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 = 3.5199994 3.5199994 3.5199994 Created orthogonal box = (0.0000000 -53.615034 0.0000000) to (26.807517 53.615034 3.5199994) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6219857 4.6219857 3.5199994 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -53.615034 0.0000000) to (26.807517 53.615034 3.5199994) create_atoms CPU = 0.001 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6219857 4.6219857 3.5199994 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -53.615034 0.0000000) to (26.807517 53.615034 3.5199994) create_atoms CPU = 0.001 seconds 466 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 926 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_400591584784_005#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3951.299 0 -3951.299 29712.119 120 0 -4100.8965 0 -4100.8965 6843.2725 Loop time of 1.96129 on 1 procs for 120 steps with 926 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3951.29901178097 -4100.89271228203 -4100.89649020032 Force two-norm initial, final = 321.03208 0.29785621 Force max component initial, final = 79.192813 0.077061412 Final line search alpha, max atom move = 1.0000000 0.077061412 Iterations, force evaluations = 120 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9027 | 1.9027 | 1.9027 | 0.0 | 97.01 Neigh | 0.035304 | 0.035304 | 0.035304 | 0.0 | 1.80 Comm | 0.013378 | 0.013378 | 0.013378 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009952 | | | 0.51 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7434.00 ave 7434 max 7434 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: 163528.0 ave 163528 max 163528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163528 Ave neighs/atom = 176.59611 Neighbor list builds = 4 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -4100.8965 0 -4100.8965 6843.2725 10118.491 125 0 -4101.0666 0 -4101.0666 -165.5789 10156.589 Loop time of 0.0602666 on 1 procs for 5 steps with 926 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 = -4100.89649020031 -4101.06614071534 -4101.06663101117 Force two-norm initial, final = 87.922399 2.7148217 Force max component initial, final = 77.432072 2.2831521 Final line search alpha, max atom move = 0.00021727329 0.00049606797 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.058396 | 0.058396 | 0.058396 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035649 | 0.00035649 | 0.00035649 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001514 | | | 2.51 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 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: 163132.0 ave 163132 max 163132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163132 Ave neighs/atom = 176.16847 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.154 | 5.154 | 5.154 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4101.0666 0 -4101.0666 -165.5789 Loop time of 2.003e-06 on 1 procs for 0 steps with 926 atoms 99.9% 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 | | 2.003e-06 | | |100.00 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 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: 162904.0 ave 162904 max 162904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162904 Ave neighs/atom = 175.92225 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.154 | 5.154 | 5.154 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 -4101.0666 -4101.0666 26.776151 107.6803 3.5226012 -165.5789 -165.5789 -210.28004 73.971042 -360.42772 2.2439289 416.57577 Loop time of 1.819e-06 on 1 procs for 0 steps with 926 atoms 219.9% 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 | | 1.819e-06 | | |100.00 Nlocal: 926.000 ave 926 max 926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7429.00 ave 7429 max 7429 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81452.0 ave 81452 max 81452 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162904.0 ave 162904 max 162904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162904 Ave neighs/atom = 175.92225 Neighbor list builds = 0 Dangerous builds = 0 926 -4101.06663098249 eV 2.24392891957594 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02