LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.04527 4.04527 4.04527 Created orthogonal box = (0 -43.7603 0) to (14.5854 43.7603 4.04527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.60978 5.60978 4.04527 Created 158 atoms create_atoms CPU = 0.000213861 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.60978 5.60978 4.04527 Created 158 atoms create_atoms CPU = 8.2016e-05 secs 158 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 19 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 306 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.474 | 4.474 | 4.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1037.0887 0 -1037.0887 -3704.189 258 0 -1040.0951 0 -1040.0951 -9303.3103 Loop time of 0.798841 on 1 procs for 258 steps with 306 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1037.08869554 -1040.0951215 -1040.0951215 Force two-norm initial, final = 4.12224 7.4118e-09 Force max component initial, final = 1.44005 1.33602e-09 Final line search alpha, max atom move = 1 1.33602e-09 Iterations, force evaluations = 258 509 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.77795 | 0.77795 | 0.77795 | 0.0 | 97.38 Neigh | 0.0017111 | 0.0017111 | 0.0017111 | 0.0 | 0.21 Comm | 0.01426 | 0.01426 | 0.01426 | 0.0 | 1.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004924 | | | 0.62 Nlocal: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836 ave 4836 max 4836 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: 64496 ave 64496 max 64496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64496 Ave neighs/atom = 210.771 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 : 258 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.475 | 4.475 | 4.475 Mbytes Step Temp E_pair E_mol TotEng Press Volume 258 0 -1040.0951 0 -1040.0951 -9303.3103 5163.8955 1258 0 -1040.2283 0 -1040.2283 -2048.848 5116.9318 Loop time of 3.20122 on 1 procs for 1000 steps with 306 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = max iterations Energy initial, next-to-last, final = -1040.0951215 -1040.22832817 -1040.22832817 Force two-norm initial, final = 37.8186 0.00368728 Force max component initial, final = 30.6202 0.0033704 Final line search alpha, max atom move = 1 0.0033704 Iterations, force evaluations = 1000 1994 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0029 | 3.0029 | 3.0029 | 0.0 | 93.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.05116 | 0.05116 | 0.05116 | 0.0 | 1.60 Output | 2.9087e-05 | 2.9087e-05 | 2.9087e-05 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1471 | | | 4.60 Nlocal: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836 ave 4836 max 4836 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: 63640 ave 63640 max 63640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63640 Ave neighs/atom = 207.974 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 4.613 | 4.613 | 4.613 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1040.2283 0 -1040.2283 -2048.848 Loop time of 2.14577e-06 on 1 procs for 0 steps with 306 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: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836 ave 4836 max 4836 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: 65160 ave 65160 max 65160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65160 Ave neighs/atom = 212.941 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.613 | 4.613 | 4.613 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 -1040.2283 -1040.2283 14.554007 87.520671 4.0171348 -2048.848 -2048.848 -0.39100235 -6145.1051 -1.047975 2.575078 202.63051 Loop time of 9.53674e-07 on 1 procs for 0 steps with 306 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: 306 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836 ave 4836 max 4836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32580 ave 32580 max 32580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 65160 ave 65160 max 65160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65160 Ave neighs/atom = 212.941 Neighbor list builds = 0 Dangerous builds = 0 306 -1040.2283281718 eV 2.57507800804035 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04