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 = 2.85532 2.85532 2.85532 Created orthogonal box = (0 -39.2571 0) to (10.6836 39.2571 6.99409) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.57871 4.36158 4.66273 Created 254 atoms create_atoms CPU = 0.000184059 secs 254 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.57871 4.36158 4.66273 Created 254 atoms create_atoms CPU = 8.51154e-05 secs 254 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 500 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2037.4762 0 -2037.4762 5016.1584 36 0 -2049.8007 0 -2049.8007 -5060.7784 Loop time of 0.0861681 on 1 procs for 36 steps with 500 atoms 104.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2037.47618114 -2049.79946639 -2049.80074932 Force two-norm initial, final = 22.2984 0.135605 Force max component initial, final = 6.11719 0.0325495 Final line search alpha, max atom move = 1 0.0325495 Iterations, force evaluations = 36 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083769 | 0.083769 | 0.083769 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015416 | 0.0015416 | 0.0015416 | 0.0 | 1.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008571 | | | 0.99 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4321 ave 4321 max 4321 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: 82840 ave 82840 max 82840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82840 Ave neighs/atom = 165.68 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -2049.8007 0 -2049.8007 -5060.7784 5866.7638 39 0 -2049.8274 0 -2049.8274 -435.16781 5851.0463 Loop time of 0.0081172 on 1 procs for 3 steps with 500 atoms 123.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2049.80074932 -2049.82734116 -2049.82735639 Force two-norm initial, final = 27.9874 0.159259 Force max component initial, final = 20.4832 0.0416495 Final line search alpha, max atom move = 0.00323082 0.000134562 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.007674 | 0.007674 | 0.007674 | 0.0 | 94.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011349 | 0.00011349 | 0.00011349 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003297 | | | 4.06 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4078 ave 4078 max 4078 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: 82896 ave 82896 max 82896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82896 Ave neighs/atom = 165.792 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.684 | 4.684 | 4.684 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2049.8274 0 -2049.8274 -435.16781 Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4078 ave 4078 max 4078 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: 82924 ave 82924 max 82924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82924 Ave neighs/atom = 165.848 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) = 4.684 | 4.684 | 4.684 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 -2049.8274 -2049.8274 10.668085 78.514158 6.9855255 -435.16781 -435.16781 9.2891443 -1303.4018 -11.390809 2.2455376 331.88483 Loop time of 9.53674e-07 on 1 procs for 0 steps with 500 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: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4078 ave 4078 max 4078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41462 ave 41462 max 41462 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82924 ave 82924 max 82924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82924 Ave neighs/atom = 165.848 Neighbor list builds = 0 Dangerous builds = 0 500 -2049.82735639032 eV 2.24553760976669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00