LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.64065 3.64065 3.64065 Created orthogonal box = (0 -56.8723 0) to (28.4344 56.8723 3.64065) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.12751 5.12751 3.64065 Created 489 atoms create_atoms CPU = 0.000457048 secs 489 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.12751 5.12751 3.64065 Created 489 atoms create_atoms CPU = 0.000309944 secs 489 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1146) 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 1 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 972 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3158.8284 0 -3158.8284 4862.4288 67 0 -3177.5726 0 -3177.5726 -1428.9965 Loop time of 2.24138 on 1 procs for 67 steps with 972 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3158.82836334 -3177.56982199 -3177.57257418 Force two-norm initial, final = 14.1165 0.136074 Force max component initial, final = 4.28893 0.0102865 Final line search alpha, max atom move = 1 0.0102865 Iterations, force evaluations = 67 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2314 | 2.2314 | 2.2314 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071008 | 0.0071008 | 0.0071008 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002836 | | | 0.13 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10428 ave 10428 max 10428 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: 308520 ave 308520 max 308520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 308520 Ave neighs/atom = 317.407 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -3177.5726 0 -3177.5726 -1428.9965 11774.785 70 0 -3177.5923 0 -3177.5923 320.00336 11760.782 Loop time of 0.107024 on 1 procs for 3 steps with 972 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 = -3177.57257418 -3177.59168052 -3177.59226385 Force two-norm initial, final = 18.9721 2.6343 Force max component initial, final = 18.8235 2.62537 Final line search alpha, max atom move = 0.000239637 0.000629136 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10599 | 0.10599 | 0.10599 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002954 | 0.0002954 | 0.0002954 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007365 | | | 0.69 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10440 ave 10440 max 10440 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: 309496 ave 309496 max 309496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309496 Ave neighs/atom = 318.412 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.97 | 5.97 | 5.97 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3177.5923 0 -3177.5923 320.00336 Loop time of 9.53674e-07 on 1 procs for 0 steps with 972 atoms 209.7% 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: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10416 ave 10416 max 10416 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: 309484 ave 309484 max 309484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309484 Ave neighs/atom = 318.399 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) = 5.97 | 5.97 | 5.97 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 -3177.5923 -3177.5923 28.458753 113.7447 3.6331988 320.00336 320.00336 357.96176 624.7346 -22.686287 2.2889851 161.47029 Loop time of 2.14577e-06 on 1 procs for 0 steps with 972 atoms 93.2% 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 | | 2.146e-06 | | |100.00 Nlocal: 972 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10416 ave 10416 max 10416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 154742 ave 154742 max 154742 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 309484 ave 309484 max 309484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 309484 Ave neighs/atom = 318.399 Neighbor list builds = 0 Dangerous builds = 0 972 -3177.59226384731 eV 2.28898507503814 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02