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 -46.701597 0.0000000) to (28.596615 46.701597 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1993846 5.3065997 5.7481360 Created 1067 atoms using lattice units in orthogonal box = (0.0000000 -46.701597 0.0000000) to (28.596615 46.701597 8.6222040) create_atoms CPU = 0.001 seconds 1067 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1993846 5.3065997 5.7481360 Created 1067 atoms using lattice units in orthogonal box = (0.0000000 -46.701597 0.0000000) to (28.596615 46.701597 8.6222040) create_atoms CPU = 0.001 seconds 1067 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 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 70 atoms, new total = 2064 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 22 3 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) = 6.499 | 6.499 | 6.499 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9098.9734 0 -9098.9734 -6012.2283 49 0 -9163.0021 0 -9163.0021 -34616.472 Loop time of 1.78543 on 1 procs for 49 steps with 2064 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 = -9098.97340115558 -9162.99446188946 -9163.0020991225 Force two-norm initial, final = 12.041088 0.27819740 Force max component initial, final = 2.1539891 0.014467199 Final line search alpha, max atom move = 1.0000000 0.014467199 Iterations, force evaluations = 49 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7442 | 1.7442 | 1.7442 | 0.0 | 97.69 Neigh | 0.026611 | 0.026611 | 0.026611 | 0.0 | 1.49 Comm | 0.006721 | 0.006721 | 0.006721 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007932 | | | 0.44 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9333.00 ave 9333 max 9333 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: 458490.0 ave 458490 max 458490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458490 Ave neighs/atom = 222.13663 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 7 22 3 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.501 | 6.501 | 6.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -9163.0021 0 -9163.0021 -34616.472 23030.038 57 0 -9165.5421 0 -9165.5421 -12064.612 22724.252 Loop time of 0.198881 on 1 procs for 8 steps with 2064 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 = -9163.0020991225 -9165.53839047216 -9165.54207668435 Force two-norm initial, final = 534.98475 5.4182081 Force max component initial, final = 394.51419 5.2967110 Final line search alpha, max atom move = 5.3911091e-05 0.00028555147 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19462 | 0.19462 | 0.19462 | 0.0 | 97.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067307 | 0.00067307 | 0.00067307 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003589 | | | 1.80 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9505.00 ave 9505 max 9505 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: 461654.0 ave 461654 max 461654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461654 Ave neighs/atom = 223.66957 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 22 3 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) = 6.639 | 6.639 | 6.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9165.5421 0 -9165.5421 -12064.612 Loop time of 1.603e-06 on 1 procs for 0 steps with 2064 atoms 187.1% 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 | | 1.603e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9588.00 ave 9588 max 9588 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: 462048.0 ave 462048 max 462048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462048 Ave neighs/atom = 223.86047 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 22 3 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) = 6.639 | 6.639 | 6.639 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 -9165.5421 -9165.5421 28.385475 93.403195 8.5710038 -12064.612 -12064.612 -69.159382 -36495.906 371.22776 2.4111456 622.02225 Loop time of 1.939e-06 on 1 procs for 0 steps with 2064 atoms 206.3% 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 | | 1.939e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9588.00 ave 9588 max 9588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231024.0 ave 231024 max 231024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 462048.0 ave 462048 max 462048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 462048 Ave neighs/atom = 223.86047 Neighbor list builds = 0 Dangerous builds = 0 2064 -9109.33663963475 eV 2.41114555768339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02