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 = 3.70049 3.70049 3.70049 Created orthogonal box = (0 -54.7659 0) to (44.7131 54.7659 9.0643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.51258 5.25117 6.04287 Created 1754 atoms create_atoms CPU = 0.000707865 secs 1754 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.51258 5.25117 6.04287 Created 1754 atoms create_atoms CPU = 0.00058794 secs 1754 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 17 41 4 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 5.44 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3472 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 17 41 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.44 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) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5120.0483 0 -5120.0483 3810.7512 88 0 -5182.6528 0 -5182.6528 -7355.5156 Loop time of 0.294296 on 1 procs for 88 steps with 3472 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5120.04831047 -5182.6489856 -5182.65276935 Force two-norm initial, final = 47.4509 0.206832 Force max component initial, final = 6.49486 0.0296452 Final line search alpha, max atom move = 1 0.0296452 Iterations, force evaluations = 88 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27198 | 0.27198 | 0.27198 | 0.0 | 92.42 Neigh | 0.0053279 | 0.0053279 | 0.0053279 | 0.0 | 1.81 Comm | 0.0066438 | 0.0066438 | 0.0066438 | 0.0 | 2.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01035 | | | 3.52 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7091 ave 7091 max 7091 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: 186824 ave 186824 max 186824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186824 Ave neighs/atom = 53.8088 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 : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -5182.6528 0 -5182.6528 -7355.5156 44392.513 91 0 -5182.9436 0 -5182.9436 -3033.6678 44215.781 Loop time of 0.010576 on 1 procs for 3 steps with 3472 atoms 94.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5182.65276935 -5182.93984135 -5182.94358603 Force two-norm initial, final = 204.305 2.31359 Force max component initial, final = 160.521 1.99045 Final line search alpha, max atom move = 4.98235e-05 9.91712e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0093307 | 0.0093307 | 0.0093307 | 0.0 | 88.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019765 | 0.00019765 | 0.00019765 | 0.0 | 1.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001048 | | | 9.91 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6931 ave 6931 max 6931 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: 186776 ave 186776 max 186776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186776 Ave neighs/atom = 53.7949 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 17 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.44 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) = 5.355 | 5.355 | 5.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5182.9436 0 -5182.9436 -3033.6678 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3472 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 | | 1.907e-06 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6971 ave 6971 max 6971 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: 186828 ave 186828 max 186828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186828 Ave neighs/atom = 53.8099 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) = 5.355 | 5.355 | 5.355 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 -5182.9436 -5182.9436 44.637044 109.53178 9.0436078 -3033.6678 -3033.6678 72.002027 -9131.4832 -41.522315 2.3160403 790.80915 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6971 ave 6971 max 6971 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93414 ave 93414 max 93414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186828 ave 186828 max 186828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186828 Ave neighs/atom = 53.8099 Neighbor list builds = 0 Dangerous builds = 0 3472 -5182.9435860265 eV 2.31604025016795 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00