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 = 3.52 3.52 3.52 Created orthogonal box = (0 -65.2898 0) to (23.0822 65.2898 4.97803) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.90474 6.07314 4.97803 Created 690 atoms create_atoms CPU = 0.000772953 secs 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.90474 6.07314 4.97803 Created 690 atoms create_atoms CPU = 0.000623941 secs 690 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 31 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.948 | 5.948 | 5.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6050.1628 0 -6050.1628 3854.2154 73 0 -6076.9382 0 -6076.9382 -6432.4124 Loop time of 0.954816 on 1 procs for 73 steps with 1368 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6050.16276009 -6076.93259951 -6076.93816687 Force two-norm initial, final = 41.4058 0.284478 Force max component initial, final = 10.7959 0.0435275 Final line search alpha, max atom move = 1 0.0435275 Iterations, force evaluations = 73 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.93134 | 0.93134 | 0.93134 | 0.0 | 97.54 Neigh | 0.0086529 | 0.0086529 | 0.0086529 | 0.0 | 0.91 Comm | 0.009635 | 0.009635 | 0.009635 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005189 | | | 0.54 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10737 ave 10737 max 10737 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: 305948 ave 305948 max 305948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305948 Ave neighs/atom = 223.646 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.948 | 5.948 | 5.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -6076.9382 0 -6076.9382 -6432.4124 15004.096 75 0 -6076.9614 0 -6076.9614 -3767.2919 14981.815 Loop time of 0.0367069 on 1 procs for 2 steps with 1368 atoms 81.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6076.93816687 -6076.96127612 -6076.96138948 Force two-norm initial, final = 43.6909 0.292029 Force max component initial, final = 33.0449 0.0441488 Final line search alpha, max atom move = 0.000663561 2.92954e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035421 | 0.035421 | 0.035421 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003252 | 0.0003252 | 0.0003252 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009608 | | | 2.62 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10656 ave 10656 max 10656 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: 306172 ave 306172 max 306172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306172 Ave neighs/atom = 223.81 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 6.086 | 6.086 | 6.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6076.9614 0 -6076.9614 -3767.2919 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10665 ave 10665 max 10665 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: 306192 ave 306192 max 306192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306192 Ave neighs/atom = 223.825 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) = 6.086 | 6.086 | 6.086 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 -6076.9614 -6076.9614 23.068028 130.57959 4.9736896 -3767.2919 -3767.2919 -4.7184413 -11297.794 0.63669594 2.3141126 349.35194 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10665 ave 10665 max 10665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153096 ave 153096 max 153096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306192 ave 306192 max 306192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306192 Ave neighs/atom = 223.825 Neighbor list builds = 0 Dangerous builds = 0 1368 -6076.96138947818 eV 2.31411264795913 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01