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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -36.9261 0) to (45.2207 36.9261 8.62325) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.75536 5.37055 5.74883 Created 1323 atoms create_atoms CPU = 0.00133991 secs 1323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.75536 5.37055 5.74883 Created 1323 atoms create_atoms CPU = 0.00112796 secs 1323 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 16 26 3 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 60 atoms, new total = 2586 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.539 | 5.539 | 5.539 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14805.98 0 -14805.98 -9440.8918 329 0 -14955.458 0 -14955.458 -13699.806 Loop time of 215.096 on 1 procs for 329 steps with 2586 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14805.980071 -14955.4452643 -14955.4581182 Force two-norm initial, final = 37.2034 0.398133 Force max component initial, final = 5.10683 0.0730781 Final line search alpha, max atom move = 0.54795 0.0400431 Iterations, force evaluations = 329 599 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 214.94 | 214.94 | 214.94 | 0.0 | 99.93 Neigh | 0.070261 | 0.070261 | 0.070261 | 0.0 | 0.03 Comm | 0.036972 | 0.036972 | 0.036972 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04505 | | | 0.02 Nlocal: 2586 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6458 ave 6458 max 6458 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: 180866 ave 180866 max 180866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180866 Ave neighs/atom = 69.9404 Neighbor list builds = 10 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 : 329 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.539 | 5.539 | 5.539 Mbytes Step Temp E_pair E_mol TotEng Press Volume 329 0 -14955.458 0 -14955.458 -13699.806 28798.571 331 0 -14955.537 0 -14955.537 -9664.9169 28745.321 Loop time of 1.73445 on 1 procs for 2 steps with 2586 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14955.4581182 -14955.5364953 -14955.5372289 Force two-norm initial, final = 120.581 0.411117 Force max component initial, final = 86.0008 0.0738625 Final line search alpha, max atom move = 0.000166538 1.2301e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7333 | 1.7333 | 1.7333 | 0.0 | 99.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020289 | 0.00020289 | 0.00020289 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009384 | | | 0.05 Nlocal: 2586 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6457 ave 6457 max 6457 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: 180716 ave 180716 max 180716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180716 Ave neighs/atom = 69.8824 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 5.295 | 5.295 | 5.295 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14955.537 0 -14955.537 -9664.9169 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2586 atoms 251.7% 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: 2586 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6473 ave 6473 max 6473 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: 180932 ave 180932 max 180932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180932 Ave neighs/atom = 69.966 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) = 5.295 | 5.295 | 5.295 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 -14955.537 -14955.537 45.18505 73.852116 8.6140911 -9664.9169 -9664.9169 -2.3323458 -28991.324 -1.0946274 2.3354729 13821.649 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2586 atoms 167.8% 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 | | 1.192e-06 | | |100.00 Nlocal: 2586 ave 2586 max 2586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6473 ave 6473 max 6473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90466 ave 90466 max 90466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180932 ave 180932 max 180932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180932 Ave neighs/atom = 69.966 Neighbor list builds = 0 Dangerous builds = 0 2586 -6331.74069576688 eV 2.33547286450606 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:03:38