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 = 3.48714 3.48714 3.48714 Created orthogonal box = (0 -37.236 0) to (21.4962 37.236 6.03991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.65689 5.22562 6.03991 Created 458 atoms create_atoms CPU = 0.000251055 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.65689 5.22562 6.03991 Created 458 atoms create_atoms CPU = 0.000167847 secs 458 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 6 20 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 7.61876 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 6 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3941.1131 0 -3941.1131 17081.973 97 0 -3983.6255 0 -3983.6255 -9647.5615 Loop time of 1.72397 on 1 procs for 97 steps with 900 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 = -3941.11309636 -3983.62205056 -3983.6255276 Force two-norm initial, final = 60.5569 0.231814 Force max component initial, final = 16.8706 0.0319736 Final line search alpha, max atom move = 1 0.0319736 Iterations, force evaluations = 97 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6982 | 1.6982 | 1.6982 | 0.0 | 98.50 Neigh | 0.013955 | 0.013955 | 0.013955 | 0.0 | 0.81 Comm | 0.0074284 | 0.0074284 | 0.0074284 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004405 | | | 0.26 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5798 ave 5798 max 5798 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: 156548 ave 156548 max 156548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156548 Ave neighs/atom = 173.942 Neighbor list builds = 3 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 : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.008 | 5.008 | 5.008 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -3983.6255 0 -3983.6255 -9647.5615 9669.0818 99 0 -3983.6392 0 -3983.6392 -8001.2569 9659.8808 Loop time of 0.046397 on 1 procs for 2 steps with 900 atoms 86.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3983.6255276 -3983.63848839 -3983.63923599 Force two-norm initial, final = 24.1854 0.809016 Force max component initial, final = 24.0559 0.690657 Final line search alpha, max atom move = 0.000223241 0.000154183 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.045818 | 0.045818 | 0.045818 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014377 | 0.00014377 | 0.00014377 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004354 | | | 0.94 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5750 ave 5750 max 5750 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: 156648 ave 156648 max 156648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156648 Ave neighs/atom = 174.053 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 = 7.61876 ghost atom cutoff = 7.61876 binsize = 3.80938, bins = 6 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.61876 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) = 5.145 | 5.145 | 5.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3983.6392 0 -3983.6392 -8001.2569 Loop time of 1.19209e-06 on 1 procs for 0 steps with 900 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: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5767 ave 5767 max 5767 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: 156676 ave 156676 max 156676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156676 Ave neighs/atom = 174.084 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) = 5.145 | 5.145 | 5.145 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 -3983.6392 -3983.6392 21.499941 74.471997 6.0331135 -8001.2569 -8001.2569 -56.752007 -23832.596 -114.42263 2.2824472 612.17169 Loop time of 2.14577e-06 on 1 procs for 0 steps with 900 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 | | 2.146e-06 | | |100.00 Nlocal: 900 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5767 ave 5767 max 5767 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78338 ave 78338 max 78338 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156676 ave 156676 max 156676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156676 Ave neighs/atom = 174.084 Neighbor list builds = 0 Dangerous builds = 0 900 -3983.63923598549 eV 2.28244719183492 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01