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 = 2.86883 2.86883 2.86883 Created orthogonal box = (0 -46.6158 0) to (9.51483 46.6158 7.02717) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.32492 4.23754 4.68478 Created 266 atoms create_atoms CPU = 0.00031209 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.32492 4.23754 4.68478 Created 266 atoms create_atoms CPU = 0.000135183 secs 266 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 2 19 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 522 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 2 19 2 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) = 5.427 | 5.427 | 5.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2102.3967 0 -2102.3967 8130.7392 118 0 -2145.1225 0 -2145.1225 -12999.419 Loop time of 0.903141 on 1 procs for 118 steps with 522 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2102.39666761 -2145.12050107 -2145.12248139 Force two-norm initial, final = 96.4924 0.192806 Force max component initial, final = 47.1133 0.0236566 Final line search alpha, max atom move = 1 0.0236566 Iterations, force evaluations = 118 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87851 | 0.87851 | 0.87851 | 0.0 | 97.27 Neigh | 0.010513 | 0.010513 | 0.010513 | 0.0 | 1.16 Comm | 0.01021 | 0.01021 | 0.01021 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003912 | | | 0.43 Nlocal: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7382 ave 7382 max 7382 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: 198452 ave 198452 max 198452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198452 Ave neighs/atom = 380.176 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 : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.428 | 5.428 | 5.428 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -2145.1225 0 -2145.1225 -12999.419 6233.69 126 0 -2145.4845 0 -2145.4845 605.37621 6182.393 Loop time of 0.0359931 on 1 procs for 8 steps with 522 atoms 83.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2145.12248139 -2145.48382051 -2145.48451185 Force two-norm initial, final = 102.802 0.428052 Force max component initial, final = 95.3182 0.0687903 Final line search alpha, max atom move = 0.00024649 1.69561e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.034649 | 0.034649 | 0.034649 | 0.0 | 96.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038195 | 0.00038195 | 0.00038195 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009623 | | | 2.67 Nlocal: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7359 ave 7359 max 7359 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: 198468 ave 198468 max 198468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198468 Ave neighs/atom = 380.207 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 = 2 19 2 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) = 5.566 | 5.566 | 5.566 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2145.4845 0 -2145.4845 605.37621 Loop time of 1.90735e-06 on 1 procs for 0 steps with 522 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: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7420 ave 7420 max 7420 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: 201460 ave 201460 max 201460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201460 Ave neighs/atom = 385.939 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) = 5.566 | 5.566 | 5.566 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 -2145.4845 -2145.4845 9.5035172 93.231686 6.9776424 605.37621 605.37621 -17.805904 1840.6901 -6.7555851 2.3416033 613.64733 Loop time of 1.19209e-06 on 1 procs for 0 steps with 522 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: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7420 ave 7420 max 7420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100730 ave 100730 max 100730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201460 ave 201460 max 201460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201460 Ave neighs/atom = 385.939 Neighbor list builds = 0 Dangerous builds = 0 522 -2145.48451184825 eV 2.34160333968695 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01