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 ######################################################################## ### 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 comm_modify vel yes 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) 1 by 1 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 * edpd/temp 1.0 Setting atom values ... 16000 settings made for edpd/temp set atom * edpd/cv 1.0E5 Setting atom values ... 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 region upper block -10.0 10.0 0.0 10.0 -5.0 5.0 region lower block -10.0 10.0 -10.0 0.0 -5.0 5.0 fix mvv all mvv/edpd 0.5 fix upper all edpd/source region upper 0.01 fix lower all edpd/source region lower -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 edpd command: doi:10.1016/j.jcp.2014.02.003 @Article{ZLi2014_JCP, author = {Li, Z. and Tang, Y.-H. and Lei, H. and Caswell, B. and Karniadakis, G. E.}, title = {Energy-Conserving Dissipative Particle Dynamics with Temperature-Dependent Properties}, journal = {Journal of Computational Physics}, year = {2014}, volume = {265}, pages = {113--127} } @Article{ZLi2015_CC, author = {Li, Z. and Tang, Y.-H. and Li, X. and Karniadakis, G. E.}, title = {Mesoscale Modeling of Phase Transition Dynamics of Thermoresponsive Polymers}, journal = {Chemical Communications}, year = {2015}, volume = {51}, pages = {11038--11040} } 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 edpd, 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) = 12.1 | 12.1 | 12.1 Mbytes Step Temp E_pair E_mol TotEng Press 0 1 48.942039 0 50.441946 201.43068 100 0.99644296 43.749732 0 45.244303 200.44316 200 0.98985852 43.699081 0 45.183776 197.29314 300 1.0062075 43.708406 0 45.217622 194.61595 400 0.99858259 43.69758 0 45.19536 196.87253 500 0.99991379 43.677571 0 45.177348 194.59785 Loop time of 50.3705 on 1 procs for 500 steps with 16000 atoms Performance: 8576.445 tau/day, 9.926 timesteps/s, 158.823 katom-step/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.879 | 44.879 | 44.879 | 0.0 | 89.10 Neigh | 4.8096 | 4.8096 | 4.8096 | 0.0 | 9.55 Comm | 0.31711 | 0.31711 | 0.31711 | 0.0 | 0.63 Output | 0.0005095 | 0.0005095 | 0.0005095 | 0.0 | 0.00 Modify | 0.29611 | 0.29611 | 0.29611 | 0.0 | 0.59 Other | | 0.06781 | | | 0.13 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14106 ave 14106 max 14106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 749963 ave 749963 max 749963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749963 Ave neighs/atom = 46.872687 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 Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Per MPI rank memory allocation (min/avg/max) = 12.6 | 12.6 | 12.6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.99991379 43.67752 0 45.177297 195.4932 100 1.0053402 43.685038 0 45.192954 196.73683 200 1.0052797 43.665955 0 45.173781 198.60396 300 0.98694632 43.650877 0 45.131204 199.11464 400 1.003189 43.639966 0 45.144655 196.20663 500 1.008172 43.625425 0 45.137589 196.69792 Loop time of 48.7446 on 1 procs for 500 steps with 16000 atoms Performance: 8862.512 tau/day, 10.258 timesteps/s, 164.121 katom-step/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.362 | 43.362 | 43.362 | 0.0 | 88.96 Neigh | 4.6255 | 4.6255 | 4.6255 | 0.0 | 9.49 Comm | 0.30073 | 0.30073 | 0.30073 | 0.0 | 0.62 Output | 0.00039502 | 0.00039502 | 0.00039502 | 0.0 | 0.00 Modify | 0.39271 | 0.39271 | 0.39271 | 0.0 | 0.81 Other | | 0.06321 | | | 0.13 Nlocal: 16000 ave 16000 max 16000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14131 ave 14131 max 14131 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 749932 ave 749932 max 749932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749932 Ave neighs/atom = 46.87075 Neighbor list builds = 182 Dangerous builds = 0 Total wall time: 0:01:39