LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -63.7222 0) to (36.7879 63.7222 6.24812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65968 5.71833 6.24812 Created 1249 atoms create_atoms CPU = 0.00203204 secs 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65968 5.71833 6.24812 Created 1249 atoms create_atoms CPU = 0.00145102 secs 1249 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 21 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2472 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 14.82 | 14.82 | 14.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8629.2309 0 -8629.2309 1345.7564 39 0 -8694.4843 0 -8694.4843 -8751.1093 Loop time of 4.00399 on 1 procs for 39 steps with 2472 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8629.23087276 -8694.4765212 -8694.48433204 Force two-norm initial, final = 48.8768 0.361323 Force max component initial, final = 9.59879 0.032808 Final line search alpha, max atom move = 1 0.032808 Iterations, force evaluations = 39 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9351 | 3.9351 | 3.9351 | 0.0 | 98.28 Neigh | 0.050383 | 0.050383 | 0.050383 | 0.0 | 1.26 Comm | 0.012369 | 0.012369 | 0.012369 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006159 | | | 0.15 Nlocal: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20311 ave 20311 max 20311 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: 1.54474e+06 ave 1.54474e+06 max 1.54474e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1544738 Ave neighs/atom = 624.894 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 14.82 | 14.82 | 14.82 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -8694.4843 0 -8694.4843 -8751.1093 29293.752 42 0 -8694.6059 0 -8694.6059 -4956.9372 29212.214 Loop time of 0.334322 on 1 procs for 3 steps with 2472 atoms 91.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8694.48433204 -8694.60588057 -8694.60588861 Force two-norm initial, final = 122.805 0.445984 Force max component initial, final = 95.2253 0.227674 Final line search alpha, max atom move = 0.00208486 0.00047467 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33047 | 0.33047 | 0.33047 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001014 | 0.001014 | 0.001014 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002841 | | | 0.85 Nlocal: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20363 ave 20363 max 20363 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: 1.54613e+06 ave 1.54613e+06 max 1.54613e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1546134 Ave neighs/atom = 625.459 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 14.33 | 14.33 | 14.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8694.6059 0 -8694.6059 -4956.9372 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2472 atoms 139.8% 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: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20363 ave 20363 max 20363 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: 1.54717e+06 ave 1.54717e+06 max 1.54717e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1547174 Ave neighs/atom = 625.879 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) = 14.33 | 14.33 | 14.33 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 -8694.6059 -8694.6059 36.741153 127.44432 6.2386584 -4956.9372 -4956.9372 12.471185 -14878.221 -5.0622375 2.3372282 1038.712 Loop time of 1.90735e-06 on 1 procs for 0 steps with 2472 atoms 157.3% 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: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 20363 ave 20363 max 20363 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 773587 ave 773587 max 773587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.54717e+06 ave 1.54717e+06 max 1.54717e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1547174 Ave neighs/atom = 625.879 Neighbor list builds = 0 Dangerous builds = 0 2472 -8694.6058886109 eV 2.33722824209686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05