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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549139 52.111839 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504087 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549139 52.111839 8.6256130) create_atoms CPU = 0.003 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2457842 4.9970257 5.7504087 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -52.111839 0.0000000) to (42.549139 52.111839 8.6256130) create_atoms CPU = 0.002 seconds 1759 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 ghost atom cutoff = 6 binsize = 3, bins = 15 35 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3510 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_700541006254_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 ghost atom cutoff = 6 binsize = 3, bins = 15 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.692 | 5.692 | 5.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14939.084 0 -14939.084 68858.394 74 0 -15555.158 0 -15555.158 13568.51 Loop time of 14.7776 on 1 procs for 74 steps with 3510 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14939.0844765864 -15555.1445549821 -15555.15784583 Force two-norm initial, final = 599.84496 0.44923053 Force max component initial, final = 98.677633 0.047076840 Final line search alpha, max atom move = 1.0000000 0.047076840 Iterations, force evaluations = 74 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.665 | 14.665 | 14.665 | 0.0 | 99.24 Neigh | 0.066391 | 0.066391 | 0.066391 | 0.0 | 0.45 Comm | 0.017558 | 0.017558 | 0.017558 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02846 | | | 0.19 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8564.00 ave 8564 max 8564 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: 273382.0 ave 273382 max 273382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273382 Ave neighs/atom = 77.886610 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 ghost atom cutoff = 6 binsize = 3, bins = 15 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.691 | 5.691 | 5.691 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -15555.158 0 -15555.158 13568.51 38251.383 84 0 -15557.792 0 -15557.792 -61.204656 38528.446 Loop time of 1.39063 on 1 procs for 10 steps with 3510 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15555.15784583 -15557.7917851171 -15557.7921437515 Force two-norm initial, final = 674.17453 2.8631014 Force max component initial, final = 628.62007 1.8950069 Final line search alpha, max atom move = 0.00017886898 0.00033895795 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3823 | 1.3823 | 1.3823 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010288 | 0.0010288 | 0.0010288 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007334 | | | 0.53 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8499.00 ave 8499 max 8499 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: 273176.0 ave 273176 max 273176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273176 Ave neighs/atom = 77.827920 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.830 | 5.830 | 5.830 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15557.792 0 -15557.792 -61.204656 Loop time of 1.999e-06 on 1 procs for 0 steps with 3510 atoms 150.1% 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 | | 1.999e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 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: 272884.0 ave 272884 max 272884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272884 Ave neighs/atom = 77.744729 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 5.830 | 5.830 | 5.830 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 -15557.792 -15557.792 42.494493 105.16247 8.6216037 -61.204656 -61.204656 -78.701234 -58.626543 -46.286192 2.1955835 1626.794 Loop time of 2.421e-06 on 1 procs for 0 steps with 3510 atoms 247.8% 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 | | 2.421e-06 | | |100.00 Nlocal: 3510.00 ave 3510 max 3510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8504.00 ave 8504 max 8504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136442.0 ave 136442 max 136442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272884.0 ave 272884 max 272884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272884 Ave neighs/atom = 77.744729 Neighbor list builds = 0 Dangerous builds = 0 3510 -15557.7921437515 eV 2.19558345645872 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16