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 = 3.65836 3.65836 3.65836 Created orthogonal box = (0 -50.2979 0) to (13.6883 50.2979 8.96113) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.86643 5.58824 5.97408 Created 507 atoms create_atoms CPU = 0.000383139 secs 507 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.86643 5.58824 5.97408 Created 507 atoms create_atoms CPU = 0.000258923 secs 507 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 22 atoms, new total = 992 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3936.8072 0 -3936.8072 -2857.16 613 0 -3993.8749 0 -3993.8749 -70868.161 Loop time of 4.22637 on 1 procs for 613 steps with 992 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3936.80715086 -3993.87147044 -3993.87493197 Force two-norm initial, final = 10.4113 0.200579 Force max component initial, final = 2.09895 0.0660595 Final line search alpha, max atom move = 0.945104 0.0624331 Iterations, force evaluations = 613 1205 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1015 | 4.1015 | 4.1015 | 0.0 | 97.05 Neigh | 0.05245 | 0.05245 | 0.05245 | 0.0 | 1.24 Comm | 0.042857 | 0.042857 | 0.042857 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02954 | | | 0.70 Nlocal: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5496 ave 5496 max 5496 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: 147576 ave 147576 max 147576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147576 Ave neighs/atom = 148.766 Neighbor list builds = 11 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 : 613 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.046 | 5.046 | 5.046 Mbytes Step Temp E_pair E_mol TotEng Press Volume 613 0 -3993.8749 0 -3993.8749 -70868.161 12339.375 692 0 -4030.6625 0 -4030.6625 -10699.163 11826.002 Loop time of 0.298934 on 1 procs for 79 steps with 992 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 = -3993.87493197 -4030.65955782 -4030.66254763 Force two-norm initial, final = 1065.86 6.34162 Force max component initial, final = 1064.23 4.7375 Final line search alpha, max atom move = 0.000348639 0.00165168 Iterations, force evaluations = 79 84 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28548 | 0.28548 | 0.28548 | 0.0 | 95.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0027411 | 0.0027411 | 0.0027411 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01071 | | | 3.58 Nlocal: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5491 ave 5491 max 5491 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: 147584 ave 147584 max 147584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147584 Ave neighs/atom = 148.774 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.183 | 5.183 | 5.183 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4030.6625 0 -4030.6625 -10699.163 Loop time of 1.90735e-06 on 1 procs for 0 steps with 992 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: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 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: 158130 ave 158130 max 158130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158130 Ave neighs/atom = 159.405 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) = 5.183 | 5.183 | 5.183 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 -4030.6625 -4030.6625 12.772745 100.59572 9.2039488 -10699.163 -10699.163 598.90045 -32545.724 -150.66409 2.2546014 2937.5113 Loop time of 9.53674e-07 on 1 procs for 0 steps with 992 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: 992 ave 992 max 992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5639 ave 5639 max 5639 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79065 ave 79065 max 79065 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158130 ave 158130 max 158130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158130 Ave neighs/atom = 159.405 Neighbor list builds = 0 Dangerous builds = 0 992 -4030.66254762697 eV 2.25460139799468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04