LAMMPS (28 Jul 2021) using 1 OpenMP thread(s) per MPI task units lj atom_style full boundary p p p special_bonds lj/coul 1 1 1 newton on on # save an extra atom type for bond particles read_data data.chain Reading data file ... orthogonal box = (0.0000000 0.0000000 0.0000000) to (10.000000 10.000000 10.000000) 1 by 1 by 1 MPI processor grid reading atoms ... 3000 atoms reading velocities ... 3000 velocities scanning bonds ... 1 = max bonds/atom reading bonds ... 2700 bonds Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 1 1 1 special bond factors coul: 1 1 1 2 = max # of 1-2 neighbors 2 = max # of special neighbors special bonds CPU = 0.000 seconds read_data CPU = 0.013 seconds neighbor 2.0 bin neigh_modify every 10 check yes bond_style harmonic bond_coeff * 225.0 0.85 comm_modify vel yes comm_modify cutoff 3.6 # must use pair hybrid, since srp bond particles # do not interact with other atoms types pair_style hybrid dpd 1.0 1.0 373692 srp 0.8 1 mid pair_coeff 1 1 dpd 60.0 4.5 1.0 pair_coeff 1 2 none pair_coeff 2 2 srp 100.0 # auto normalization of thermo quantities is turned off by pair srp # just divide by natoms variable natoms equal count(all) variable nPotEng equal c_thermo_pe/v_natoms thermo 50 thermo_style custom step temp pe v_nPotEng press atoms v_natoms lx ly lz fix 1 all nve timestep 0.01 #restart 500 mid-run-*.restart run 1000 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - @Article{Sirk2012 author = {T. Sirk and Y. Sliozberg and J. Brennan and M. Lisal and J. Andzelm}, title = {An enhanced entangled polymer model for dissipative particle dynamics}, journal = {J.~Chem.~Phys.}, year = 2012, volume = 136, pages = {134903} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Using type 2 for bond particles Thermo normalization turned off by pair srp (src/MISC/pair_srp.cpp:486) Neighbor list info ... update every 10 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 3 ghost atom cutoff = 3.6 binsize = 1.5, bins = 7 7 7 3 neighbor lists, perpetual/occasional/extra = 3 0 0 (1) pair dpd, perpetual, skip from (3) attributes: half, newton on pair build: skip stencil: none bin: none (2) pair srp, perpetual, skip from (3) attributes: half, newton on pair build: skip stencil: none bin: none (3) neighbor class addition, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard Removed/inserted 0/2700 bond particles. (src/MISC/fix_srp.cpp:250) Per MPI rank memory allocation (min/avg/max) = 21.70 | 21.70 | 21.70 Mbytes Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz 0 0.98262092 31772.336 10.590779 60.690437 5700 3000 10 10 10 50 0.99678169 31789.37 10.596457 61.967133 5700 3000 10 10 10 100 1.016953 31770.946 10.590315 61.808425 5700 3000 10 10 10 150 1.0151677 31737.965 10.579322 61.034423 5700 3000 10 10 10 200 0.99241972 31766.458 10.588819 60.99902 5700 3000 10 10 10 250 1.0101747 31816.098 10.605366 61.484391 5700 3000 10 10 10 300 1.0058287 31824.98 10.608327 60.656545 5700 3000 10 10 10 350 1.0093409 31839.963 10.613321 61.485931 5700 3000 10 10 10 400 1.029692 31713.44 10.571147 61.442428 5700 3000 10 10 10 450 1.0292264 31739.234 10.579745 61.026996 5700 3000 10 10 10 500 1.0141131 31796.032 10.598677 61.099407 5700 3000 10 10 10 550 0.99860738 31887.879 10.629293 61.412249 5700 3000 10 10 10 600 1.0104436 31830.675 10.610225 60.725018 5700 3000 10 10 10 650 1.0060939 31871.441 10.623814 61.12217 5700 3000 10 10 10 700 1.0394405 31724.09 10.574697 60.652294 5700 3000 10 10 10 750 1.0094386 31827.328 10.609109 61.274573 5700 3000 10 10 10 800 0.99986353 31777.205 10.592402 60.652922 5700 3000 10 10 10 850 0.9762615 31752.585 10.584195 61.448972 5700 3000 10 10 10 900 0.99324534 31794.723 10.598241 61.191199 5700 3000 10 10 10 950 1.0139717 31719.123 10.573041 61.876053 5700 3000 10 10 10 1000 0.99850758 31774.801 10.5916 60.960607 5700 3000 10 10 10 Deleted 2700 atoms, new total = 3000 Loop time of 6.54135 on 1 procs for 1000 steps with 3000 atoms Performance: 132082.911 tau/day, 152.874 timesteps/s 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5403 | 4.5403 | 4.5403 | 0.0 | 69.41 Bond | 0.030682 | 0.030682 | 0.030682 | 0.0 | 0.47 Neigh | 1.7065 | 1.7065 | 1.7065 | 0.0 | 26.09 Comm | 0.20647 | 0.20647 | 0.20647 | 0.0 | 3.16 Output | 0.00084543 | 0.00084543 | 0.00084543 | 0.0 | 0.01 Modify | 0.034479 | 0.034479 | 0.034479 | 0.0 | 0.53 Other | | 0.022 | | | 0.34 Nlocal: 3000.00 ave 3000 max 3000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12269.0 ave 12269 max 12269 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 0 Ave neighs/atom = 0.0000000 Ave special neighs/atom = 1.8000000 Neighbor list builds = 21 Dangerous builds = 0 #write_restart end-run.restart Total wall time: 0:00:06