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 = 3.64613 3.64613 3.64613 Created orthogonal box = (0 -42.2106 0) to (29.8448 42.2106 5.1564) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.79079 6.29954 5.1564 Created 538 atoms create_atoms CPU = 0.000316858 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.79079 6.29954 5.1564 Created 538 atoms create_atoms CPU = 0.000206947 secs 538 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 7 20 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 8.65905 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 1058 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4063.5039 0 -4063.5039 4682.6971 105 0 -4120.6844 0 -4120.6844 -20628.628 Loop time of 0.770735 on 1 procs for 105 steps with 1058 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4063.50386262 -4120.68037147 -4120.68442519 Force two-norm initial, final = 42.6376 0.260709 Force max component initial, final = 14.6725 0.020104 Final line search alpha, max atom move = 1 0.020104 Iterations, force evaluations = 105 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74759 | 0.74759 | 0.74759 | 0.0 | 97.00 Neigh | 0.0092459 | 0.0092459 | 0.0092459 | 0.0 | 1.20 Comm | 0.0087452 | 0.0087452 | 0.0087452 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005152 | | | 0.67 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7942 ave 7942 max 7942 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: 232436 ave 232436 max 232436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232436 Ave neighs/atom = 219.694 Neighbor list builds = 2 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 : 105 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.43 | 5.43 | 5.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 105 0 -4120.6844 0 -4120.6844 -20628.628 12991.732 119 0 -4122.8594 0 -4122.8594 1886.7738 12807.849 Loop time of 0.072212 on 1 procs for 14 steps with 1058 atoms 96.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4120.68442519 -4122.85942915 -4122.85944789 Force two-norm initial, final = 348.46 0.556472 Force max component initial, final = 320.708 0.232919 Final line search alpha, max atom move = 0.00140511 0.000327277 Iterations, force evaluations = 14 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068882 | 0.068882 | 0.068882 | 0.0 | 95.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072908 | 0.00072908 | 0.00072908 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002601 | | | 3.60 Nlocal: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7924 ave 7924 max 7924 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: 233392 ave 233392 max 233392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233392 Ave neighs/atom = 220.597 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 = 8.65905 ghost atom cutoff = 8.65905 binsize = 4.32953, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.65905 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) = 5.568 | 5.568 | 5.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4122.8594 0 -4122.8594 1886.7738 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1058 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: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7987 ave 7987 max 7987 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: 236116 ave 236116 max 236116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236116 Ave neighs/atom = 223.172 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) = 5.568 | 5.568 | 5.568 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 -4122.8594 -4122.8594 29.46354 84.421194 5.1492002 1886.7738 1886.7738 -28.764426 5711.9771 -22.891237 2.3713576 1085.119 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1058 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: 1058 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7987 ave 7987 max 7987 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118058 ave 118058 max 118058 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 236116 ave 236116 max 236116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236116 Ave neighs/atom = 223.172 Neighbor list builds = 0 Dangerous builds = 0 1058 -4122.85944789206 eV 2.37135757267637 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00