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 = 4.0333018 4.0333018 4.0333018 Created orthogonal box = (0.0000000 -48.734572 0.0000000) to (59.687417 48.734572 9.8795315) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7234509 6.0083718 6.5863543 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -48.734572 0.0000000) to (59.687417 48.734572 9.8795315) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7234509 6.0083718 6.5863543 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -48.734572 0.0000000) to (59.687417 48.734572 9.8795315) create_atoms CPU = 0.003 seconds 1756 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 = 15 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_577453891941_005#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 = 15 23 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) = 6.991 | 6.991 | 6.991 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11462.601 0 -11462.601 19535.869 49 0 -11782.767 0 -11782.767 4670.7765 Loop time of 2.80791 on 1 procs for 49 steps with 3506 atoms 96.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11462.6013319564 -11782.7587468966 -11782.7666397726 Force two-norm initial, final = 233.93391 0.25880340 Force max component initial, final = 44.066552 0.051880863 Final line search alpha, max atom move = 1.0000000 0.051880863 Iterations, force evaluations = 49 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7737 | 2.7737 | 2.7737 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013693 | 0.013693 | 0.013693 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0205 | | | 0.73 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994.0 ave 10994 max 10994 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: 496208.0 ave 496208 max 496208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496208 Ave neighs/atom = 141.53109 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 23 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) = 6.991 | 6.991 | 6.991 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -11782.767 0 -11782.767 4670.7765 57475.966 57 0 -11783.797 0 -11783.797 -29.204961 57806.02 Loop time of 0.299838 on 1 procs for 8 steps with 3506 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11782.7666397727 -11783.7895627837 -11783.7965641753 Force two-norm initial, final = 331.93616 1.8934207 Force max component initial, final = 298.17630 1.2998912 Final line search alpha, max atom move = 6.8169136e-05 8.8612463e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29235 | 0.29235 | 0.29235 | 0.0 | 97.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092647 | 0.00092647 | 0.00092647 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006563 | | | 2.19 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994.0 ave 10994 max 10994 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: 509152.0 ave 509152 max 509152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 509152 Ave neighs/atom = 145.22305 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 = 15 24 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) = 7.129 | 7.129 | 7.129 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11783.797 0 -11783.797 -29.204961 Loop time of 2.009e-06 on 1 procs for 0 steps with 3506 atoms 199.1% 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 | | 2.009e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994.0 ave 10994 max 10994 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: 503012.0 ave 503012 max 503012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503012 Ave neighs/atom = 143.47176 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 = 15 24 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) = 7.129 | 7.129 | 7.129 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 -11783.797 -11783.797 59.658141 98.217439 9.8654012 -29.204961 -29.204961 -36.010673 -27.894877 -23.709332 2.5395371 1967.9895 Loop time of 2.608e-06 on 1 procs for 0 steps with 3506 atoms 230.1% 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 | | 2.608e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10994.0 ave 10994 max 10994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251506.0 ave 251506 max 251506 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 503012.0 ave 503012 max 503012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503012 Ave neighs/atom = 143.47176 Neighbor list builds = 0 Dangerous builds = 0 3506 -11783.7965641754 eV 2.53953705285084 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03