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 = 3.31169 3.31169 3.31169 Created orthogonal box = (0 -33.776 0) to (16.8864 33.776 3.31169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.89685 3.89685 3.31169 Created 210 atoms create_atoms CPU = 0.00010705 secs 210 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.89685 3.89685 3.31169 Created 210 atoms create_atoms CPU = 4.91142e-05 secs 210 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 19 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 417 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1427.5767 0 -1427.5767 235008.5 60 0 -1607.942 0 -1607.942 130730.3 Loop time of 0.241949 on 1 procs for 60 steps with 417 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 = -1427.57668248 -1607.94041285 -1607.94199494 Force two-norm initial, final = 206.735 0.222324 Force max component initial, final = 46.7311 0.0291534 Final line search alpha, max atom move = 0.417216 0.0121633 Iterations, force evaluations = 60 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23661 | 0.23661 | 0.23661 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037761 | 0.0037761 | 0.0037761 | 0.0 | 1.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001567 | | | 0.65 Nlocal: 417 ave 417 max 417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5433 ave 5433 max 5433 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: 83392 ave 83392 max 83392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83392 Ave neighs/atom = 199.981 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 : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.495 | 4.495 | 4.495 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1607.942 0 -1607.942 130730.3 3777.6701 308 0 -1662.6307 0 -1662.6307 -25948.707 4933.3906 Loop time of 0.392767 on 1 procs for 248 steps with 417 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1607.94199494 -1662.6290125 -1662.63066091 Force two-norm initial, final = 361.511 3.72394 Force max component initial, final = 266.185 2.82892 Final line search alpha, max atom move = 0.000526498 0.00148942 Iterations, force evaluations = 248 257 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36869 | 0.36869 | 0.36869 | 0.0 | 93.87 Neigh | 0.0026109 | 0.0026109 | 0.0026109 | 0.0 | 0.66 Comm | 0.0054877 | 0.0054877 | 0.0054877 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01598 | | | 4.07 Nlocal: 417 ave 417 max 417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4083 ave 4083 max 4083 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: 64888 ave 64888 max 64888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64888 Ave neighs/atom = 155.607 Neighbor list builds = 2 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 6 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1662.6307 0 -1662.6307 -25948.707 Loop time of 9.53674e-07 on 1 procs for 0 steps with 417 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: 417 ave 417 max 417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4073 ave 4073 max 4073 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: 62350 ave 62350 max 62350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62350 Ave neighs/atom = 149.52 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) = 4.612 | 4.612 | 4.612 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 -1662.6307 -1662.6307 19.275114 67.552063 3.788872 -25948.707 -25948.707 353.48045 -79250.703 1051.1032 2.3235212 198.91544 Loop time of 1.90735e-06 on 1 procs for 0 steps with 417 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: 417 ave 417 max 417 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4073 ave 4073 max 4073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31175 ave 31175 max 31175 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62350 ave 62350 max 62350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62350 Ave neighs/atom = 149.52 Neighbor list builds = 0 Dangerous builds = 0 417 -1662.63066091099 eV 2.32352120419965 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00