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 -36.0771 0) to (18.0368 36.0771 3.60735) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.05029 5.05029 3.60735 Created 202 atoms create_atoms CPU = 0.000507116 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.05029 5.05029 3.60735 Created 202 atoms create_atoms CPU = 0.000207901 secs 202 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 = 3 12 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 401 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 = 3 12 1 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) = 5.347 | 5.347 | 5.347 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1345.4218 0 -1345.4218 47982.964 91 0 -1408.3826 0 -1408.3826 9226.1528 Loop time of 1.45761 on 1 procs for 91 steps with 401 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 = -1345.42175449 -1408.38134169 -1408.3826345 Force two-norm initial, final = 59.7228 0.145482 Force max component initial, final = 15.0649 0.023488 Final line search alpha, max atom move = 1 0.023488 Iterations, force evaluations = 91 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4135 | 1.4135 | 1.4135 | 0.0 | 96.98 Neigh | 0.028664 | 0.028664 | 0.028664 | 0.0 | 1.97 Comm | 0.012225 | 0.012225 | 0.012225 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00319 | | | 0.22 Nlocal: 401 ave 401 max 401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9663 ave 9663 max 9663 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: 254402 ave 254402 max 254402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254402 Ave neighs/atom = 634.419 Neighbor list builds = 3 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.348 | 5.348 | 5.348 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -1408.3826 0 -1408.3826 9226.1528 4694.7152 105 0 -1408.6013 0 -1408.6013 1135.0518 4721.4682 Loop time of 0.197856 on 1 procs for 14 steps with 401 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 = -1408.3826345 -1408.60116833 -1408.6012807 Force two-norm initial, final = 38.7364 1.45412 Force max component initial, final = 38.7353 1.1796 Final line search alpha, max atom move = 0.0169215 0.0199606 Iterations, force evaluations = 14 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19225 | 0.19225 | 0.19225 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014961 | 0.0014961 | 0.0014961 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004111 | | | 2.08 Nlocal: 401 ave 401 max 401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9703 ave 9703 max 9703 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: 254510 ave 254510 max 254510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254510 Ave neighs/atom = 634.688 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 = 3 12 1 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) = 5.486 | 5.486 | 5.486 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1408.6013 0 -1408.6013 1135.0518 Loop time of 9.53674e-07 on 1 procs for 0 steps with 401 atoms 209.7% 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 | | 9.537e-07 | | |100.00 Nlocal: 401 ave 401 max 401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719 ave 9719 max 9719 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: 254648 ave 254648 max 254648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254648 Ave neighs/atom = 635.032 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) = 5.486 | 5.486 | 5.486 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 -1408.6013 -1408.6013 17.939952 72.154269 3.6474872 1135.0518 1135.0518 398.13587 2735.3146 271.70498 2.2702433 135.87654 Loop time of 1.90735e-06 on 1 procs for 0 steps with 401 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: 401 ave 401 max 401 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9719 ave 9719 max 9719 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127324 ave 127324 max 127324 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 254648 ave 254648 max 254648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254648 Ave neighs/atom = 635.032 Neighbor list builds = 0 Dangerous builds = 0 401 -1408.60128069603 eV 2.2702433164326 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01