LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified) using 1 OpenMP thread(s) per MPI task # QEq Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015) boundary p p p units real atom_style charge read_data data.water Reading data file ... orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) 1 by 2 by 2 MPI processor grid reading atoms ... 3000 atoms read_data CPU = 0.009 seconds variable x index 1 variable y index 1 variable z index 1 replicate $x $y $z replicate 1 $y $z replicate 1 1 $z replicate 1 1 1 Replication is creating a 1x1x1 = 1 times larger system... orthogonal box = (0 0 0) to (31.043046 31.043046 31.043046) 1 by 2 by 2 MPI processor grid 3000 atoms replicate CPU = 0.002 seconds pair_style reaxff NULL safezone 3.0 mincap 150 pair_coeff * * qeq_ff.water O H WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxff_ffield.cpp:294) neighbor 0.5 bin neigh_modify every 1 delay 0 check yes velocity all create 300.0 4928459 rot yes dist gaussian fix 1 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 400 fix 2 all nvt temp 300 300 50.0 timestep 0.5 thermo 10 thermo_style custom step temp press density vol run 20 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - pair reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, number = {4--5}, pages = {245--259} } - fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005 @Article{Aktulga12, author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama}, title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques}, journal = {Parallel Computing}, year = 2012, volume = 38, pages = {245--259} } CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.5 ghost atom cutoff = 10.5 binsize = 5.25, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair reaxff, perpetual attributes: half, newton off, ghost pair build: half/bin/ghost/newtoff stencil: full/ghost/bin/3d bin: standard (2) fix qeq/reaxff, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 260.5 | 262.2 | 263.6 Mbytes Step Temp Press Density Volume 0 300 780.34006 1 29915.273 10 301.29205 5433.7414 1 29915.273 20 297.90652 1572.6111 1 29915.273 Loop time of 1.21853 on 4 procs for 20 steps with 3000 atoms Performance: 0.709 ns/day, 33.848 hours/ns, 16.413 timesteps/s, 49.240 katom-step/s 99.1% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81943 | 0.83131 | 0.84443 | 1.2 | 68.22 Neigh | 0.040127 | 0.040506 | 0.040961 | 0.2 | 3.32 Comm | 0.0025704 | 0.015716 | 0.027606 | 8.9 | 1.29 Output | 3.3504e-05 | 3.7908e-05 | 5.1038e-05 | 0.0 | 0.00 Modify | 0.33037 | 0.33079 | 0.33116 | 0.1 | 27.15 Other | | 0.0001712 | | | 0.01 Nlocal: 750 ave 759 max 735 min Histogram: 1 0 0 0 0 1 0 0 0 2 Nghost: 6230.5 ave 6256 max 6190 min Histogram: 1 0 0 0 0 1 0 0 1 1 Neighs: 277008 ave 280943 max 271394 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 1108032 Ave neighs/atom = 369.344 Neighbor list builds = 2 Dangerous builds = 0 Total wall time: 0:00:01