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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -54.4062 0) to (22.21 54.4062 7.69376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.33039 4.71493 5.12917 Created 602 atoms create_atoms CPU = 0.000394106 secs 602 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.33039 4.71493 5.12917 Created 602 atoms create_atoms CPU = 0.000270844 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1188 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.346 | 6.346 | 6.346 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7796.6282 0 -7796.6282 22183.293 755 0 -7999.2331 0 -7999.2331 -15498.16 Loop time of 17.0671 on 1 procs for 755 steps with 1188 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 = -7796.628182 -7999.22517427 -7999.23311615 Force two-norm initial, final = 283.987 0.558178 Force max component initial, final = 93.175 0.103545 Final line search alpha, max atom move = 0.535588 0.0554573 Iterations, force evaluations = 755 1493 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.728 | 16.728 | 16.728 | 0.0 | 98.01 Neigh | 0.1987 | 0.1987 | 0.1987 | 0.0 | 1.16 Comm | 0.097668 | 0.097668 | 0.097668 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04295 | | | 0.25 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10526 ave 10526 max 10526 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: 480006 ave 480006 max 480006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480006 Ave neighs/atom = 404.045 Neighbor list builds = 16 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 : 755 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.347 | 6.347 | 6.347 Mbytes Step Temp E_pair E_mol TotEng Press Volume 755 0 -7999.2331 0 -7999.2331 -15498.16 18593.652 767 0 -8005.6869 0 -8005.6869 35251.825 18263.155 Loop time of 0.131996 on 1 procs for 12 steps with 1188 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 = -7999.23311615 -8005.68474326 -8005.68690336 Force two-norm initial, final = 987.715 1.57835 Force max component initial, final = 752.225 0.201498 Final line search alpha, max atom move = 6.30128e-05 1.2697e-05 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12913 | 0.12913 | 0.12913 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075245 | 0.00075245 | 0.00075245 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002117 | | | 1.60 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10530 ave 10530 max 10530 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: 480510 ave 480510 max 480510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 480510 Ave neighs/atom = 404.47 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.489 | 6.489 | 6.489 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8005.6869 0 -8005.6869 35251.825 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1188 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: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10698 ave 10698 max 10698 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: 488802 ave 488802 max 488802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488802 Ave neighs/atom = 411.449 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) = 6.489 | 6.489 | 6.489 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 -8005.6869 -8005.6869 22.059104 108.81243 7.6086825 35251.825 35251.825 -17.556818 105767.98 5.0518522 2.536828 3510.0819 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1188 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 | | 2.146e-06 | | |100.00 Nlocal: 1188 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10698 ave 10698 max 10698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244401 ave 244401 max 244401 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 488802 ave 488802 max 488802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488802 Ave neighs/atom = 411.449 Neighbor list builds = 0 Dangerous builds = 0 1188 -8005.68690335829 eV 2.53682801293017 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17