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 = 3.49194 3.49194 3.49194 Created orthogonal box = (0 -49.1394 0) to (11.5815 49.1394 4.93835) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2643 5.95587 4.93835 Created 266 atoms create_atoms CPU = 0.000366926 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2643 5.95587 4.93835 Created 266 atoms create_atoms CPU = 0.000244141 secs 266 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 4 29 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 6.85342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 526 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 4 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2306.1104 0 -2306.1104 21468.828 52 0 -2328.1283 0 -2328.1283 1907.167 Loop time of 0.40362 on 1 procs for 52 steps with 526 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2306.1104426 -2328.12600014 -2328.12830172 Force two-norm initial, final = 48.562 0.185091 Force max component initial, final = 13.4943 0.0374242 Final line search alpha, max atom move = 1 0.0374242 Iterations, force evaluations = 52 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39641 | 0.39641 | 0.39641 | 0.0 | 98.21 Neigh | 0.0021901 | 0.0021901 | 0.0021901 | 0.0 | 0.54 Comm | 0.0032201 | 0.0032201 | 0.0032201 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001797 | | | 0.45 Nlocal: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 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: 69892 ave 69892 max 69892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69892 Ave neighs/atom = 132.875 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.533 | 4.533 | 4.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -2328.1283 0 -2328.1283 1907.167 5620.8835 54 0 -2328.135 0 -2328.135 2533.149 5618.8954 Loop time of 0.0176799 on 1 procs for 2 steps with 526 atoms 113.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2328.12830172 -2328.13437457 -2328.13496827 Force two-norm initial, final = 9.90231 1.52894 Force max component initial, final = 9.33695 1.50688 Final line search alpha, max atom move = 0.0002781 0.000419063 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.017222 | 0.017222 | 0.017222 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011563 | 0.00011563 | 0.00011563 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003419 | | | 1.93 Nlocal: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 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: 70056 ave 70056 max 70056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70056 Ave neighs/atom = 133.186 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 4 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 4.67 | 4.67 | 4.67 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2328.135 0 -2328.135 2533.149 Loop time of 9.53674e-07 on 1 procs for 0 steps with 526 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: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 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: 70064 ave 70064 max 70064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70064 Ave neighs/atom = 133.202 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) = 4.67 | 4.67 | 4.67 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 -2328.135 -2328.135 11.569484 98.278846 4.9417061 2533.149 2533.149 -429.22886 8079.4255 -50.74945 2.2818903 237.11458 Loop time of 2.14577e-06 on 1 procs for 0 steps with 526 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: 526 ave 526 max 526 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35032 ave 35032 max 35032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70064 ave 70064 max 70064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70064 Ave neighs/atom = 133.202 Neighbor list builds = 0 Dangerous builds = 0 526 -2328.13496826812 eV 2.28189028585916 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00