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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -52.879184 0.0000000) to (37.391230 52.879184 5.7021090) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9565078 6.7636166 5.7021090 Created 687 atoms using lattice units in orthogonal box = (0.0000000 -52.879184 0.0000000) to (37.391230 52.879184 5.7021090) create_atoms CPU = 0.002 seconds 687 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9565078 6.7636166 5.7021090 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -52.879184 0.0000000) to (37.391230 52.879184 5.7021090) create_atoms CPU = 0.002 seconds 695 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1376 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.497 | 5.497 | 5.497 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4378.0499 0 -4378.0499 22820.969 72 0 -4614.3115 0 -4614.3115 2442.0164 Loop time of 1.74867 on 1 procs for 72 steps with 1376 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 = -4378.04988088297 -4614.30758079448 -4614.3115137912 Force two-norm initial, final = 246.55850 0.14747583 Force max component initial, final = 41.047463 0.030673628 Final line search alpha, max atom move = 1.0000000 0.030673628 Iterations, force evaluations = 72 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.713 | 1.713 | 1.713 | 0.0 | 97.96 Neigh | 0.014453 | 0.014453 | 0.014453 | 0.0 | 0.83 Comm | 0.01142 | 0.01142 | 0.01142 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009758 | | | 0.56 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8420.00 ave 8420 max 8420 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: 242588.0 ave 242588 max 242588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 242588 Ave neighs/atom = 176.29942 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.492 | 5.492 | 5.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -4614.3115 0 -4614.3115 2442.0164 22548.622 75 0 -4614.3717 0 -4614.3717 -0.46618672 22616.587 Loop time of 0.0741742 on 1 procs for 3 steps with 1376 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 = -4614.3115137912 -4614.3696813096 -4614.37171761918 Force two-norm initial, final = 61.065402 0.59527274 Force max component initial, final = 45.351736 0.44139370 Final line search alpha, max atom move = 0.00017933322 7.9156556e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.072267 | 0.072267 | 0.072267 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035975 | 0.00035975 | 0.00035975 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001547 | | | 2.09 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8112.00 ave 8112 max 8112 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: 241420.0 ave 241420 max 241420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241420 Ave neighs/atom = 175.45058 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.630 | 5.630 | 5.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4614.3717 0 -4614.3717 -0.46618672 Loop time of 1.69e-06 on 1 procs for 0 steps with 1376 atoms 177.5% 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 | | 1.69e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8112.00 ave 8112 max 8112 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: 241200.0 ave 241200 max 241200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241200 Ave neighs/atom = 175.29070 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 5.630 | 5.630 | 5.630 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 -4614.3717 -4614.3717 37.416579 105.97174 5.7039136 -0.46618672 -0.46618672 31.28987 -7.6089407 -25.07949 2.6686381 1258.9781 Loop time of 2.539e-06 on 1 procs for 0 steps with 1376 atoms 236.3% 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 | | 2.539e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8112.00 ave 8112 max 8112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120600.0 ave 120600 max 120600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241200.0 ave 241200 max 241200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241200 Ave neighs/atom = 175.29070 Neighbor list builds = 0 Dangerous builds = 0 1376 -4614.37171761918 eV 2.66863810726138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02