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 = 4.07372 4.07372 4.07372 Created orthogonal box = (0 -46.8075 0) to (33.095 46.8075 5.76111) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0144 6.38229 5.76111 Created 532 atoms create_atoms CPU = 0.000355959 secs 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0144 6.38229 5.76111 Created 532 atoms create_atoms CPU = 0.000236034 secs 532 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 8 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3185.8427 0 -3185.8427 4414.3631 30 0 -3206.0522 0 -3206.0522 -296.15856 Loop time of 0.365103 on 1 procs for 30 steps with 1048 atoms 101.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3185.84267383 -3206.04955613 -3206.05221549 Force two-norm initial, final = 28.0265 0.116389 Force max component initial, final = 5.24757 0.0178421 Final line search alpha, max atom move = 1 0.0178421 Iterations, force evaluations = 30 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35494 | 0.35494 | 0.35494 | 0.0 | 97.22 Neigh | 0.0058551 | 0.0058551 | 0.0058551 | 0.0 | 1.60 Comm | 0.0026875 | 0.0026875 | 0.0026875 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001616 | | | 0.44 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7287 ave 7287 max 7287 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: 207408 ave 207408 max 207408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207408 Ave neighs/atom = 197.908 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 : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.422 | 5.422 | 5.422 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -3206.0522 0 -3206.0522 -296.15856 17849.031 32 0 -3206.0594 0 -3206.0594 366.46229 17824.774 Loop time of 0.0345769 on 1 procs for 2 steps with 1048 atoms 86.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3206.05221549 -3206.05903671 -3206.05944472 Force two-norm initial, final = 12.9154 0.117203 Force max component initial, final = 11.3152 0.0195213 Final line search alpha, max atom move = 0.000616455 1.2034e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033751 | 0.033751 | 0.033751 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021005 | 0.00021005 | 0.00021005 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006156 | | | 1.78 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7287 ave 7287 max 7287 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: 207320 ave 207320 max 207320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207320 Ave neighs/atom = 197.824 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.56 | 5.56 | 5.56 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3206.0594 0 -3206.0594 366.46229 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7287 ave 7287 max 7287 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: 207352 ave 207352 max 207352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207352 Ave neighs/atom = 197.855 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) = 5.56 | 5.56 | 5.56 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 -3206.0594 -3206.0594 33.08881 93.615063 5.7543618 366.46229 366.46229 0.32640519 1098.6455 0.41493498 2.6376466 490.52092 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7287 ave 7287 max 7287 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103676 ave 103676 max 103676 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 207352 ave 207352 max 207352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207352 Ave neighs/atom = 197.855 Neighbor list builds = 0 Dangerous builds = 0 1048 -3356.02343851669 eV 2.63764661719125 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00