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 = 3.56184 3.56184 3.56184 Created orthogonal box = (0 -41.2348 0) to (29.1549 41.2348 5.0372) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65692 6.15392 5.0372 Created 538 atoms create_atoms CPU = 0.00137901 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65692 6.15392 5.0372 Created 538 atoms create_atoms CPU = 0.00108385 secs 538 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 20 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 8.5097 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1058 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5097 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) = 5.443 | 5.443 | 5.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4097.9887 0 -4097.9887 5019.9959 106 0 -4155.6406 0 -4155.6406 -22370.132 Loop time of 1.31208 on 1 procs for 106 steps with 1058 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4097.98873244 -4155.63703872 -4155.64055577 Force two-norm initial, final = 43.9127 0.256902 Force max component initial, final = 15.1042 0.0360875 Final line search alpha, max atom move = 1 0.0360875 Iterations, force evaluations = 106 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2693 | 1.2693 | 1.2693 | 0.0 | 96.74 Neigh | 0.021309 | 0.021309 | 0.021309 | 0.0 | 1.62 Comm | 0.013527 | 0.013527 | 0.013527 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007982 | | | 0.61 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7987 ave 7987 max 7987 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: 236388 ave 236388 max 236388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236388 Ave neighs/atom = 223.429 Neighbor list builds = 2 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 : 106 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.443 | 5.443 | 5.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 106 0 -4155.6406 0 -4155.6406 -22370.132 12111.396 120 0 -4157.8376 0 -4157.8376 1962.3687 11939.726 Loop time of 0.126634 on 1 procs for 14 steps with 1058 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4155.64055577 -4157.83760433 -4157.83764016 Force two-norm initial, final = 351.107 0.517873 Force max component initial, final = 323.211 0.143564 Final line search alpha, max atom move = 0.000867065 0.000124479 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1214 | 0.1214 | 0.1214 | 0.0 | 95.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011163 | 0.0011163 | 0.0011163 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004115 | | | 3.25 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7969 ave 7969 max 7969 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: 236444 ave 236444 max 236444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236444 Ave neighs/atom = 223.482 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5097 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) = 5.58 | 5.58 | 5.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4157.8376 0 -4157.8376 1962.3687 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1058 atoms 314.6% 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: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 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: 237568 ave 237568 max 237568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237568 Ave neighs/atom = 224.544 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) = 5.58 | 5.58 | 5.58 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 -4157.8376 -4157.8376 28.78186 82.469597 5.030158 1962.3687 1962.3687 -16.004608 5922.3484 -19.237693 2.3175298 1031.7833 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1058 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: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8041 ave 8041 max 8041 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118784 ave 118784 max 118784 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237568 ave 237568 max 237568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237568 Ave neighs/atom = 224.544 Neighbor list builds = 0 Dangerous builds = 0 1058 -4157.83764016022 eV 2.3175297635372 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01