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 = 3.56184 3.56184 3.56184 Created orthogonal box = (0 -38.5307 0) to (12.8424 38.5307 3.56184) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.93938 4.93938 3.56184 Created 158 atoms create_atoms CPU = 0.000153065 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.93938 4.93938 3.56184 Created 158 atoms create_atoms CPU = 4.60148e-05 secs 158 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 19 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 8.5097 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 312 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5097 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1188.3666 0 -1188.3666 33569.597 29 0 -1220.0484 0 -1220.0484 6928.0433 Loop time of 0.0597529 on 1 procs for 29 steps with 312 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1188.36658329 -1220.04755042 -1220.04838693 Force two-norm initial, final = 50.1781 0.128329 Force max component initial, final = 16.2635 0.0253525 Final line search alpha, max atom move = 1 0.0253525 Iterations, force evaluations = 29 51 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05793 | 0.05793 | 0.05793 | 0.0 | 96.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013251 | 0.0013251 | 0.0013251 | 0.0 | 2.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004978 | | | 0.83 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064 ave 5064 max 5064 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: 70020 ave 70020 max 70020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70020 Ave neighs/atom = 224.423 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -1220.0484 0 -1220.0484 6928.0433 3524.9798 37 0 -1220.1382 0 -1220.1382 899.66566 3536.9608 Loop time of 0.012265 on 1 procs for 8 steps with 312 atoms 163.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1220.04838693 -1220.1381026 -1220.13819501 Force two-norm initial, final = 23.7037 0.432856 Force max component initial, final = 23.5597 0.22558 Final line search alpha, max atom move = 0.00280752 0.000633322 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011414 | 0.011414 | 0.011414 | 0.0 | 93.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023961 | 0.00023961 | 0.00023961 | 0.0 | 1.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006111 | | | 4.98 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064 ave 5064 max 5064 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: 69752 ave 69752 max 69752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69752 Ave neighs/atom = 223.564 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5097 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1220.1382 0 -1220.1382 899.66566 Loop time of 1.19209e-06 on 1 procs for 0 steps with 312 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: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064 ave 5064 max 5064 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: 69720 ave 69720 max 69720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69720 Ave neighs/atom = 223.462 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) = 4.619 | 4.619 | 4.619 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 -1220.1382 -1220.1382 12.793858 77.061425 3.5874982 899.66566 899.66566 101.79748 2661.2339 -64.034347 2.2296648 120.56718 Loop time of 2.14577e-06 on 1 procs for 0 steps with 312 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: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5064 ave 5064 max 5064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34860 ave 34860 max 34860 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69720 ave 69720 max 69720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69720 Ave neighs/atom = 223.462 Neighbor list builds = 0 Dangerous builds = 0 312 -1220.13819501345 eV 2.22966482495121 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00