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 = 3.6584 3.6584 3.6584 Created orthogonal box = (0 -62.5185 0) to (31.2574 62.5185 3.6584) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.71002 4.71002 3.6584 Created 586 atoms create_atoms CPU = 0.000246048 secs 586 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.71002 4.71002 3.6584 Created 586 atoms create_atoms CPU = 0.000109911 secs 586 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 = 8 30 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1162 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 = 8 30 1 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) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4479.2112 0 -4479.2112 6815.9697 135 0 -4512.8766 0 -4512.8766 -4396.5183 Loop time of 1.46304 on 1 procs for 135 steps with 1162 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4479.21117365 -4512.8725107 -4512.87655794 Force two-norm initial, final = 31.7993 0.205525 Force max component initial, final = 7.56742 0.0306435 Final line search alpha, max atom move = 1 0.0306435 Iterations, force evaluations = 135 255 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4354 | 1.4354 | 1.4354 | 0.0 | 98.11 Neigh | 0.00525 | 0.00525 | 0.00525 | 0.0 | 0.36 Comm | 0.015273 | 0.015273 | 0.015273 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007065 | | | 0.48 Nlocal: 1162 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10076 ave 10076 max 10076 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: 236728 ave 236728 max 236728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236728 Ave neighs/atom = 203.725 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 : 135 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 135 0 -4512.8766 0 -4512.8766 -4396.5183 14298.251 165 0 -4517.8248 0 -4517.8248 -7793.0767 14315.658 Loop time of 0.162175 on 1 procs for 30 steps with 1162 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4512.87655794 -4517.82268257 -4517.82480738 Force two-norm initial, final = 255.096 3.13933 Force max component initial, final = 218.18 1.36487 Final line search alpha, max atom move = 0.000353161 0.000482021 Iterations, force evaluations = 30 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15559 | 0.15559 | 0.15559 | 0.0 | 95.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015759 | 0.0015759 | 0.0015759 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005007 | | | 3.09 Nlocal: 1162 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10074 ave 10074 max 10074 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: 238332 ave 238332 max 238332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238332 Ave neighs/atom = 205.105 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 = 8 30 1 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) = 5.612 | 5.612 | 5.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4517.8248 0 -4517.8248 -7793.0767 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1162 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: 1162 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10189 ave 10189 max 10189 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: 240600 ave 240600 max 240600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240600 Ave neighs/atom = 207.057 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) = 5.612 | 5.612 | 5.612 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 -4517.8248 -4517.8248 30.450723 125.03695 3.7598917 -7793.0767 -7793.0767 148.81146 -23395.561 -132.48023 2.2546148 620.52656 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1162 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: 1162 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10189 ave 10189 max 10189 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120300 ave 120300 max 120300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240600 ave 240600 max 240600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240600 Ave neighs/atom = 207.057 Neighbor list builds = 0 Dangerous builds = 0 1162 -4517.82480738391 eV 2.25461480544534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01