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 -63.8299 0) to (22.566 63.8299 4.984) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0543 5.44859 4.984 Created 658 atoms create_atoms CPU = 0.000404835 secs 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0543 5.44859 4.984 Created 658 atoms create_atoms CPU = 0.000271082 secs 658 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 = 8 41 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 12 atoms, new total = 1304 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 = 8 41 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) = 5.076 | 5.076 | 5.076 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5770.1123 0 -5770.1123 8648.3787 57 0 -5803.7542 0 -5803.7542 -3437.4095 Loop time of 0.224496 on 1 procs for 57 steps with 1304 atoms 102.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5770.11229746 -5803.74844236 -5803.75417117 Force two-norm initial, final = 56.32 0.261918 Force max component initial, final = 16.2995 0.0434566 Final line search alpha, max atom move = 0.799826 0.0347577 Iterations, force evaluations = 57 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21419 | 0.21419 | 0.21419 | 0.0 | 95.41 Neigh | 0.0027668 | 0.0027668 | 0.0027668 | 0.0 | 1.23 Comm | 0.0043852 | 0.0043852 | 0.0043852 | 0.0 | 1.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003152 | | | 1.40 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466 ave 6466 max 6466 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: 112320 ave 112320 max 112320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112320 Ave neighs/atom = 86.135 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.076 | 5.076 | 5.076 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -5803.7542 0 -5803.7542 -3437.4095 14357.771 60 0 -5803.837 0 -5803.837 -725.44127 14337.527 Loop time of 0.0131059 on 1 procs for 3 steps with 1304 atoms 152.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5803.75417117 -5803.83420035 -5803.83704157 Force two-norm initial, final = 67.2351 1.13308 Force max component initial, final = 66.3766 0.846872 Final line search alpha, max atom move = 0.000108059 9.15121e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012307 | 0.012307 | 0.012307 | 0.0 | 93.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018907 | 0.00018907 | 0.00018907 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006099 | | | 4.65 Nlocal: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6480 ave 6480 max 6480 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: 112356 ave 112356 max 112356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112356 Ave neighs/atom = 86.1626 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 = 8 41 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5803.837 0 -5803.837 -725.44127 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466 ave 6466 max 6466 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: 112372 ave 112372 max 112372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112372 Ave neighs/atom = 86.1748 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) = 5.213 | 5.213 | 5.213 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 -5803.837 -5803.837 22.586181 127.65974 4.972531 -725.44127 -725.44127 -78.215841 -2003.6903 -94.417635 2.3240028 407.31359 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1304 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: 1304 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6466 ave 6466 max 6466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56186 ave 56186 max 56186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112372 ave 112372 max 112372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112372 Ave neighs/atom = 86.1748 Neighbor list builds = 0 Dangerous builds = 0 1304 -5803.83704156716 eV 2.32400280038791 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00