LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -36.243135 0.0000000) to (18.119755 36.243135 3.6239511) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0735315 5.0735315 3.6239511 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.243135 0.0000000) to (18.119755 36.243135 3.6239511) create_atoms CPU = 0.001 seconds 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0735315 5.0735315 3.6239511 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -36.243135 0.0000000) to (18.119755 36.243135 3.6239511) create_atoms CPU = 0.000 seconds 202 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 399 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_427873955970_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1638.55 0 -1638.55 22816.997 40 0 -1666.5213 0 -1666.5213 -509.15788 Loop time of 1.74595 on 1 procs for 40 steps with 399 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1638.55003184787 -1666.51976432577 -1666.52126381201 Force two-norm initial, final = 33.448725 0.11754513 Force max component initial, final = 11.751541 0.032595853 Final line search alpha, max atom move = 1.0000000 0.032595853 Iterations, force evaluations = 40 64 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7381 | 1.7381 | 1.7381 | 0.0 | 99.55 Neigh | 0.0029736 | 0.0029736 | 0.0029736 | 0.0 | 0.17 Comm | 0.002571 | 0.002571 | 0.002571 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002322 | | | 0.13 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3796.00 ave 3796 max 3796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52696.0 ave 52696 max 52696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52696 Ave neighs/atom = 132.07018 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1666.5213 0 -1666.5213 -509.15788 4759.8187 72 0 -1668.0646 0 -1668.0646 -12271.328 4793.1992 Loop time of 0.910662 on 1 procs for 32 steps with 399 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1666.52126381201 -1668.06391976424 -1668.06463450446 Force two-norm initial, final = 65.236664 2.9351670 Force max component initial, final = 58.363755 1.9216644 Final line search alpha, max atom move = 0.00070873538 0.0013619516 Iterations, force evaluations = 32 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90424 | 0.90424 | 0.90424 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010805 | 0.0010805 | 0.0010805 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005337 | | | 0.59 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3796.00 ave 3796 max 3796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52744.0 ave 52744 max 52744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52744 Ave neighs/atom = 132.19048 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1668.0646 0 -1668.0646 -12271.328 Loop time of 1.862e-06 on 1 procs for 0 steps with 399 atoms 214.8% 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 | | 1.862e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3856.00 ave 3856 max 3856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52402.0 ave 52402 max 52402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52402 Ave neighs/atom = 131.33333 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.594 | 4.594 | 4.594 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 -1668.0646 -1668.0646 17.696168 72.48627 3.7367194 -12271.328 -12271.328 627.3203 -38013.123 571.81858 2.3419031 183.12171 Loop time of 3.311e-06 on 1 procs for 0 steps with 399 atoms 181.2% 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 | | 3.311e-06 | | |100.00 Nlocal: 399.000 ave 399 max 399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3856.00 ave 3856 max 3856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26201.0 ave 26201 max 26201 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52402.0 ave 52402 max 52402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52402 Ave neighs/atom = 131.33333 Neighbor list builds = 0 Dangerous builds = 0 399 -1668.06463450446 eV 2.34190305221012 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03