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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -59.3767 0) to (20.9914 59.3767 5.71314) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.44222 6.59696 5.71314 Created 434 atoms create_atoms CPU = 0.000442028 secs 434 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.44222 6.59696 5.71314 Created 434 atoms create_atoms CPU = 0.00031209 secs 434 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 4 21 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 856 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.874 | 5.874 | 5.874 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2428.1866 0 -2428.1866 3906.8385 61 0 -2458.563 0 -2458.563 -4217.502 Loop time of 0.967921 on 1 procs for 61 steps with 856 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2428.18660908 -2458.56083309 -2458.56295223 Force two-norm initial, final = 30.2249 0.142405 Force max component initial, final = 8.81002 0.0294369 Final line search alpha, max atom move = 1 0.0294369 Iterations, force evaluations = 61 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94776 | 0.94776 | 0.94776 | 0.0 | 97.92 Neigh | 0.0086489 | 0.0086489 | 0.0086489 | 0.0 | 0.89 Comm | 0.0084147 | 0.0084147 | 0.0084147 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003099 | | | 0.32 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10645 ave 10645 max 10645 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: 345484 ave 345484 max 345484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 345484 Ave neighs/atom = 403.603 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 : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.874 | 5.874 | 5.874 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -2458.563 0 -2458.563 -4217.502 14241.718 69 0 -2458.7711 0 -2458.7711 -422.95963 14168.987 Loop time of 0.088948 on 1 procs for 8 steps with 856 atoms 89.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2458.56295223 -2458.77002656 -2458.77105557 Force two-norm initial, final = 59.1646 0.400677 Force max component initial, final = 58.4325 0.24684 Final line search alpha, max atom move = 0.00036295 8.95906e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.086573 | 0.086573 | 0.086573 | 0.0 | 97.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061226 | 0.00061226 | 0.00061226 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001763 | | | 1.98 Nlocal: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10486 ave 10486 max 10486 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: 338048 ave 338048 max 338048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338048 Ave neighs/atom = 394.916 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 6.011 | 6.011 | 6.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2458.7711 0 -2458.7711 -422.95963 Loop time of 1.19209e-06 on 1 procs for 0 steps with 856 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: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10634 ave 10634 max 10634 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: 346516 ave 346516 max 346516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346516 Ave neighs/atom = 404.808 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) = 6.011 | 6.011 | 6.011 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 -2458.7711 -2458.7711 20.833907 118.75342 5.7269311 -422.95963 -422.95963 21.350229 -1318.2083 27.979142 2.5712535 635.40157 Loop time of 1.90735e-06 on 1 procs for 0 steps with 856 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: 856 ave 856 max 856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10634 ave 10634 max 10634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 173258 ave 173258 max 173258 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 346516 ave 346516 max 346516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 346516 Ave neighs/atom = 404.808 Neighbor list builds = 0 Dangerous builds = 0 856 -2458.77105557384 eV 2.57125347736847 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01