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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -50.094724 0.0000000) to (17.710069 50.094724 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8300189 3.7948213 4.3599177 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.094724 0.0000000) to (17.710069 50.094724 4.3599177) create_atoms CPU = 0.001 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8300189 3.7948213 4.3599177 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.094724 0.0000000) to (17.710069 50.094724 4.3599177) create_atoms CPU = 0.000 seconds 266 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 30 2 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 528 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.254 | 5.254 | 5.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3251.0203 0 -3251.0203 83291.168 65 0 -3422.6488 0 -3422.6488 6240.7 Loop time of 18.2711 on 1 procs for 65 steps with 528 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 = -3251.0203262672 -3422.64611093412 -3422.64881719998 Force two-norm initial, final = 309.39814 0.26141951 Force max component initial, final = 71.421724 0.044824243 Final line search alpha, max atom move = 1.0000000 0.044824243 Iterations, force evaluations = 65 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.243 | 18.243 | 18.243 | 0.0 | 99.84 Neigh | 0.020496 | 0.020496 | 0.020496 | 0.0 | 0.11 Comm | 0.0041971 | 0.0041971 | 0.0041971 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003776 | | | 0.02 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3681.00 ave 3681 max 3681 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: 38244.0 ave 38244 max 38244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38244 Ave neighs/atom = 72.431818 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.254 | 5.254 | 5.254 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -3422.6488 0 -3422.6488 6240.7 7736.0726 75 0 -3423.3434 0 -3423.3434 -2698.1349 7765.4076 Loop time of 1.91123 on 1 procs for 10 steps with 528 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 = -3422.64881719998 -3423.34251532893 -3423.34339447275 Force two-norm initial, final = 143.41562 6.1252395 Force max component initial, final = 135.53816 4.7533034 Final line search alpha, max atom move = 0.016638249 0.079086649 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.909 | 1.909 | 1.909 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037552 | 0.00037552 | 0.00037552 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001867 | | | 0.10 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3671.00 ave 3671 max 3671 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: 37848.0 ave 37848 max 37848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37848 Ave neighs/atom = 71.681818 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.392 | 5.392 | 5.392 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3423.3434 0 -3423.3434 -2698.1349 Loop time of 1.807e-06 on 1 procs for 0 steps with 528 atoms 110.7% 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 | | 1.807e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3677.00 ave 3677 max 3677 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: 37860.0 ave 37860 max 37860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37860 Ave neighs/atom = 71.704545 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.392 | 5.392 | 5.392 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 -3423.3434 -3423.3434 17.626147 100.18945 4.3972879 -2698.1349 -2698.1349 976.06503 -9862.5044 792.03464 2.4766456 813.54241 Loop time of 1.939e-06 on 1 procs for 0 steps with 528 atoms 103.1% 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 | | 1.939e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3677.00 ave 3677 max 3677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18930.0 ave 18930 max 18930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37860.0 ave 37860 max 37860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37860 Ave neighs/atom = 71.704545 Neighbor list builds = 0 Dangerous builds = 0 528 -3423.34339447275 eV 2.47664556337651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21