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 -49.6925 0) to (20.2857 49.6925 7.02717) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.86857 4.30643 4.68478 Created 602 atoms create_atoms CPU = 0.000394106 secs 602 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.86857 4.30643 4.68478 Created 602 atoms create_atoms CPU = 0.000265837 secs 602 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 = 4 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1200 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 = 4 20 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) = 6.341 | 6.341 | 6.341 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4772.9776 0 -4772.9776 33236.472 107 0 -4933.3708 0 -4933.3708 5095.2555 Loop time of 1.81484 on 1 procs for 107 steps with 1200 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 = -4772.97762302 -4933.36644191 -4933.37082568 Force two-norm initial, final = 171.745 0.291012 Force max component initial, final = 30.4749 0.0364445 Final line search alpha, max atom move = 1 0.0364445 Iterations, force evaluations = 107 203 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7827 | 1.7827 | 1.7827 | 0.0 | 98.23 Neigh | 0.013018 | 0.013018 | 0.013018 | 0.0 | 0.72 Comm | 0.013046 | 0.013046 | 0.013046 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00612 | | | 0.34 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10424 ave 10424 max 10424 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: 463376 ave 463376 max 463376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463376 Ave neighs/atom = 386.147 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 : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.342 | 6.342 | 6.342 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -4933.3708 0 -4933.3708 5095.2555 14167.423 110 0 -4933.4591 0 -4933.4591 1219.8503 14199.493 Loop time of 0.049782 on 1 procs for 3 steps with 1200 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4933.37082568 -4933.45677076 -4933.45907999 Force two-norm initial, final = 76.9892 1.74062 Force max component initial, final = 76.4119 1.43571 Final line search alpha, max atom move = 0.000104963 0.000150697 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.048601 | 0.048601 | 0.048601 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031018 | 0.00031018 | 0.00031018 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008709 | | | 1.75 Nlocal: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10468 ave 10468 max 10468 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: 464544 ave 464544 max 464544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 464544 Ave neighs/atom = 387.12 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 = 4 20 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) = 6.479 | 6.479 | 6.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4933.4591 0 -4933.4591 1219.8503 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1200 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: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10436 ave 10436 max 10436 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: 463156 ave 463156 max 463156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463156 Ave neighs/atom = 385.963 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) = 6.479 | 6.479 | 6.479 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 -4933.4591 -4933.4591 20.333493 99.384932 7.0265202 1219.8503 1219.8503 -104.43074 3925.9629 -161.98114 2.304327 1003.3495 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1200 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: 1200 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10436 ave 10436 max 10436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231578 ave 231578 max 231578 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463156 ave 463156 max 463156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463156 Ave neighs/atom = 385.963 Neighbor list builds = 0 Dangerous builds = 0 1200 -4933.4590799878 eV 2.30432700617712 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02