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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -42.532323 0.0000000) to (52.091244 42.532323 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9950508 5.2437110 5.7481360 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -42.532323 0.0000000) to (52.091244 42.532323 8.6222040) create_atoms CPU = 0.007 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9950508 5.2437110 5.7481360 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -42.532323 0.0000000) to (52.091244 42.532323 8.6222040) create_atoms CPU = 0.006 seconds 1755 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 16 25 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 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 3495 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_776437554506_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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.545 | 6.545 | 6.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14858.864 0 -14858.864 25269.891 72 0 -15500.68 0 -15500.68 4021.9705 Loop time of 5.02422 on 1 procs for 72 steps with 3495 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 = -14858.8643528237 -15500.6661419682 -15500.6796672956 Force two-norm initial, final = 292.06403 0.42262222 Force max component initial, final = 33.068297 0.076279830 Final line search alpha, max atom move = 1.0000000 0.076279830 Iterations, force evaluations = 72 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7453 | 4.7453 | 4.7453 | 0.0 | 94.45 Neigh | 0.20503 | 0.20503 | 0.20503 | 0.0 | 4.08 Comm | 0.029662 | 0.029662 | 0.029662 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04422 | | | 0.88 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9756.00 ave 9756 max 9756 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: 463292.0 ave 463292 max 463292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463292 Ave neighs/atom = 132.55851 Neighbor list builds = 3 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.547 | 6.547 | 6.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -15500.68 0 -15500.68 4021.9705 38206.048 77 0 -15501.115 0 -15501.115 -126.64587 38296.204 Loop time of 0.271797 on 1 procs for 5 steps with 3495 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 = -15500.6796672957 -15501.1138209272 -15501.1148876125 Force two-norm initial, final = 227.03865 7.4611868 Force max component initial, final = 222.15966 6.6371574 Final line search alpha, max atom move = 8.4321417e-05 0.00055965452 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26309 | 0.26309 | 0.26309 | 0.0 | 96.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015184 | 0.0015184 | 0.0015184 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007191 | | | 2.65 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9982.00 ave 9982 max 9982 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: 463458.0 ave 463458 max 463458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463458 Ave neighs/atom = 132.60601 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.685 | 6.685 | 6.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15501.115 0 -15501.115 -126.64587 Loop time of 6.165e-06 on 1 procs for 0 steps with 3495 atoms 0.0% 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 | | 6.165e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10009.0 ave 10009 max 10009 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: 463242.0 ave 463242 max 463242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463242 Ave neighs/atom = 132.54421 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 = 6.85 ghost atom cutoff = 6.85 binsize = 3.425, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85 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) = 6.685 | 6.685 | 6.685 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 -15501.115 -15501.115 52.038589 85.417381 8.615569 -126.64587 -126.64587 -277.3943 33.845346 -136.38864 2.2111694 1424.7793 Loop time of 6.826e-06 on 1 procs for 0 steps with 3495 atoms 336.9% 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 | | 6.826e-06 | | |100.00 Nlocal: 3495.00 ave 3495 max 3495 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10009.0 ave 10009 max 10009 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 231621.0 ave 231621 max 231621 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 463242.0 ave 463242 max 463242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 463242 Ave neighs/atom = 132.54421 Neighbor list builds = 0 Dangerous builds = 0 3495 -15501.1148876125 eV 2.21116942657823 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06