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 = 3.51962 3.51962 3.51962 Created orthogonal box = (0 -63.7465 0) to (22.5366 63.7465 4.97749) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.04639 5.44148 4.97749 Created 658 atoms create_atoms CPU = 0.000611067 secs 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.04639 5.44148 4.97749 Created 658 atoms create_atoms CPU = 0.000454903 secs 658 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 6 34 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 7.56501 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.507 | 5.507 | 5.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5762.1749 0 -5762.1749 6348.7143 30 0 -5792.54 0 -5792.54 -6259.9734 Loop time of 0.22372 on 1 procs for 30 steps with 1304 atoms 102.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5762.17493065 -5792.53434287 -5792.54003755 Force two-norm initial, final = 44.4171 0.260713 Force max component initial, final = 11.9287 0.029945 Final line search alpha, max atom move = 1 0.029945 Iterations, force evaluations = 30 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21473 | 0.21473 | 0.21473 | 0.0 | 95.98 Neigh | 0.0043359 | 0.0043359 | 0.0043359 | 0.0 | 1.94 Comm | 0.0027628 | 0.0027628 | 0.0027628 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001887 | | | 0.84 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416 ave 8416 max 8416 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: 225728 ave 225728 max 225728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225728 Ave neighs/atom = 173.104 Neighbor list builds = 1 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) = 5.508 | 5.508 | 5.508 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -5792.54 0 -5792.54 -6259.9734 14301.597 33 0 -5792.6056 0 -5792.6056 -2544.913 14271.354 Loop time of 0.0220232 on 1 procs for 3 steps with 1304 atoms 90.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5792.54003755 -5792.60483748 -5792.60562813 Force two-norm initial, final = 61.1309 0.270811 Force max component initial, final = 58.4116 0.0294217 Final line search alpha, max atom move = 0.000138248 4.06749e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.02105 | 0.02105 | 0.02105 | 0.0 | 95.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024748 | 0.00024748 | 0.00024748 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007257 | | | 3.30 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416 ave 8416 max 8416 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: 225936 ave 225936 max 225936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225936 Ave neighs/atom = 173.264 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 = 7.56501 ghost atom cutoff = 7.56501 binsize = 3.7825, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.56501 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) = 5.645 | 5.645 | 5.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5792.6056 0 -5792.6056 -2544.913 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1304 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 | | 1.192e-06 | | |100.00 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416 ave 8416 max 8416 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: 226040 ave 226040 max 226040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226040 Ave neighs/atom = 173.344 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) = 5.645 | 5.645 | 5.645 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 -5792.6056 -5792.6056 22.534684 127.49304 4.9673783 -2544.913 -2544.913 -2.8037799 -7632.6158 0.68070743 2.3025029 407.95805 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8416 ave 8416 max 8416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113020 ave 113020 max 113020 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226040 ave 226040 max 226040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226040 Ave neighs/atom = 173.344 Neighbor list builds = 0 Dangerous builds = 0 1304 -5792.60562813439 eV 2.30250287501921 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00