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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8499780 5.2799873 5.9032052 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8499780 5.2799873 5.9032052 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.599905 0.0000000) to (8.0832967 39.599905 8.8548078) create_atoms CPU = 0.001 seconds 242 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 2 19 3 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 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_318213562153_000#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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1614.2604 0 -1614.2604 26275.133 120 0 -1678.6526 0 -1678.6526 1192.7376 Loop time of 1.30094 on 1 procs for 120 steps with 476 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1614.26044229782 -1678.65126752622 -1678.65262432671 Force two-norm initial, final = 156.26071 0.10897355 Force max component initial, final = 54.911605 0.027754927 Final line search alpha, max atom move = 1.0000000 0.027754927 Iterations, force evaluations = 120 227 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2641 | 1.2641 | 1.2641 | 0.0 | 97.17 Neigh | 0.020334 | 0.020334 | 0.020334 | 0.0 | 1.56 Comm | 0.0094701 | 0.0094701 | 0.0094701 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007041 | | | 0.54 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4738.00 ave 4738 max 4738 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: 98616.0 ave 98616 max 98616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98616 Ave neighs/atom = 207.17647 Neighbor list builds = 3 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.973 | 4.973 | 4.973 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -1678.6526 0 -1678.6526 1192.7376 5668.8086 126 0 -1678.725 0 -1678.725 40.927924 5673.8412 Loop time of 0.0460705 on 1 procs for 6 steps with 476 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 = -1678.65262432671 -1678.72374050659 -1678.72504564364 Force two-norm initial, final = 22.944402 0.40432640 Force max component initial, final = 21.791684 0.26174537 Final line search alpha, max atom move = 0.00045963236 0.00012030664 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044343 | 0.044343 | 0.044343 | 0.0 | 96.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030459 | 0.00030459 | 0.00030459 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001423 | | | 3.09 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4661.00 ave 4661 max 4661 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: 99644.0 ave 99644 max 99644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99644 Ave neighs/atom = 209.33613 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 5.111 | 5.111 | 5.111 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1678.725 0 -1678.725 40.927924 Loop time of 1.752e-06 on 1 procs for 0 steps with 476 atoms 114.2% 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 | | 1.752e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4726.00 ave 4726 max 4726 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: 100268.0 ave 100268 max 100268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100268 Ave neighs/atom = 210.64706 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 = 8.4662927 ghost atom cutoff = 8.4662927 binsize = 4.2331463, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.466292682285578 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) = 5.111 | 5.111 | 5.111 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 -1678.725 -1678.725 8.0636214 79.654044 8.8336302 40.927924 40.927924 22.757384 26.291631 73.734758 2.2922649 315.56528 Loop time of 2.354e-06 on 1 procs for 0 steps with 476 atoms 169.9% 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 | | 2.354e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4726.00 ave 4726 max 4726 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50134.0 ave 50134 max 50134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 100268.0 ave 100268 max 100268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100268 Ave neighs/atom = 210.64706 Neighbor list builds = 0 Dangerous builds = 0 476 -1678.72504564364 eV 2.29226491072436 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01