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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -38.0853 0) to (31.0939 38.0853 7.69376) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.44199 4.40406 5.12917 Created 590 atoms create_atoms CPU = 0.000871181 secs 590 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.44199 4.40406 5.12917 Created 590 atoms create_atoms CPU = 0.000653982 secs 590 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 14 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1179 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 14 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.307 | 6.307 | 6.307 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7149.2713 0 -7149.2713 139232.57 300 0 -7900.5315 0 -7900.5315 32814.352 Loop time of 14.6108 on 1 procs for 300 steps with 1179 atoms 69.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7149.27131975 -7900.52444652 -7900.53154345 Force two-norm initial, final = 719.952 0.524276 Force max component initial, final = 116.786 0.184314 Final line search alpha, max atom move = 0.510904 0.094167 Iterations, force evaluations = 300 564 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.222 | 14.222 | 14.222 | 0.0 | 97.34 Neigh | 0.26437 | 0.26437 | 0.26437 | 0.0 | 1.81 Comm | 0.087598 | 0.087598 | 0.087598 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03677 | | | 0.25 Nlocal: 1179 ave 1179 max 1179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9517 ave 9517 max 9517 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: 488900 ave 488900 max 488900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 488900 Ave neighs/atom = 414.673 Neighbor list builds = 11 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 : 300 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.307 | 6.307 | 6.307 Mbytes Step Temp E_pair E_mol TotEng Press Volume 300 0 -7900.5315 0 -7900.5315 32814.352 18222.23 314 0 -7903.9965 0 -7903.9965 15504.406 18327.306 Loop time of 0.514129 on 1 procs for 14 steps with 1179 atoms 64.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7900.53154345 -7903.99551366 -7903.99647245 Force two-norm initial, final = 533.869 2.98486 Force max component initial, final = 514.578 0.782608 Final line search alpha, max atom move = 0.000116248 9.09766e-05 Iterations, force evaluations = 14 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49486 | 0.49486 | 0.49486 | 0.0 | 96.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014534 | 0.0014534 | 0.0014534 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01781 | | | 3.46 Nlocal: 1179 ave 1179 max 1179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9515 ave 9515 max 9515 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: 489014 ave 489014 max 489014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489014 Ave neighs/atom = 414.77 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 6 14 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 6.442 | 6.442 | 6.442 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7903.9965 0 -7903.9965 15504.406 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1179 atoms 314.6% 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: 1179 ave 1179 max 1179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9536 ave 9536 max 9536 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: 486284 ave 486284 max 486284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486284 Ave neighs/atom = 412.455 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) = 6.442 | 6.442 | 6.442 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 -7903.9965 -7903.9965 31.459808 76.170582 7.6481306 15504.406 15504.406 11.85015 46433.358 68.010019 2.4839418 8066.7023 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1179 atoms 314.6% 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: 1179 ave 1179 max 1179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9536 ave 9536 max 9536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 243142 ave 243142 max 243142 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 486284 ave 486284 max 486284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 486284 Ave neighs/atom = 412.455 Neighbor list builds = 0 Dangerous builds = 0 1179 -7903.99647245308 eV 2.4839417831743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15