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 2 by 2 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 = 0.011 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) = 10.35 | 10.35 | 10.35 Mbytes Step Temp PotEng v_nPotEng Press Atoms v_natoms Lx Ly Lz 0 0.98262092 31772.336 10.590779 60.908146 5700 3000 10 10 10 50 1.0094645 31632.293 10.544098 61.107394 5700 3000 10 10 10 100 1.0067657 31633.525 10.544508 61.721089 5700 3000 10 10 10 150 0.99163624 31751.06 10.583687 60.437789 5700 3000 10 10 10 200 0.98701756 31674.754 10.558251 60.897782 5700 3000 10 10 10 250 0.99422545 31689.944 10.563315 61.748317 5700 3000 10 10 10 300 0.98351268 31756.124 10.585375 61.164735 5700 3000 10 10 10 350 0.99570183 31840.098 10.613366 61.210337 5700 3000 10 10 10 400 1.0025719 31832.008 10.610669 61.270633 5700 3000 10 10 10 450 0.99464256 31812.213 10.604071 60.625168 5700 3000 10 10 10 500 0.98753036 31822.577 10.607526 61.007786 5700 3000 10 10 10 550 0.98085348 31779.406 10.593135 61.268608 5700 3000 10 10 10 600 1.0031999 31849.695 10.616565 61.938464 5700 3000 10 10 10 650 1.0102644 31912.564 10.637521 61.298438 5700 3000 10 10 10 700 1.0238545 31799.622 10.599874 61.424427 5700 3000 10 10 10 750 1.0186874 31781.261 10.593754 60.706143 5700 3000 10 10 10 800 1.0245821 31738.473 10.579491 61.550865 5700 3000 10 10 10 850 1.0179726 31720.521 10.573507 61.881576 5700 3000 10 10 10 900 1.0154591 31760.887 10.586962 61.673156 5700 3000 10 10 10 950 0.99349056 31834.644 10.611548 61.624864 5700 3000 10 10 10 1000 1.0033121 31820.089 10.606696 60.698277 5700 3000 10 10 10 Deleted 2700 atoms, new total = 3000 Loop time of 2.18923 on 4 procs for 1000 steps with 3000 atoms Performance: 394659.660 tau/day, 456.782 timesteps/s 98.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2744 | 1.2921 | 1.3222 | 1.6 | 59.02 Bond | 0.0092027 | 0.0093722 | 0.009696 | 0.2 | 0.43 Neigh | 0.47767 | 0.47768 | 0.47769 | 0.0 | 21.82 Comm | 0.34932 | 0.37877 | 0.39403 | 2.9 | 17.30 Output | 0.001045 | 0.0015711 | 0.003145 | 2.3 | 0.07 Modify | 0.015498 | 0.016073 | 0.017271 | 0.6 | 0.73 Other | | 0.01362 | | | 0.62 Nlocal: 750.000 ave 754 max 743 min Histogram: 1 0 0 0 0 0 1 0 0 2 Nghost: 6941.25 ave 6967 max 6911 min Histogram: 1 0 0 0 0 1 1 0 0 1 Neighs: 0.00000 ave 0 max 0 min Histogram: 4 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: 0:00:02