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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897097 62.179117 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226304 5.5798612 6.0968188 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897097 62.179117 6.0968188) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226304 5.5798612 6.0968188 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.179117 0.0000000) to (35.897097 62.179117 6.0968188) create_atoms CPU = 0.007 seconds 1249 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2472 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_444394830472_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.249 | 5.249 | 5.249 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10882.941 0 -10882.941 5890.2338 25 0 -10941.253 0 -10941.253 -2474.9849 Loop time of 4.89844 on 1 procs for 25 steps with 2472 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 = -10882.9406655013 -10941.2442688041 -10941.2534312363 Force two-norm initial, final = 95.399275 0.63383652 Force max component initial, final = 20.618987 0.074899989 Final line search alpha, max atom move = 0.16683641 0.012496045 Iterations, force evaluations = 25 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.876 | 4.876 | 4.876 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0090256 | 0.0090256 | 0.0090256 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01344 | | | 0.27 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7170.00 ave 7170 max 7170 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: 191400.0 ave 191400 max 191400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191400 Ave neighs/atom = 77.427184 Neighbor list builds = 0 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.249 | 5.249 | 5.249 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -10941.253 0 -10941.253 -2474.9849 27216.807 27 0 -10941.27 0 -10941.27 -795.65268 27191.074 Loop time of 0.451655 on 1 procs for 2 steps with 2472 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 = -10941.2534312363 -10941.2700850231 -10941.2703002685 Force two-norm initial, final = 48.991347 0.65135384 Force max component initial, final = 38.667761 0.12356350 Final line search alpha, max atom move = 0.00033208000 4.1032967e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44761 | 0.44761 | 0.44761 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076811 | 0.00076811 | 0.00076811 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003278 | | | 0.73 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209.00 ave 7209 max 7209 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: 191498.0 ave 191498 max 191498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191498 Ave neighs/atom = 77.466828 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.387 | 5.387 | 5.387 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10941.27 0 -10941.27 -795.65268 Loop time of 6.505e-06 on 1 procs for 0 steps with 2472 atoms 169.1% 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 | | 6.505e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209.00 ave 7209 max 7209 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: 191508.0 ave 191508 max 191508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191508 Ave neighs/atom = 77.470874 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 ghost atom cutoff = 6 binsize = 3, bins = 12 42 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.387 | 5.387 | 5.387 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 -10941.27 -10941.27 35.875379 124.35823 6.094742 -795.65268 -795.65268 -0.064398511 -2379.6154 -7.2782377 2.2534837 1069.5378 Loop time of 6.806e-06 on 1 procs for 0 steps with 2472 atoms 279.2% 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 | | 6.806e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7209.00 ave 7209 max 7209 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95754.0 ave 95754 max 95754 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191508.0 ave 191508 max 191508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191508 Ave neighs/atom = 77.470874 Neighbor list builds = 0 Dangerous builds = 0 2472 -10941.2703002685 eV 2.25348373446447 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06