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 = 4.04526 4.04526 4.04526 Created orthogonal box = (0 -55.6172 0) to (15.136 55.6172 9.90882) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.48685 6.17924 6.60588 Created 508 atoms create_atoms CPU = 0.00026083 secs 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.48685 6.17924 6.60588 Created 508 atoms create_atoms CPU = 0.000240088 secs 508 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 27 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1000 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3385.6327 0 -3385.6327 2669.9838 57 0 -3401.7529 0 -3401.7529 -1903.8029 Loop time of 0.417051 on 1 procs for 57 steps with 1000 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3385.6326691 -3401.74997873 -3401.75289023 Force two-norm initial, final = 24.1123 0.116239 Force max component initial, final = 5.39863 0.0184189 Final line search alpha, max atom move = 1 0.0184189 Iterations, force evaluations = 57 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40692 | 0.40692 | 0.40692 | 0.0 | 97.57 Neigh | 0.003264 | 0.003264 | 0.003264 | 0.0 | 0.78 Comm | 0.0038481 | 0.0038481 | 0.0038481 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003018 | | | 0.72 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5636 ave 5636 max 5636 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: 141136 ave 141136 max 141136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141136 Ave neighs/atom = 141.136 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3401.7529 0 -3401.7529 -1903.8029 16682.894 59 0 -3401.7827 0 -3401.7827 97.387665 16640.54 Loop time of 0.0165589 on 1 procs for 2 steps with 1000 atoms 120.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3401.75289023 -3401.77940997 -3401.78271403 Force two-norm initial, final = 32.6214 2.67041 Force max component initial, final = 26.4197 2.44797 Final line search alpha, max atom move = 0.000102755 0.000251541 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015999 | 0.015999 | 0.015999 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001297 | 0.0001297 | 0.0001297 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004303 | | | 2.60 Nlocal: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5577 ave 5577 max 5577 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: 140896 ave 140896 max 140896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140896 Ave neighs/atom = 140.896 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 4 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.176 | 5.176 | 5.176 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3401.7827 0 -3401.7827 97.387665 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5577 ave 5577 max 5577 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: 140984 ave 140984 max 140984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140984 Ave neighs/atom = 140.984 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) = 5.176 | 5.176 | 5.176 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 -3401.7827 -3401.7827 15.12137 111.23435 9.8932127 97.387665 97.387665 235.46663 158.63843 -101.94207 2.5762853 497.8076 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1000 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: 1000 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5577 ave 5577 max 5577 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70492 ave 70492 max 70492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 140984 ave 140984 max 140984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140984 Ave neighs/atom = 140.984 Neighbor list builds = 0 Dangerous builds = 0 1000 -3401.78271402611 eV 2.57628533559878 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00