LAMMPS (28 Mar 2023 - Development) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task ######################################################################## ### Pure diffusion with a reaction source term analog of a periodic ### ### Poiseuille flow problem using transport DPD (tDPD) simulation ### ### ### ### Created : Zhen Li (zhen_li@brown.edu) ### ### Division of Applied Mathematics, Brown University. ### ### ### ### tDPD system setup follows Fig.1 in the publication: ### ### Z. Li, A. Yazdani, A. Tartakovsky and G.E. Karniadakis. ### ### "Transport dissipative particle dynamics model for mesoscopic ### ### advection-diffusion-reaction problems. J. Chem. Phys., ### ### 2015, 143: 014101. DOI: 10.1063/1.4923254 ### ######################################################################## units lj dimension 3 boundary p p p neighbor 0.2 bin neigh_modify every 1 delay 0 check yes atom_style tdpd 2 comm_modify vel yes region tdpd block -10 10 -10 10 -5 5 units box create_box 1 tdpd 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 using lattice units in orthogonal box = (-10 -10 -5) to (10 10 5) create_atoms CPU = 0.002 seconds mass 1 1.0 set atom * cc 1 1.0 Setting atom values ... 16000 settings made for cc index 1 set atom * cc 2 1.0 Setting atom values ... 16000 settings made for cc index 2 pair_style tdpd 1.0 1.58 9872598 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 compute mythermo all temp thermo 50 thermo_modify temp mythermo thermo_modify flush yes velocity all create 1.0 432982 loop local dist gaussian fix mvv all mvv/tdpd 0.5 fix upper1 all tdpd/source 1 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 0.01 fix lower1 all tdpd/source 1 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 -0.01 fix upper2 all tdpd/source 2 cuboid 0.0 5.0 0.0 20.0 10.0 10.0 -0.01 fix lower2 all tdpd/source 2 cuboid 0.0 -5.0 0.0 20.0 10.0 10.0 0.01 timestep 0.01 run 500 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair tdpd command: doi:10.1063/1.4923254 @Article{ZLi2015_JCP, author = {Li, Z. and Yazdani, A. and Tartakovsky, A. and Karniadakis, G. E.}, title = {Transport Dissipative Particle Dynamics Model for Mesoscopic Advection-Diffusion-Reaction Problems}, journal = {The Journal of Chemical Physics}, year = {2015}, volume = {143}, number = {1}, pages = {014101} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule 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 tdpd, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 5.337 | 5.351 | 5.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 48.942039 0 50.441946 199.59508 50 1.0164166 43.95706 0 45.48159 198.02944 100 0.99583217 43.760777 0 45.254431 198.26943 150 1.0025022 43.730114 0 45.233774 198.402 200 0.99563635 43.72379 0 45.217151 197.6948 250 1.0117752 43.724349 0 45.241917 195.70427 300 0.98950567 43.72333 0 45.207496 197.582 350 0.99351667 43.719413 0 45.209595 194.69504 400 1.0050663 43.715857 0 45.223362 198.50199 450 1.003148 43.712337 0 45.216965 196.26462 500 0.99888463 43.712357 0 45.21059 195.78645 Loop time of 16.464 on 4 procs for 500 steps with 16000 atoms Performance: 26239.140 tau/day, 30.369 timesteps/s, 485.910 katom-step/s 99.6% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.166 | 14.302 | 14.373 | 2.1 | 86.87 Neigh | 1.406 | 1.4132 | 1.4179 | 0.4 | 8.58 Comm | 0.53805 | 0.61257 | 0.75493 | 10.7 | 3.72 Output | 0.00041375 | 0.00062178 | 0.00091415 | 0.0 | 0.00 Modify | 0.088249 | 0.089209 | 0.090198 | 0.2 | 0.54 Other | | 0.04683 | | | 0.28 Nlocal: 4000 ave 4013 max 3992 min Histogram: 1 1 0 1 0 0 0 0 0 1 Nghost: 5990 ave 6012 max 5980 min Histogram: 2 0 1 0 0 0 0 0 0 1 Neighs: 187350 ave 188412 max 186633 min Histogram: 1 0 1 1 0 0 0 0 0 1 Total # of neighbors = 749401 Ave neighs/atom = 46.837562 Neighbor list builds = 182 Dangerous builds = 0 reset_timestep 0 compute cc1 all tdpd/cc/atom 1 compute cc2 all tdpd/cc/atom 2 compute bin all chunk/atom bin/1d y 0.0 1.0 fix stat all ave/chunk 1 100 100 bin c_cc1 c_cc2 norm sample file cc.profile run 100 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 5.588 | 5.602 | 5.61 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.99888463 43.712357 0 45.21059 197.42728 50 1.0015386 43.71567 0 45.217884 198.28372 100 1.0053363 43.718221 0 45.226131 195.45072 Loop time of 3.09095 on 4 procs for 100 steps with 16000 atoms Performance: 27952.588 tau/day, 32.353 timesteps/s, 517.641 katom-step/s 99.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6867 | 2.6999 | 2.7131 | 0.8 | 87.35 Neigh | 0.2523 | 0.25332 | 0.25501 | 0.2 | 8.20 Comm | 0.087738 | 0.10048 | 0.11401 | 4.0 | 3.25 Output | 0.00014184 | 0.00015461 | 0.00015946 | 0.0 | 0.01 Modify | 0.028066 | 0.028154 | 0.02831 | 0.1 | 0.91 Other | | 0.008906 | | | 0.29 Nlocal: 4000 ave 4024 max 3988 min Histogram: 2 0 1 0 0 0 0 0 0 1 Nghost: 5977 ave 6004 max 5941 min Histogram: 1 0 0 0 0 1 1 0 0 1 Neighs: 187313 ave 188798 max 186723 min Histogram: 2 1 0 0 0 0 0 0 0 1 Total # of neighbors = 749253 Ave neighs/atom = 46.828313 Neighbor list builds = 35 Dangerous builds = 0 Total wall time: 0:00:19