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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -57.011439 0.0000000) to (34.910017 57.011439 8.8671532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6306479 5.5168857 5.9114354 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.011439 0.0000000) to (34.910017 57.011439 8.8671532) create_atoms CPU = 0.002 seconds 1491 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6306479 5.5168857 5.9114354 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -57.011439 0.0000000) to (34.910017 57.011439 8.8671532) create_atoms CPU = 0.002 seconds 1491 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2952 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.938 | 6.938 | 6.938 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10376.733 0 -10376.733 789.29432 68 0 -10425.416 0 -10425.416 -6530.1508 Loop time of 3.26067 on 1 procs for 68 steps with 2952 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10376.7328008809 -10425.4076125459 -10425.4158303855 Force two-norm initial, final = 35.597912 0.31959329 Force max component initial, final = 4.7167048 0.082841793 Final line search alpha, max atom move = 1.0000000 0.082841793 Iterations, force evaluations = 68 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1976 | 3.1976 | 3.1976 | 0.0 | 98.07 Neigh | 0.031094 | 0.031094 | 0.031094 | 0.0 | 0.95 Comm | 0.013753 | 0.013753 | 0.013753 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01824 | | | 0.56 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10424.0 ave 10424 max 10424 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: 512694.0 ave 512694 max 512694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 512694 Ave neighs/atom = 173.67683 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.938 | 6.938 | 6.938 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -10425.416 0 -10425.416 -6530.1508 35296.063 71 0 -10425.714 0 -10425.714 -852.8489 35146.797 Loop time of 0.127956 on 1 procs for 3 steps with 2952 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 = -10425.4158303854 -10425.7094034557 -10425.7142344642 Force two-norm initial, final = 198.95514 3.9243268 Force max component initial, final = 149.63221 3.4367777 Final line search alpha, max atom move = 4.6058781e-05 0.00015829379 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12495 | 0.12495 | 0.12495 | 0.0 | 97.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043593 | 0.00043593 | 0.00043593 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002566 | | | 2.01 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10417.0 ave 10417 max 10417 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: 513022.0 ave 513022 max 513022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513022 Ave neighs/atom = 173.78794 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.076 | 7.076 | 7.076 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10425.714 0 -10425.714 -852.8489 Loop time of 2.114e-06 on 1 procs for 0 steps with 2952 atoms 189.2% 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 | | 2.114e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10420.0 ave 10420 max 10420 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: 513386.0 ave 513386 max 513386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513386 Ave neighs/atom = 173.91125 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 30 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 7.076 | 7.076 | 7.076 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 -10425.714 -10425.714 34.843929 114.02288 8.8464013 -852.8489 -852.8489 156.36988 -2630.2696 -84.646949 2.3282871 984.24864 Loop time of 2.615e-06 on 1 procs for 0 steps with 2952 atoms 229.4% 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 | | 2.615e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10420.0 ave 10420 max 10420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 256693.0 ave 256693 max 256693 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 513386.0 ave 513386 max 513386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 513386 Ave neighs/atom = 173.91125 Neighbor list builds = 0 Dangerous builds = 0 2952 -10425.7142344642 eV 2.3282870724091 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04