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 = 3.1435003 3.1435003 3.1435003 Created orthogonal box = (0.0000000 -40.010227 0.0000000) to (9.4305009 40.010227 4.4455807) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2391671 4.4455807 4.4455807 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -40.010227 0.0000000) to (9.4305009 40.010227 4.4455807) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2391671 4.4455807 4.4455807 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -40.010227 0.0000000) to (9.4305009 40.010227 4.4455807) create_atoms CPU = 0.000 seconds 110 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 2 16 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 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 216 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_534363225491_004#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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 2 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1219.3486 0 -1219.3486 165179.86 63 0 -1433.9244 0 -1433.9244 16229.277 Loop time of 0.354867 on 1 procs for 63 steps with 216 atoms 96.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1219.34856850464 -1433.92317870086 -1433.92437745581 Force two-norm initial, final = 532.38903 0.21604053 Force max component initial, final = 187.38724 0.031172837 Final line search alpha, max atom move = 1.0000000 0.031172837 Iterations, force evaluations = 63 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34414 | 0.34414 | 0.34414 | 0.0 | 96.98 Neigh | 0.0037864 | 0.0037864 | 0.0037864 | 0.0 | 1.07 Comm | 0.0047321 | 0.0047321 | 0.0047321 | 0.0 | 1.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002209 | | | 0.62 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4413.00 ave 4413 max 4413 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: 59616.0 ave 59616 max 59616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59616 Ave neighs/atom = 276.00000 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 2 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1433.9244 0 -1433.9244 16229.277 3354.7817 656 0 -1451.4627 0 -1451.4627 791.75319 3356.2172 Loop time of 2.17449 on 1 procs for 593 steps with 216 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1433.92437745581 -1451.46127258551 -1451.46267603778 Force two-norm initial, final = 190.99913 4.0361924 Force max component initial, final = 172.68430 2.6919325 Final line search alpha, max atom move = 0.00039378709 0.0010600483 Iterations, force evaluations = 593 723 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.018 | 2.018 | 2.018 | 0.0 | 92.81 Neigh | 0.024736 | 0.024736 | 0.024736 | 0.0 | 1.14 Comm | 0.025984 | 0.025984 | 0.025984 | 0.0 | 1.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1057 | | | 4.86 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 58464.0 ave 58464 max 58464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58464 Ave neighs/atom = 270.66667 Neighbor list builds = 7 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 2 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1451.4627 0 -1451.4627 791.75319 Loop time of 2.028e-06 on 1 procs for 0 steps with 216 atoms 147.9% 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 | | 2.028e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 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: 58480.0 ave 58480 max 58480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58480 Ave neighs/atom = 270.74074 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 = 10.01655 ghost atom cutoff = 10.01655 binsize = 5.008275, bins = 2 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.01655 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) = 4.608 | 4.608 | 4.608 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 -1451.4627 -1451.4627 9.6016153 72.749415 4.8048104 791.75319 791.75319 757.97129 1168.2962 448.99207 2.6213183 1200.1189 Loop time of 1.952e-06 on 1 procs for 0 steps with 216 atoms 204.9% 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 | | 1.952e-06 | | |100.00 Nlocal: 216.000 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4222.00 ave 4222 max 4222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29240.0 ave 29240 max 29240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58480.0 ave 58480 max 58480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58480 Ave neighs/atom = 270.74074 Neighbor list builds = 0 Dangerous builds = 0 216 -1451.46267603778 eV 2.6213182840101 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02