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 = 3.52422 3.52422 3.52422 Created orthogonal box = (0 -43.5957 0) to (14.5307 43.5957 3.52422) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.27375 4.27375 3.52422 Created 206 atoms create_atoms CPU = 0.000201941 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.27375 4.27375 3.52422 Created 206 atoms create_atoms CPU = 6.48499e-05 secs 206 atoms in group lower Displacing atoms ... 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 5 28 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 6.31717 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1785.0856 0 -1785.0856 1156.2223 68 0 -1794.0244 0 -1794.0244 -3574.0335 Loop time of 0.124493 on 1 procs for 68 steps with 404 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1785.0855993 -1794.02301776 -1794.02442979 Force two-norm initial, final = 15.0462 0.116824 Force max component initial, final = 4.69856 0.0157578 Final line search alpha, max atom move = 1 0.0157578 Iterations, force evaluations = 68 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1189 | 0.1189 | 0.1189 | 0.0 | 95.51 Neigh | 0.0012672 | 0.0012672 | 0.0012672 | 0.0 | 1.02 Comm | 0.0028286 | 0.0028286 | 0.0028286 | 0.0 | 2.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001494 | | | 1.20 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3480 ave 3480 max 3480 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: 34508 ave 34508 max 34508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34508 Ave neighs/atom = 85.4158 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -1794.0244 0 -1794.0244 -3574.0335 4465.0311 70 0 -1794.0445 0 -1794.0445 1349.8255 4453.4315 Loop time of 0.00412011 on 1 procs for 2 steps with 404 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1794.02442979 -1794.04317476 -1794.04454046 Force two-norm initial, final = 21.7227 0.765553 Force max component initial, final = 15.8855 0.585267 Final line search alpha, max atom move = 0.00021787 0.000127512 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0038218 | 0.0038218 | 0.0038218 | 0.0 | 92.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.8678e-05 | 7.8678e-05 | 7.8678e-05 | 0.0 | 1.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002196 | | | 5.33 Nlocal: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476 ave 3476 max 3476 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: 34528 ave 34528 max 34528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34528 Ave neighs/atom = 85.4653 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1794.0445 0 -1794.0445 1349.8255 Loop time of 1.19209e-06 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476 ave 3476 max 3476 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: 34536 ave 34536 max 34536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34536 Ave neighs/atom = 85.4851 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) = 4.597 | 4.597 | 4.597 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 -1794.0445 -1794.0445 14.513122 87.191448 3.5193305 1349.8255 1349.8255 210.30165 4010.1976 -171.02265 2.2832454 195.89134 Loop time of 9.53674e-07 on 1 procs for 0 steps with 404 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: 404 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3476 ave 3476 max 3476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17268 ave 17268 max 17268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34536 ave 34536 max 34536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34536 Ave neighs/atom = 85.4851 Neighbor list builds = 0 Dangerous builds = 0 404 -1794.04454045742 eV 2.28324541424286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00