LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.86883 2.86883 2.86883 Created orthogonal box = (0 -43.3213 0) to (30.6307 43.3213 4.05714) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.83643 4.17984 4.05714 Created 458 atoms create_atoms CPU = 0.00107408 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.83643 4.17984 4.05714 Created 458 atoms create_atoms CPU = 0.000880003 secs 458 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 916 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.829 | 5.829 | 5.829 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3537.2158 0 -3537.2158 62965.301 40 0 -3759.2357 0 -3759.2357 14178.625 Loop time of 0.821786 on 1 procs for 40 steps with 916 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 = -3537.21579781 -3759.23238974 -3759.23568489 Force two-norm initial, final = 182.663 0.285849 Force max component initial, final = 33.0692 0.0416543 Final line search alpha, max atom move = 1 0.0416543 Iterations, force evaluations = 40 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79971 | 0.79971 | 0.79971 | 0.0 | 97.31 Neigh | 0.012995 | 0.012995 | 0.012995 | 0.0 | 1.58 Comm | 0.0064602 | 0.0064602 | 0.0064602 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002617 | | | 0.32 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10577 ave 10577 max 10577 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 356624 ave 356624 max 356624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356624 Ave neighs/atom = 389.328 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.829 | 5.829 | 5.829 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -3759.2357 0 -3759.2357 14178.625 10767.333 52 0 -3760.6793 0 -3760.6793 -6784.0826 10898.714 Loop time of 0.131631 on 1 procs for 12 steps with 916 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 = -3759.23568489 -3760.67846462 -3760.67933007 Force two-norm initial, final = 260.04 0.636245 Force max component initial, final = 254.732 0.0905854 Final line search alpha, max atom move = 0.000189507 1.71665e-05 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12787 | 0.12787 | 0.12787 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097466 | 0.00097466 | 0.00097466 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002788 | | | 2.12 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10583 ave 10583 max 10583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 357068 ave 357068 max 357068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357068 Ave neighs/atom = 389.812 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.967 | 5.967 | 5.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3760.6793 0 -3760.6793 -6784.0826 Loop time of 9.53674e-07 on 1 procs for 0 steps with 916 atoms 209.7% 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 | | 9.537e-07 | | |100.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10532 ave 10532 max 10532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346316 ave 346316 max 346316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346316 Ave neighs/atom = 378.074 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.967 | 5.967 | 5.967 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 -3760.6793 -3760.6793 30.659215 86.642511 4.1028268 -6784.0826 -6784.0826 -0.44210715 -20338.339 -13.466553 2.2730561 863.52915 Loop time of 1.90735e-06 on 1 procs for 0 steps with 916 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 916 ave 916 max 916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10532 ave 10532 max 10532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173158 ave 173158 max 173158 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346316 ave 346316 max 346316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346316 Ave neighs/atom = 378.074 Neighbor list builds = 0 Dangerous builds = 0 916 -3760.67933007063 eV 2.27305611776325 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01