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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -46.701920 0.0000000) to (28.596813 46.701920 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1994205 5.3066364 5.7481757 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -46.701920 0.0000000) to (28.596813 46.701920 8.6222635) create_atoms CPU = 0.005 seconds 1074 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1994205 5.3066364 5.7481757 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -46.701920 0.0000000) to (28.596813 46.701920 8.6222635) create_atoms CPU = 0.004 seconds 1074 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 23 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2112 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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 -9290.7557 0 -9290.7557 18859.573 39 0 -9381.872 0 -9381.872 4954.3111 Loop time of 3.33699 on 1 procs for 39 steps with 2112 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 = -9290.75566414093 -9381.86498461707 -9381.87198633768 Force two-norm initial, final = 87.882588 0.22485356 Force max component initial, final = 7.8347857 0.015392989 Final line search alpha, max atom move = 1.0000000 0.015392989 Iterations, force evaluations = 39 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3058 | 3.3058 | 3.3058 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.015231 | 0.015231 | 0.015231 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01592 | | | 0.48 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9311.00 ave 9311 max 9311 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: 474360.0 ave 474360 max 474360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 474360 Ave neighs/atom = 224.60227 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.490 | 6.490 | 6.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -9381.872 0 -9381.872 4954.3111 23030.516 41 0 -9381.9095 0 -9381.9095 2345.3156 23063.862 Loop time of 0.180294 on 1 procs for 2 steps with 2112 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9381.87198633774 -9381.90768570959 -9381.90954993102 Force two-norm initial, final = 63.471267 0.24528141 Force max component initial, final = 56.411797 0.056822358 Final line search alpha, max atom move = 0.00011332469 6.4393761e-06 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17669 | 0.17669 | 0.17669 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086297 | 0.00086297 | 0.00086297 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002743 | | | 1.52 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9684.00 ave 9684 max 9684 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: 472128.0 ave 472128 max 472128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472128 Ave neighs/atom = 223.54545 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 6.628 | 6.628 | 6.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9381.9095 0 -9381.9095 2345.3156 Loop time of 6.776e-06 on 1 procs for 0 steps with 2112 atoms 177.1% 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 | | 6.776e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9684.00 ave 9684 max 9684 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: 472128.0 ave 472128 max 472128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472128 Ave neighs/atom = 223.54545 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 6.628 | 6.628 | 6.628 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 -9381.9095 -9381.9095 28.631374 93.40384 8.624325 2345.3156 2345.3156 3.9520472 7029.743 2.2517446 2.3569154 656.30868 Loop time of 7.157e-06 on 1 procs for 0 steps with 2112 atoms 293.4% 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 | | 7.157e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9684.00 ave 9684 max 9684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 236064.0 ave 236064 max 236064 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 472128.0 ave 472128 max 472128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 472128 Ave neighs/atom = 223.54545 Neighbor list builds = 0 Dangerous builds = 0 2112 -9324.33346932942 eV 2.35691542494859 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04