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 = 3.52247 3.52247 3.52247 Created orthogonal box = (0 -53.1916 0) to (37.6097 53.1916 4.98152) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.93837 5.13218 4.98152 Created 916 atoms create_atoms CPU = 0.000415087 secs 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.93837 5.13218 4.98152 Created 916 atoms create_atoms CPU = 0.000319004 secs 916 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 11 30 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 1800 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 5.58 | 5.58 | 5.58 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7915.4096 0 -7915.4096 11717.292 104 0 -7987.5182 0 -7987.5182 -11329.916 Loop time of 0.980886 on 1 procs for 104 steps with 1800 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 = -7915.40956304 -7987.51072628 -7987.51815098 Force two-norm initial, final = 101.972 0.393763 Force max component initial, final = 20.251 0.0448907 Final line search alpha, max atom move = 1 0.0448907 Iterations, force evaluations = 104 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94839 | 0.94839 | 0.94839 | 0.0 | 96.69 Neigh | 0.012235 | 0.012235 | 0.012235 | 0.0 | 1.25 Comm | 0.011758 | 0.011758 | 0.011758 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008504 | | | 0.87 Nlocal: 1800 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9472 ave 9472 max 9472 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: 250328 ave 250328 max 250328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250328 Ave neighs/atom = 139.071 Neighbor list builds = 2 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 : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.581 | 5.581 | 5.581 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -7987.5182 0 -7987.5182 -11329.916 19931.252 107 0 -7987.7513 0 -7987.7513 -3836.0201 19846.293 Loop time of 0.029773 on 1 procs for 3 steps with 1800 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7987.51815098 -7987.74825476 -7987.75131225 Force two-norm initial, final = 152.287 2.13017 Force max component initial, final = 111.78 1.66984 Final line search alpha, max atom move = 6.63134e-05 0.000110733 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02854 | 0.02854 | 0.02854 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030065 | 0.00030065 | 0.00030065 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009322 | | | 3.13 Nlocal: 1800 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9456 ave 9456 max 9456 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: 250424 ave 250424 max 250424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250424 Ave neighs/atom = 139.124 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 5.718 | 5.718 | 5.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7987.7513 0 -7987.7513 -3836.0201 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1800 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: 1800 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9456 ave 9456 max 9456 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: 250480 ave 250480 max 250480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250480 Ave neighs/atom = 139.156 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) = 5.718 | 5.718 | 5.718 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 -7987.7513 -7987.7513 37.535446 106.38323 4.9700944 -3836.0201 -3836.0201 134.53904 -11543.529 -99.070031 2.369743 646.48246 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1800 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 | | 1.907e-06 | | |100.00 Nlocal: 1800 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9456 ave 9456 max 9456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 125240 ave 125240 max 125240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 250480 ave 250480 max 250480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 250480 Ave neighs/atom = 139.156 Neighbor list builds = 0 Dangerous builds = 0 1800 -7987.75131225259 eV 2.36974301457234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01