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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2341415 6.0612802 5.1100000 Created 685 atoms using lattice units in orthogonal box = (0.0000000 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) create_atoms CPU = 0.006 seconds 685 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2341415 6.0612802 5.1100000 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -47.388190 0.0000000) to (33.508511 47.388190 5.1100000) create_atoms CPU = 0.005 seconds 693 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 32 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 2 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4291.9141 0 -4291.9141 86413.89 54 0 -4856.1551 0 -4856.1551 4905.3493 Loop time of 4.68901 on 1 procs for 54 steps with 1376 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4291.91406728511 -4856.15066625134 -4856.15512768445 Force two-norm initial, final = 570.90659 0.20975175 Force max component initial, final = 97.215670 0.045148174 Final line search alpha, max atom move = 1.0000000 0.045148174 Iterations, force evaluations = 54 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.626 | 4.626 | 4.626 | 0.0 | 98.66 Neigh | 0.035488 | 0.035488 | 0.035488 | 0.0 | 0.76 Comm | 0.012592 | 0.012592 | 0.012592 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01495 | | | 0.32 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5435.00 ave 5435 max 5435 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: 106396.0 ave 106396 max 106396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106396 Ave neighs/atom = 77.322674 Neighbor list builds = 2 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 32 2 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -4856.1551 0 -4856.1551 4905.3493 16228.416 58 0 -4856.2755 0 -4856.2755 -3.5377714 16284.476 Loop time of 0.372733 on 1 procs for 4 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 = -4856.15512768444 -4856.27501176304 -4856.27547921382 Force two-norm initial, final = 91.525414 0.48525388 Force max component initial, final = 71.756725 0.30871187 Final line search alpha, max atom move = 0.00018419698 5.6863795e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36858 | 0.36858 | 0.36858 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00087937 | 0.00087937 | 0.00087937 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003278 | | | 0.88 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5435.00 ave 5435 max 5435 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: 106360.0 ave 106360 max 106360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106360 Ave neighs/atom = 77.296512 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 32 2 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) = 5.185 | 5.185 | 5.185 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4856.2755 0 -4856.2755 -3.5377714 Loop time of 6.705e-06 on 1 procs for 0 steps with 1376 atoms 179.0% 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 | | 6.705e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5435.00 ave 5435 max 5435 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: 106272.0 ave 106272 max 106272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106272 Ave neighs/atom = 77.232558 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 32 2 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) = 5.185 | 5.185 | 5.185 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 -4856.2755 -4856.2755 33.548994 95.033609 5.1076023 -3.5377714 -3.5377714 30.409849 -24.181554 -16.841609 2.3986661 1010.4695 Loop time of 6.705e-06 on 1 procs for 0 steps with 1376 atoms 253.5% 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 | | 6.705e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5435.00 ave 5435 max 5435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53136.0 ave 53136 max 53136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106272.0 ave 106272 max 106272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106272 Ave neighs/atom = 77.232558 Neighbor list builds = 0 Dangerous builds = 0 1376 -4856.27547921382 eV 2.39866607224451 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05