LAMMPS (21 Nov 2023 - Development - patch_21Nov2023-758-ge33590b2fc-modified) using 1 OpenMP thread(s) per MPI task variable nrun equal 1000 variable dump_count equal 10 variable nwall equal 4 variable w1 equal 67 variable w2 equal 71 variable w3 equal 75 variable w4 equal 79 variable x_cylinder equal 20 variable y_cylinder equal 17 variable r_cylinder equal 4 variable MASS equal 1 variable TEMP equal 0.4 variable VFLOW equal 0.5 units lj atom_style atomic lattice fcc 0.3 Lattice spacing in x,y,z = 2.3712622 2.3712622 2.3712622 region sim_box block 0 84 0 34 0 10 boundary p p p create_box 2 sim_box Created orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622) 1 by 1 by 1 MPI processor grid region reg_cylinder cylinder z ${x_cylinder} ${y_cylinder} ${r_cylinder} EDGE EDGE region reg_cylinder cylinder z 20 ${y_cylinder} ${r_cylinder} EDGE EDGE region reg_cylinder cylinder z 20 17 ${r_cylinder} EDGE EDGE region reg_cylinder cylinder z 20 17 4 EDGE EDGE create_atoms 1 box Created 114240 atoms using lattice units in orthogonal box = (0 0 0) to (199.18603 80.622915 23.712622) create_atoms CPU = 0.010 seconds ## setup obstacle ## group g_obst region reg_cylinder 1950 atoms in group g_obst group g_flow subtract all g_obst 112290 atoms in group g_flow set group g_obst type 2 Setting atom values ... 1950 settings made for type mass 1 ${MASS} mass 1 1 mass 2 ${MASS} mass 2 1 velocity g_flow create ${TEMP} 4928459 rot yes dist gaussian velocity g_flow create 0.4 4928459 rot yes dist gaussian velocity g_obst set 0.0 0.0 0.0 pair_style lj/cut 1.122462 pair_coeff 1 1 1.0 1.0 pair_coeff 1 2 1.0 1.0 pair_coeff 2 2 1.0 1.0 pair_modify shift yes neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 g_flow nve fix 2 g_flow wall/flow x ${VFLOW} ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 ${TEMP} 123 ${nwall} ${w1} ${w2} ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 ${nwall} ${w1} ${w2} ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 4 ${w1} ${w2} ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 ${w2} ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 ${w3} ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 ${w4} fix 2 g_flow wall/flow x 0.5 0.4 123 4 67 71 75 79 variable dump_every equal ${nrun}/${dump_count} variable dump_every equal 1000/${dump_count} variable dump_every equal 1000/10 variable thermo_every equal ${dump_every} variable thermo_every equal 100 variable restart_every equal ${nrun}/10 variable restart_every equal 1000/10 ##### uncomment for grid aggregation ##### #variable gr_Nx equal 42 #variable gr_Ny equal 17 #variable gr_Nz equal 1 #variable gr_Nevery equal ${dump_every} #variable gr_Nrepeat equal 1 #variable gr_Nfreq equal ${dump_every} #fix 3 g_flow ave/grid ${gr_Nevery} ${gr_Nrepeat} ${gr_Nfreq} ${gr_Nx} ${gr_Ny} ${gr_Nz} vx vy vz density/mass norm all ave one #compute ct_gridId g_flow property/grid ${gr_Nx} ${gr_Ny} ${gr_Nz} id #dump dmp_grid g_flow grid ${dump_every} grid.lammpstrj c_ct_gridId:grid:data f_3:grid:data[*] ########################################## #dump dmp_coord all atom ${dump_every} dump.lammpstrj #compute ct_Temp g_flow temp/com #thermo_style custom step temp epair emol etotal press c_ct_Temp #restart ${restart_every} flow.restart timestep 0.005 thermo ${thermo_every} thermo 100 run ${nrun} run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - fix wall/flow command: doi:10.1177/10943420231213013 @Article{Pavlov-etal-IJHPCA-2024, author = {Daniil Pavlov and Vladislav Galigerov and Daniil Kolotinskii and Vsevolod Nikolskiy and Vladimir Stegailov}, title = {GPU-based molecular dynamics of fluid flows: Reaching for turbulence}, journal = {The International Journal of High Performance Computing Applications}, year = 2024, volume = 38, number = 1, pages = 34-49 } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 20 steps, delay = 0 steps, check = no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 1.422462 ghost atom cutoff = 1.422462 binsize = 0.711231, bins = 281 114 34 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, 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) = 26.69 | 26.69 | 26.69 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.39317221 0 0 0.58975315 0.11795063 100 0.3671684 0.045118445 0 0.59586622 0.27378331 200 0.3732041 0.036897471 0 0.59669873 0.24917809 300 0.37432305 0.036501844 0 0.5979815 0.24715194 400 0.37603886 0.035350565 0 0.59940392 0.24480762 500 0.37617142 0.036949771 0 0.60120196 0.24862985 600 0.37751983 0.036484268 0 0.60275905 0.24784635 700 0.37787831 0.037327783 0 0.60414029 0.25060427 800 0.37959242 0.036206184 0 0.60558983 0.2476903 900 0.38019033 0.036874395 0 0.6071549 0.24984211 1000 0.38070666 0.037068948 0 0.60812395 0.25041936 Loop time of 5.61598 on 1 procs for 1000 steps with 114240 atoms Performance: 76923.319 tau/day, 178.063 timesteps/s, 20.342 Matom-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 | 2.6351 | 2.6351 | 2.6351 | 0.0 | 46.92 Neigh | 1.2994 | 1.2994 | 1.2994 | 0.0 | 23.14 Comm | 0.26576 | 0.26576 | 0.26576 | 0.0 | 4.73 Output | 0.0030531 | 0.0030531 | 0.0030531 | 0.0 | 0.05 Modify | 1.3019 | 1.3019 | 1.3019 | 0.0 | 23.18 Other | | 0.1107 | | | 1.97 Nlocal: 114240 ave 114240 max 114240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20119 ave 20119 max 20119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164018 ave 164018 max 164018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164018 Ave neighs/atom = 1.4357318 Neighbor list builds = 50 Dangerous builds not checked Total wall time: 0:00:05