LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8602 2.8602 2.8602 Created orthogonal box = (0 -29.7269 0) to (21.0181 29.7269 4.04493) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.67068 3.85311 4.04493 Created 218 atoms create_atoms CPU = 0.000177145 secs 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.67068 3.85311 4.04493 Created 218 atoms create_atoms CPU = 6.69956e-05 secs 218 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 23 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 10 atoms, new total = 426 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.819 | 4.819 | 4.819 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1773.9166 0 -1773.9166 11213.42 47 0 -1809.1369 0 -1809.1369 -14975.832 Loop time of 1.07735 on 1 procs for 47 steps with 426 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1773.91662597 -1809.13518407 -1809.13685716 Force two-norm initial, final = 64.3153 0.157923 Force max component initial, final = 16.8583 0.0291019 Final line search alpha, max atom move = 1 0.0291019 Iterations, force evaluations = 47 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0704 | 1.0704 | 1.0704 | 0.0 | 99.36 Neigh | 0.0042031 | 0.0042031 | 0.0042031 | 0.0 | 0.39 Comm | 0.0016611 | 0.0016611 | 0.0016611 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001072 | | | 0.10 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2602 ave 2602 max 2602 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: 24400 ave 24400 max 24400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24400 Ave neighs/atom = 57.277 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.819 | 4.819 | 4.819 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -1809.1369 0 -1809.1369 -14975.832 5054.5521 53 0 -1809.3332 0 -1809.3332 -1302.9443 5015.4123 Loop time of 0.135777 on 1 procs for 6 steps with 426 atoms 103.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1809.13685716 -1809.33300792 -1809.33316935 Force two-norm initial, final = 69.3764 0.60995 Force max component initial, final = 55.4728 0.205053 Final line search alpha, max atom move = 0.00081284 0.000166675 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13508 | 0.13508 | 0.13508 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016141 | 0.00016141 | 0.00016141 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005331 | | | 0.39 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2594 ave 2594 max 2594 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: 24404 ave 24404 max 24404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24404 Ave neighs/atom = 57.2864 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1809.3332 0 -1809.3332 -1302.9443 Loop time of 9.53674e-07 on 1 procs for 0 steps with 426 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606 ave 2606 max 2606 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: 24412 ave 24412 max 24412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24412 Ave neighs/atom = 57.3052 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) = 4.957 | 4.957 | 4.957 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 -1809.3332 -1809.3332 20.956875 59.453766 4.025323 -1302.9443 -1302.9443 -65.313506 -3878.4166 34.897168 2.2622074 410.86262 Loop time of 9.53674e-07 on 1 procs for 0 steps with 426 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 426 ave 426 max 426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2606 ave 2606 max 2606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12206 ave 12206 max 12206 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24412 ave 24412 max 24412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24412 Ave neighs/atom = 57.3052 Neighbor list builds = 0 Dangerous builds = 0 426 -1809.33316935399 eV 2.26220739330173 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01