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 = 4.0333 4.0333 4.0333 Created orthogonal box = (0 -53.5118 0) to (18.9179 53.5118 5.70395) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.87922 6.08043 5.70395 Created 359 atoms create_atoms CPU = 0.000333071 secs 359 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.87922 6.08043 5.70395 Created 359 atoms create_atoms CPU = 0.000239849 secs 359 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 26 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 704 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2367.3434 0 -2367.3434 1787.108 13 0 -2369.5134 0 -2369.5134 1572.261 Loop time of 0.0779762 on 1 procs for 13 steps with 704 atoms 102.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2367.34337392 -2369.51226307 -2369.51336053 Force two-norm initial, final = 7.3012 0.0430915 Force max component initial, final = 1.31763 0.00304012 Final line search alpha, max atom move = 1 0.00304012 Iterations, force evaluations = 13 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076621 | 0.076621 | 0.076621 | 0.0 | 98.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085187 | 0.00085187 | 0.00085187 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005035 | | | 0.65 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014 ave 5014 max 5014 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: 99040 ave 99040 max 99040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99040 Ave neighs/atom = 140.682 Neighbor list builds = 0 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 : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -2369.5134 0 -2369.5134 1572.261 11548.553 14 0 -2369.5144 0 -2369.5144 1120.3898 11555.065 Loop time of 0.00932193 on 1 procs for 1 steps with 704 atoms 107.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2369.51336053 -2369.51336053 -2369.51438089 Force two-norm initial, final = 5.14515 0.272143 Force max component initial, final = 3.91368 0.226208 Final line search alpha, max atom move = 0.000255514 5.77993e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0089717 | 0.0089717 | 0.0089717 | 0.0 | 96.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.5367e-05 | 9.5367e-05 | 9.5367e-05 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002549 | | | 2.73 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014 ave 5014 max 5014 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: 99040 ave 99040 max 99040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99040 Ave neighs/atom = 140.682 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.094 | 5.094 | 5.094 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2369.5144 0 -2369.5144 1120.3898 Loop time of 9.53674e-07 on 1 procs for 0 steps with 704 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014 ave 5014 max 5014 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: 99040 ave 99040 max 99040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99040 Ave neighs/atom = 140.682 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) = 5.094 | 5.094 | 5.094 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 -2369.5144 -2369.5144 18.923618 107.02366 5.7054309 1120.3898 1120.3898 20.069654 3372.4731 -31.373215 2.6989092 280.84184 Loop time of 1.90735e-06 on 1 procs for 0 steps with 704 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5014 ave 5014 max 5014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49520 ave 49520 max 49520 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99040 ave 99040 max 99040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99040 Ave neighs/atom = 140.682 Neighbor list builds = 0 Dangerous builds = 0 704 -2369.51438089288 eV 2.69890920529428 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00