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 = 3.59279 3.59279 3.59279 Created orthogonal box = (0 -46.9854 0) to (22.1474 46.9854 5.08097) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.66262 5.76969 5.08097 Created 464 atoms create_atoms CPU = 0.000387907 secs 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.66262 5.76969 5.08097 Created 464 atoms create_atoms CPU = 0.000272989 secs 464 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 = 6.98409 ghost atom cutoff = 6.98409 binsize = 3.49204, bins = 7 27 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 6.98409 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 904 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 = 6.98409 ghost atom cutoff = 6.98409 binsize = 3.49204, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.98409 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) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3142.617 0 -3142.617 7502.4089 30 0 -3161.9813 0 -3161.9813 -2792.6182 Loop time of 0.383271 on 1 procs for 30 steps with 904 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3142.61697869 -3161.97844475 -3161.98133455 Force two-norm initial, final = 38.3824 0.157167 Force max component initial, final = 8.2924 0.0158175 Final line search alpha, max atom move = 1 0.0158175 Iterations, force evaluations = 30 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37979 | 0.37979 | 0.37979 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020821 | 0.0020821 | 0.0020821 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001395 | | | 0.36 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5354 ave 5354 max 5354 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: 119488 ave 119488 max 119488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119488 Ave neighs/atom = 132.177 Neighbor list builds = 0 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -3161.9813 0 -3161.9813 -2792.6182 10574.56 32 0 -3161.9856 0 -3161.9856 -1632.8793 10565.339 Loop time of 0.0348749 on 1 procs for 2 steps with 904 atoms 114.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3161.98133455 -3161.98517515 -3161.98563091 Force two-norm initial, final = 12.4089 0.164307 Force max component initial, final = 10.1524 0.0339659 Final line search alpha, max atom move = 0.00055186 1.87444e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0342 | 0.0342 | 0.0342 | 0.0 | 98.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016212 | 0.00016212 | 0.00016212 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005128 | | | 1.47 Nlocal: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396 ave 5396 max 5396 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: 119632 ave 119632 max 119632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119632 Ave neighs/atom = 132.336 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 = 6.98409 ghost atom cutoff = 6.98409 binsize = 3.49204, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.98409 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3161.9856 0 -3161.9856 -1632.8793 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396 ave 5396 max 5396 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: 119664 ave 119664 max 119664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119664 Ave neighs/atom = 132.372 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) = 5.125 | 5.125 | 5.125 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 -3161.9856 -3161.9856 22.130191 93.970747 5.08049 -1632.8793 -1632.8793 -0.33023031 -4893.1573 -5.1502617 2.4011818 539.44635 Loop time of 9.53674e-07 on 1 procs for 0 steps with 904 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: 904 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5396 ave 5396 max 5396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59832 ave 59832 max 59832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119664 ave 119664 max 119664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119664 Ave neighs/atom = 132.372 Neighbor list builds = 0 Dangerous builds = 0 904 -3161.98563091318 eV 2.40118182952425 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00