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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -41.601777 0.0000000) to (14.708449 41.601777 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0564203 6.1179084 5.0449565 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.601777 0.0000000) to (14.708449 41.601777 5.0449565) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0564203 6.1179084 5.0449565 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.601777 0.0000000) to (14.708449 41.601777 5.0449565) create_atoms CPU = 0.001 seconds 274 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 30 2 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 540 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_196726067688_000#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2194.1213 0 -2194.1213 32942.867 133 0 -2279.5278 0 -2279.5278 43032.409 Loop time of 3.80148 on 1 procs for 133 steps with 540 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 = -2194.12125633294 -2279.52591741395 -2279.52778293158 Force two-norm initial, final = 181.97821 0.17662509 Force max component initial, final = 60.772350 0.023807115 Final line search alpha, max atom move = 1.0000000 0.023807115 Iterations, force evaluations = 133 253 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7833 | 3.7833 | 3.7833 | 0.0 | 99.52 Neigh | 0.0028566 | 0.0028566 | 0.0028566 | 0.0 | 0.08 Comm | 0.007573 | 0.007573 | 0.007573 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007793 | | | 0.21 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3002.00 ave 3002 max 3002 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: 32144.0 ave 32144 max 32144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32144 Ave neighs/atom = 59.525926 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -2279.5278 0 -2279.5278 43032.409 6173.9939 144 0 -2280.9054 0 -2280.9054 671.02696 6261.6672 Loop time of 0.186851 on 1 procs for 11 steps with 540 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 = -2279.52778293158 -2280.90412449482 -2280.90540186065 Force two-norm initial, final = 292.10735 5.3488363 Force max component initial, final = 202.35444 4.3537586 Final line search alpha, max atom move = 0.00022129625 0.00096347044 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18492 | 0.18492 | 0.18492 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032129 | 0.00032129 | 0.00032129 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001611 | | | 0.86 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3002.00 ave 3002 max 3002 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: 32528.0 ave 32528 max 32528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32528 Ave neighs/atom = 60.237037 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2280.9054 0 -2280.9054 671.02696 Loop time of 1.832e-06 on 1 procs for 0 steps with 540 atoms 163.8% 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 | | 1.832e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2964.00 ave 2964 max 2964 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: 31260.0 ave 31260 max 31260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31260 Ave neighs/atom = 57.888889 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.627 | 4.627 | 4.627 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 -2280.9054 -2280.9054 14.857686 83.22965 5.0636158 671.02696 671.02696 1125.3018 280.14531 607.63382 2.3785105 418.13369 Loop time of 1.948e-06 on 1 procs for 0 steps with 540 atoms 154.0% 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 | | 1.948e-06 | | |100.00 Nlocal: 540.000 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2964.00 ave 2964 max 2964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15630.0 ave 15630 max 15630 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31260.0 ave 31260 max 31260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31260 Ave neighs/atom = 57.888889 Neighbor list builds = 0 Dangerous builds = 0 540 -2280.90540186065 eV 2.37851048931099 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04