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 -40.746946 0.0000000) to (28.812442 40.746946 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5904738 6.0816338 4.9780318 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -40.746946 0.0000000) to (28.812442 40.746946 4.9780318) create_atoms CPU = 0.006 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5904738 6.0816338 4.9780318 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.746946 0.0000000) to (28.812442 40.746946 4.9780318) create_atoms CPU = 0.004 seconds 538 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4466.8488 0 -4466.8488 68718.579 68 0 -4749.8188 0 -4749.8188 1191.0523 Loop time of 3.4055 on 1 procs for 68 steps with 1070 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 = -4466.84884393835 -4749.81465658555 -4749.81879966977 Force two-norm initial, final = 665.35174 0.21943146 Force max component initial, final = 219.95813 0.020644664 Final line search alpha, max atom move = 1.0000000 0.020644664 Iterations, force evaluations = 68 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2953 | 3.2953 | 3.2953 | 0.0 | 96.76 Neigh | 0.069177 | 0.069177 | 0.069177 | 0.0 | 2.03 Comm | 0.023311 | 0.023311 | 0.023311 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01772 | | | 0.52 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8173.00 ave 8173 max 8173 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: 241048.0 ave 241048 max 241048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241048 Ave neighs/atom = 225.27850 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.444 | 5.444 | 5.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -4749.8188 0 -4749.8188 1191.0523 11688.608 73 0 -4750.0177 0 -4750.0177 -60.901212 11697.016 Loop time of 0.216459 on 1 procs for 5 steps with 1070 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 = -4749.81879966976 -4750.01754460537 -4750.01771519415 Force two-norm initial, final = 81.466551 0.83109756 Force max component initial, final = 67.686295 0.53129411 Final line search alpha, max atom move = 0.00044305524 0.00023539264 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2108 | 0.2108 | 0.2108 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013018 | 0.0013018 | 0.0013018 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004355 | | | 2.01 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8173.00 ave 8173 max 8173 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: 241076.0 ave 241076 max 241076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241076 Ave neighs/atom = 225.30467 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.582 | 5.582 | 5.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4750.0177 0 -4750.0177 -60.901212 Loop time of 6.375e-06 on 1 procs for 0 steps with 1070 atoms 203.9% 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 | | 6.375e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8155.00 ave 8155 max 8155 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: 240800.0 ave 240800 max 240800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240800 Ave neighs/atom = 225.04673 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.582 | 5.582 | 5.582 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 -4750.0177 -4750.0177 28.715785 81.789045 4.980343 -60.901212 -60.901212 -64.938711 -73.036566 -44.728358 2.3022381 507.33838 Loop time of 6.675e-06 on 1 procs for 0 steps with 1070 atoms 254.7% 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 | | 6.675e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8155.00 ave 8155 max 8155 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120400.0 ave 120400 max 120400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 240800.0 ave 240800 max 240800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240800 Ave neighs/atom = 225.04673 Neighbor list builds = 0 Dangerous builds = 0 1070 -4720.88020664615 eV 2.30223812004253 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04