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 = 3.99461 3.99461 3.99461 Created orthogonal box = (0 -52.3928 0) to (37.0445 52.3928 5.64923) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.892 6.70089 5.64923 Created 693 atoms create_atoms CPU = 0.000620127 secs 693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.892 6.70089 5.64923 Created 693 atoms create_atoms CPU = 0.000479937 secs 693 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 10 28 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 7.6001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1368 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4462.3089 0 -4462.3089 3043.6405 55 0 -4484.9812 0 -4484.9812 -2324.5945 Loop time of 0.896156 on 1 procs for 55 steps with 1368 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4462.30889738 -4484.97731558 -4484.98124494 Force two-norm initial, final = 21.684 0.14166 Force max component initial, final = 4.32715 0.021016 Final line search alpha, max atom move = 1 0.021016 Iterations, force evaluations = 55 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88467 | 0.88467 | 0.88467 | 0.0 | 98.72 Neigh | 0.0038068 | 0.0038068 | 0.0038068 | 0.0 | 0.42 Comm | 0.0044732 | 0.0044732 | 0.0044732 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003211 | | | 0.36 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6928 ave 6928 max 6928 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: 179472 ave 179472 max 179472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179472 Ave neighs/atom = 131.193 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -4484.9812 0 -4484.9812 -2324.5945 21928.765 57 0 -4484.9996 0 -4484.9996 -1448.1089 21880.224 Loop time of 0.0417199 on 1 procs for 2 steps with 1368 atoms 95.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4484.98124494 -4484.99741776 -4484.99958829 Force two-norm initial, final = 21.6977 1.4805 Force max component initial, final = 19.2482 1.44599 Final line search alpha, max atom move = 0.000142851 0.000206561 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04107 | 0.04107 | 0.04107 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016212 | 0.00016212 | 0.00016212 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004878 | | | 1.17 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6911 ave 6911 max 6911 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: 179588 ave 179588 max 179588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179588 Ave neighs/atom = 131.278 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4484.9996 0 -4484.9996 -1448.1089 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6919 ave 6919 max 6919 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: 179642 ave 179642 max 179642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179642 Ave neighs/atom = 131.317 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) = 5.216 | 5.216 | 5.216 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 -4484.9996 -4484.9996 37.021105 104.78558 5.6402823 -1448.1089 -1448.1089 105.8154 -4429.4443 -20.697766 2.6125613 1242.1857 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6919 ave 6919 max 6919 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89821 ave 89821 max 89821 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179642 ave 179642 max 179642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179642 Ave neighs/atom = 131.317 Neighbor list builds = 0 Dangerous builds = 0 1368 -4484.99958828784 eV 2.61256132997899 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01