LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified) using 1 OpenMP thread(s) per MPI task # ACKS2 Water, CITE: Achtyl et al., Nat. Comm., 6 6539 (2015) boundary p p s 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 ... WARNING: Non-zero imageflag(s) in z direction for non-periodic boundary reset to zero (src/read_data.cpp:1548) 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 0.0012889577) to (31.043046 31.043046 31.045309) 2 by 1 by 2 MPI processor grid 3000 atoms replicate CPU = 0.001 seconds pair_style reaxff NULL safezone 3.0 mincap 150 pair_coeff * * acks2_ff.water O H Reading potential file acks2_ff.water with DATE: 2021-09-21 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 acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff maxiter 1000 fix 2 all nvt temp 300 300 50.0 fix 3 all efield 0.0 0.0 1.0 fix 4 all wall/reflect zlo EDGE zhi EDGE 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 acks2/reaxff command: doi:10.1137/18M1224684 @Article{O'Hearn2020, author = {K. A. {O'Hearn} and A. Alperen and H. M. Aktulga}, title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms}, journal = {SIAM J.\ Sci.\ Comput.}, year = 2020, volume = 42, number = 1, pages = {1--22} } 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 acks2/reaxff, perpetual, copy from (1) attributes: half, newton off pair build: copy stencil: none bin: none Per MPI rank memory allocation (min/avg/max) = 198.5 | 199.3 | 199.9 Mbytes Step Temp Press Density Volume 0 300 -20760.178 0.99996859 29916.212 10 396.27472 -18425.294 1.0000143 29914.845 20 518.59015 -10012.352 1.0000209 29914.647 Loop time of 3.14386 on 4 procs for 20 steps with 3000 atoms Performance: 0.275 ns/day, 87.329 hours/ns, 6.362 timesteps/s, 19.085 katom-step/s 99.2% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66121 | 0.66884 | 0.68146 | 1.0 | 21.27 Neigh | 0.095801 | 0.09707 | 0.098006 | 0.3 | 3.09 Comm | 0.0018538 | 0.014557 | 0.022268 | 6.8 | 0.46 Output | 3.5758e-05 | 4.0192e-05 | 5.2801e-05 | 0.0 | 0.00 Modify | 2.3621 | 2.3631 | 2.3644 | 0.1 | 75.17 Other | | 0.0002583 | | | 0.01 Nlocal: 750 ave 758 max 737 min Histogram: 1 0 0 0 0 0 1 0 1 1 Nghost: 4219.5 ave 4233 max 4198 min Histogram: 1 0 0 0 1 0 0 0 0 2 Neighs: 230733 ave 233430 max 225532 min Histogram: 1 0 0 0 0 0 0 0 2 1 Total # of neighbors = 922931 Ave neighs/atom = 307.64367 Neighbor list builds = 7 Dangerous builds = 0 Total wall time: 0:00:03