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 -53.0516 0) to (18.7556 53.0516 4.04493) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.79793 4.93476 4.04493 Created 346 atoms create_atoms CPU = 0.000456095 secs 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.79793 4.93476 4.04493 Created 346 atoms create_atoms CPU = 0.00029707 secs 346 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 40 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 8 atoms, new total = 684 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 40 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) = 4.897 | 4.897 | 4.897 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2898.9686 0 -2898.9686 1664.5228 15 0 -2915.9866 0 -2915.9866 -3939.7171 Loop time of 0.645332 on 1 procs for 15 steps with 684 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 = -2898.96863185 -2915.98378691 -2915.98662838 Force two-norm initial, final = 36.2481 0.217538 Force max component initial, final = 9.3004 0.0607372 Final line search alpha, max atom move = 1 0.0607372 Iterations, force evaluations = 15 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.64413 | 0.64413 | 0.64413 | 0.0 | 99.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067973 | 0.00067973 | 0.00067973 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005195 | | | 0.08 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39376 ave 39376 max 39376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39376 Ave neighs/atom = 57.5673 Neighbor list builds = 0 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 : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.897 | 4.897 | 4.897 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -2915.9866 0 -2915.9866 -3939.7171 8049.5016 17 0 -2916.012 0 -2916.012 -213.37245 8032.0584 Loop time of 0.0609119 on 1 procs for 2 steps with 684 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2915.98662838 -2916.0102975 -2916.01199269 Force two-norm initial, final = 32.2704 2.20904 Force max component initial, final = 26.9779 2.14602 Final line search alpha, max atom move = 0.000130718 0.000280524 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060604 | 0.060604 | 0.060604 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.534e-05 | 7.534e-05 | 7.534e-05 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002325 | | | 0.38 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39408 ave 39408 max 39408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39408 Ave neighs/atom = 57.614 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 40 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2916.012 0 -2916.012 -213.37245 Loop time of 1.19209e-06 on 1 procs for 0 steps with 684 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 | | 1.192e-06 | | |100.00 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 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: 39424 ave 39424 max 39424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39424 Ave neighs/atom = 57.6374 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) = 5.035 | 5.035 | 5.035 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 -2916.012 -2916.012 18.741587 106.10317 4.0391703 -213.37245 -213.37245 427.75408 -977.23456 -90.636868 2.2884287 329.74822 Loop time of 1.19209e-06 on 1 procs for 0 steps with 684 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 | | 1.192e-06 | | |100.00 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3478 ave 3478 max 3478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19712 ave 19712 max 19712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39424 ave 39424 max 39424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39424 Ave neighs/atom = 57.6374 Neighbor list builds = 0 Dangerous builds = 0 684 -2916.01199269075 eV 2.28842869150363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00