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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -42.654952 0.0000000) to (34.827623 42.654952 8.6176017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9753746 4.9328856 5.7450678 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -42.654952 0.0000000) to (34.827623 42.654952 8.6176017) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9753746 4.9328856 5.7450678 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.654952 0.0000000) to (34.827623 42.654952 8.6176017) create_atoms CPU = 0.001 seconds 1184 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_832600236922_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.487 | 6.487 | 6.487 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9545.0925 0 -9545.0925 74271.801 56 0 -10191.736 0 -10191.736 -595.72169 Loop time of 2.33276 on 1 procs for 56 steps with 2336 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 = -9545.0924978582 -10191.7279019312 -10191.7362667667 Force two-norm initial, final = 810.87050 0.26943554 Force max component initial, final = 124.31733 0.017371810 Final line search alpha, max atom move = 1.0000000 0.017371810 Iterations, force evaluations = 56 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2783 | 2.2783 | 2.2783 | 0.0 | 97.67 Neigh | 0.029313 | 0.029313 | 0.029313 | 0.0 | 1.26 Comm | 0.011132 | 0.011132 | 0.011132 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01398 | | | 0.60 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9407.00 ave 9407 max 9407 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: 461568.0 ave 461568 max 461568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461568 Ave neighs/atom = 197.58904 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.485 | 6.485 | 6.485 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -10191.736 0 -10191.736 -595.72169 25604.111 58 0 -10191.798 0 -10191.798 -312.79114 25600.675 Loop time of 0.0908251 on 1 procs for 2 steps with 2336 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 = -10191.7362667666 -10191.7906880168 -10191.7976610818 Force two-norm initial, final = 59.181020 12.401672 Force max component initial, final = 37.158219 11.030397 Final line search alpha, max atom move = 3.6267476e-05 0.00040004466 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.088837 | 0.088837 | 0.088837 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032238 | 0.00032238 | 0.00032238 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001666 | | | 1.83 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9099.00 ave 9099 max 9099 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: 462496.0 ave 462496 max 462496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462496 Ave neighs/atom = 197.98630 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.623 | 6.623 | 6.623 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10191.798 0 -10191.798 -312.79114 Loop time of 2.667e-06 on 1 procs for 0 steps with 2336 atoms 187.5% 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 | | 2.667e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9105.00 ave 9105 max 9105 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: 462464.0 ave 462464 max 462464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462464 Ave neighs/atom = 197.97260 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 ghost atom cutoff = 8 binsize = 4, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.623 | 6.623 | 6.623 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 -10191.798 -10191.798 34.801622 85.436702 8.6100853 -312.79114 -312.79114 -689.80406 92.985774 -341.55514 2.1944998 1227.8379 Loop time of 2.799e-06 on 1 procs for 0 steps with 2336 atoms 285.8% 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 | | 2.799e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9105.00 ave 9105 max 9105 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231232.0 ave 231232 max 231232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 462464.0 ave 462464 max 462464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462464 Ave neighs/atom = 197.97260 Neighbor list builds = 0 Dangerous builds = 0 2336 -10191.7976610818 eV 2.19449983188901 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03