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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -42.822648 0.0000000) to (21.411324 42.822648 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0507910 4.0507910 3.5200000 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -42.822648 0.0000000) to (21.411324 42.822648 3.5200000) create_atoms CPU = 0.002 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0507910 4.0507910 3.5200000 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -42.822648 0.0000000) to (21.411324 42.822648 3.5200000) create_atoms CPU = 0.001 seconds 298 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 592 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2593.0442 0 -2593.0442 3144.2493 63 0 -2622.707 0 -2622.707 7638.7533 Loop time of 2.48905 on 1 procs for 63 steps with 592 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2593.04423683838 -2622.70470002438 -2622.70704691614 Force two-norm initial, final = 15.706160 0.14923697 Force max component initial, final = 4.5361061 0.014421346 Final line search alpha, max atom move = 1.0000000 0.014421346 Iterations, force evaluations = 63 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4594 | 2.4594 | 2.4594 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017989 | 0.017989 | 0.017989 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01168 | | | 0.47 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6514.00 ave 6514 max 6514 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: 147008.0 ave 147008 max 147008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147008 Ave neighs/atom = 248.32432 Neighbor list builds = 0 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2622.707 0 -2622.707 7638.7533 6454.9027 66 0 -2622.7758 0 -2622.7758 -3.9039167 6482.3933 Loop time of 0.127791 on 1 procs for 3 steps with 592 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2622.70704691613 -2622.7740346312 -2622.7758440545 Force two-norm initial, final = 53.559596 0.19620100 Force max component initial, final = 34.622264 0.098570481 Final line search alpha, max atom move = 0.00036025228 3.5510241e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12461 | 0.12461 | 0.12461 | 0.0 | 97.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083559 | 0.00083559 | 0.00083559 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00235 | | | 1.84 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 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: 146464.0 ave 146464 max 146464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146464 Ave neighs/atom = 247.40541 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2622.7758 0 -2622.7758 -3.9039167 Loop time of 6.085e-06 on 1 procs for 0 steps with 592 atoms 180.8% 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 | | 6.085e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 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: 146288.0 ave 146288 max 146288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146288 Ave neighs/atom = 247.10811 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.075 | 5.075 | 5.075 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 -2622.7758 -2622.7758 21.438263 85.692195 3.528617 -3.9039167 -3.9039167 -24.393152 10.191696 2.4897061 2.2463196 181.86133 Loop time of 6.545e-06 on 1 procs for 0 steps with 592 atoms 244.5% 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 | | 6.545e-06 | | |100.00 Nlocal: 592.000 ave 592 max 592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73144.0 ave 73144 max 73144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146288.0 ave 146288 max 146288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146288 Ave neighs/atom = 247.10811 Neighbor list builds = 0 Dangerous builds = 0 592 -2622.7758440545 eV 2.24631960391495 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03