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 = 3.63366 3.63366 3.63366 Created orthogonal box = (0 -41.1138 0) to (17.8012 41.1138 6.29369) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.93375 5.13877 6.29369 Created 396 atoms create_atoms CPU = 0.000296116 secs 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.93375 5.13877 6.29369 Created 396 atoms create_atoms CPU = 0.000166893 secs 396 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 29 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 752 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3059.1085 0 -3059.1085 -5313.0225 25 0 -3073.2723 0 -3073.2723 -19852.718 Loop time of 5.95463 on 1 procs for 25 steps with 752 atoms 69.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3059.10854864 -3073.26946457 -3073.27229621 Force two-norm initial, final = 9.49712 0.153809 Force max component initial, final = 1.90052 0.0140207 Final line search alpha, max atom move = 1 0.0140207 Iterations, force evaluations = 25 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.9529 | 5.9529 | 5.9529 | 0.0 | 99.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087261 | 0.00087261 | 0.00087261 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008075 | | | 0.01 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3400 ave 3400 max 3400 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: 40272 ave 40272 max 40272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40272 Ave neighs/atom = 53.5532 Neighbor list builds = 0 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -3073.2723 0 -3073.2723 -19852.718 9212.4092 35 0 -3073.7461 0 -3073.7461 -8516.3808 9131.1784 Loop time of 1.51623 on 1 procs for 10 steps with 752 atoms 86.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3073.27229621 -3073.74603916 -3073.74605028 Force two-norm initial, final = 114.017 0.357665 Force max component initial, final = 106.883 0.142245 Final line search alpha, max atom move = 0.00318842 0.000453536 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5149 | 1.5149 | 1.5149 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025749 | 0.00025749 | 0.00025749 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001045 | | | 0.07 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3400 ave 3400 max 3400 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: 42280 ave 42280 max 42280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42280 Ave neighs/atom = 56.2234 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 7 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.68 | 4.68 | 4.68 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3073.7461 0 -3073.7461 -8516.3808 Loop time of 9.53674e-07 on 1 procs for 0 steps with 752 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: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3400 ave 3400 max 3400 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: 42720 ave 42720 max 42720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42720 Ave neighs/atom = 56.8085 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) = 4.68 | 4.68 | 4.68 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 -3073.7461 -3073.7461 17.646935 82.227654 6.2927378 -8516.3808 -8516.3808 24.492074 -25598.589 24.954801 2.4351502 385.43643 Loop time of 1.90735e-06 on 1 procs for 0 steps with 752 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 | | 1.907e-06 | | |100.00 Nlocal: 752 ave 752 max 752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3400 ave 3400 max 3400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21360 ave 21360 max 21360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42720 ave 42720 max 42720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42720 Ave neighs/atom = 56.8085 Neighbor list builds = 0 Dangerous builds = 0 752 -1919.24931551979 eV 2.43515016464622 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08