.58 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 compute mythermo all temp thermo 100 thermo_modify temp mythermo thermo_modify flush yes velocity all create 1.0 432982 loop local dist gaussian fix mvv all mvv/edpd 0.5 fix upper all edpd/source cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix lower all edpd/source cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 timestep 0.01 run 500 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.78 ghost atom cutoff = 1.78 binsize = 0.89, bins = 23 23 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair edpd, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d/newton bin: standard Per MPI rank memory allocation (min/avg/max) = 4.969 | 4.979 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 48.948932 0 50.448838 199.51547 100 1.0106415 43.744371 0 45.260239 196.39598 200 1.0053215 43.714413 0 45.222301 195.35298 300 0.99886399 43.713356 0 45.211559 196.74821 400 1.0035264 43.699086 0 45.204282 195.47446 500 1.0025285 43.698051 0 45.20175 197.27042 Loop time of 21.165 on 4 procs for 500 steps with 16000 atoms Performance: 20411.046 tau/day, 23.624 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.713 | 19.101 | 19.41 | 6.0 | 90.25 Neigh | 1.2687 | 1.2925 | 1.3177 | 1.5 | 6.11 Comm | 0.33013 | 0.66337 | 1.0747 | 34.3 | 3.13 Output | 0.00023484 | 0.00028092 | 0.00036526 | 0.0 | 0.00 Modify | 0.073931 | 0.075277 | 0.076306 | 0.3 | 0.36 Other | | 0.03227 | | | 0.15 Nlocal: 4000 ave 4067 max 3930 min Histogram: 1 1 0 0 0 0 0 0 0 2 Nghost: 5997.5 ave 6052 max 5943 min Histogram: 1 0 1 0 0 0 0 1 0 1 Neighs: 187388 ave 193157 max 181221 min Histogram: 1 1 0 0 0 0 0 0 0 2 Total # of neighbors = 749552 Ave neighs/atom = 46.847 Neighbor list builds = 181 Dangerous builds = 0 reset_timestep 0 compute temp all edpd/temp/atom compute ccT all chunk/atom bin/1d y 0.0 1.0 fix stat all ave/chunk 1 500 500 ccT c_temp density/number norm sample file temp.profile run 500 Per MPI rank memory allocation (min/avg/max) = 5.221 | 5.23 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.0025285 43.69801 0 45.201708 194.00452 100 0.9885969 43.679927 0 45.16273 196.28442 200 1.0028463 43.663067 0 45.167242 198.25592 300 1.0027516 43.648817 0 45.152851 198.82226 400 0.99695312 43.641469 0 45.136805 197.97499 500 0.98202292 43.627163 0 45.100105 199.16319 Loop time of 21.576 on 4 procs for 500 steps with 16000 atoms Performance: 20022.203 tau/day, 23.174 timesteps/s 99.8% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.438 | 19.121 | 19.812 | 14.1 | 88.62 Neigh | 1.2568 | 1.2885 | 1.325 | 2.5 | 5.97 Comm | 0.29482 | 1.0219 | 1.7352 | 63.9 | 4.74 Output | 0.00027728 | 0.00029719 | 0.0003531 | 0.0 | 0.00 Modify | 0.11153 | 0.11265 | 0.1135 | 0.2 | 0.52 Other | | 0.03194 | | | 0.15 Nlocal: 4000 ave 4092 max 3899 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 5974 ave 6019 max 5915 min Histogram: 1 0 0 1 0 0 0 0 0 2 Neighs: 187414 ave 196149 max 178418 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 749658 Ave neighs/atom = 46.8536 Neighbor list builds = 181 Dangerous builds = 0 Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:42