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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -53.580451 0.0000000) to (43.745299 53.580451 8.8681001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3932560 5.1375043 5.9120667 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.580451 0.0000000) to (43.745299 53.580451 8.8681001) create_atoms CPU = 0.002 seconds 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3932560 5.1375043 5.9120667 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.580451 0.0000000) to (43.745299 53.580451 8.8681001) create_atoms CPU = 0.002 seconds 1758 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 = 15 36 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 52 atoms, new total = 3464 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_390178379548_001#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 = 15 36 3 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) = 5.688 | 5.688 | 5.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12139.396 0 -12139.396 3327.2595 70 0 -12219.086 0 -12219.086 -9509.0042 Loop time of 6.56145 on 1 procs for 70 steps with 3464 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 = -12139.3961678354 -12219.0748233187 -12219.0863762979 Force two-norm initial, final = 81.244535 0.30914892 Force max component initial, final = 9.8741420 0.040257391 Final line search alpha, max atom move = 1.0000000 0.040257391 Iterations, force evaluations = 70 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5307 | 6.5307 | 6.5307 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011829 | 0.011829 | 0.011829 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01895 | | | 0.29 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8399.00 ave 8399 max 8399 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: 266888.0 ave 266888 max 266888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266888 Ave neighs/atom = 77.046189 Neighbor list builds = 0 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 = 15 36 3 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 : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.685 | 5.685 | 5.685 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -12219.086 0 -12219.086 -9509.0042 41571.753 74 0 -12219.752 0 -12219.752 -1367.7364 41330.671 Loop time of 0.293176 on 1 procs for 4 steps with 3464 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 = -12219.0863762979 -12219.7471761226 -12219.7524969916 Force two-norm initial, final = 327.68918 11.369519 Force max component initial, final = 244.47200 11.257164 Final line search alpha, max atom move = 4.5071626e-05 0.00050737868 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29028 | 0.29028 | 0.29028 | 0.0 | 99.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037118 | 0.00037118 | 0.00037118 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00252 | | | 0.86 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8097.00 ave 8097 max 8097 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: 267768.0 ave 267768 max 267768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267768 Ave neighs/atom = 77.300231 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 = 15 36 3 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) = 5.824 | 5.824 | 5.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12219.752 0 -12219.752 -1367.7364 Loop time of 2.265e-06 on 1 procs for 0 steps with 3464 atoms 176.6% 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 | | 2.265e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8140.00 ave 8140 max 8140 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: 267824.0 ave 267824 max 267824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267824 Ave neighs/atom = 77.316397 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 = 15 36 3 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) = 5.824 | 5.824 | 5.824 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 -12219.752 -12219.752 43.593551 107.1609 8.8473629 -1367.7364 -1367.7364 59.440127 -4598.0108 435.36163 2.270313 1843.7093 Loop time of 2.23e-06 on 1 procs for 0 steps with 3464 atoms 224.2% 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 | | 2.23e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8140.00 ave 8140 max 8140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133912.0 ave 133912 max 133912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267824.0 ave 267824 max 267824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267824 Ave neighs/atom = 77.316397 Neighbor list builds = 0 Dangerous builds = 0 3464 -12219.7524969916 eV 2.27031303915871 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07