LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -58.673407 0.0000000) to (11.976659 58.673407 8.8453489) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4439359 5.3339461 5.8968993 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.673407 0.0000000) to (11.976659 58.673407 8.8453489) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4439359 5.3339461 5.8968993 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.673407 0.0000000) to (11.976659 58.673407 8.8453489) create_atoms CPU = 0.001 seconds 530 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_912636107108_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4057.5734 0 -4057.5734 68239.658 130 0 -4467.8295 0 -4467.8295 6297.298 Loop time of 9.90169 on 1 procs for 130 steps with 1056 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4057.57336784277 -4467.8253720034 -4467.8294992123 Force two-norm initial, final = 677.46124 0.26265241 Force max component initial, final = 192.41230 0.073938949 Final line search alpha, max atom move = 1.0000000 0.073938949 Iterations, force evaluations = 130 246 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8534 | 9.8534 | 9.8534 | 0.0 | 99.51 Neigh | 0.02324 | 0.02324 | 0.02324 | 0.0 | 0.23 Comm | 0.011541 | 0.011541 | 0.011541 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01355 | | | 0.14 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4653.00 ave 4653 max 4653 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 FullNghs: 81520.0 ave 81520 max 81520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81520 Ave neighs/atom = 77.196970 Neighbor list builds = 3 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -4467.8295 0 -4467.8295 6297.298 12431.455 135 0 -4467.9877 0 -4467.9877 -9.8505337 12476.875 Loop time of 0.320511 on 1 procs for 5 steps with 1056 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4467.8294992123 -4467.98585977717 -4467.98770781178 Force two-norm initial, final = 92.838638 1.0809818 Force max component initial, final = 77.788277 0.76341054 Final line search alpha, max atom move = 8.7600517e-05 6.6875158e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31832 | 0.31832 | 0.31832 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003467 | 0.0003467 | 0.0003467 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00184 | | | 0.57 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4587.00 ave 4587 max 4587 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 FullNghs: 81520.0 ave 81520 max 81520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81520 Ave neighs/atom = 77.196970 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.707 | 4.707 | 4.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4467.9877 0 -4467.9877 -9.8505337 Loop time of 2.459e-06 on 1 procs for 0 steps with 1056 atoms 162.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.459e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4546.00 ave 4546 max 4546 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 FullNghs: 81468.0 ave 81468 max 81468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81468 Ave neighs/atom = 77.147727 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 40 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.707 | 4.707 | 4.707 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -4467.9877 -4467.9877 11.988156 117.20107 8.8801822 -9.8505337 -9.8505337 98.124936 -64.7166 -62.959938 2.2159215 655.53928 Loop time of 2.201e-06 on 1 procs for 0 steps with 1056 atoms 227.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 2.201e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4546.00 ave 4546 max 4546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40734.0 ave 40734 max 40734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81468.0 ave 81468 max 81468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81468 Ave neighs/atom = 77.147727 Neighbor list builds = 0 Dangerous builds = 0 1056 -4467.98770781178 eV 2.21592153640656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10