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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -49.600000 0.0000000) to (20.249115 49.600000 7.0144992) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8597876 4.2986667 4.6763328 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.600000 0.0000000) to (20.249115 49.600000 7.0144992) create_atoms CPU = 0.001 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8597876 4.2986667 4.6763328 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.600000 0.0000000) to (20.249115 49.600000 7.0144992) create_atoms CPU = 0.001 seconds 601 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 = 7 34 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 = 1200 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_321233176498_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 = 7 34 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) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4966.5961 0 -4966.5961 36601.756 39 0 -5126.8652 0 -5126.8652 6076.7895 Loop time of 2.28789 on 1 procs for 39 steps with 1200 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 = -4966.59610245071 -5126.8604855524 -5126.86524949489 Force two-norm initial, final = 239.33008 0.25390331 Force max component initial, final = 57.176094 0.052585824 Final line search alpha, max atom move = 1.0000000 0.052585824 Iterations, force evaluations = 39 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2796 | 2.2796 | 2.2796 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0034751 | 0.0034751 | 0.0034751 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004782 | | | 0.21 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4539.00 ave 4539 max 4539 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: 77716.0 ave 77716 max 77716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77716 Ave neighs/atom = 64.763333 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 34 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -5126.8652 0 -5126.8652 6076.7895 14090.11 44 0 -5127.1074 0 -5127.1074 202.61225 14137.865 Loop time of 0.238849 on 1 procs for 5 steps with 1200 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5126.86524949489 -5127.10257260113 -5127.10737829568 Force two-norm initial, final = 116.80482 3.1794474 Force max component initial, final = 111.57343 2.0683370 Final line search alpha, max atom move = 0.00010907838 0.00022561086 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23675 | 0.23675 | 0.23675 | 0.0 | 99.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034095 | 0.00034095 | 0.00034095 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001757 | | | 0.74 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4547.00 ave 4547 max 4547 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: 77228.0 ave 77228 max 77228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77228 Ave neighs/atom = 64.356667 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 = 7 34 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) = 4.743 | 4.743 | 4.743 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5127.1074 0 -5127.1074 202.61225 Loop time of 2.392e-06 on 1 procs for 0 steps with 1200 atoms 167.2% 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 | | 2.392e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4540.00 ave 4540 max 4540 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: 77180.0 ave 77180 max 77180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77180 Ave neighs/atom = 64.316667 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 = 7 34 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) = 4.743 | 4.743 | 4.743 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 -5127.1074 -5127.1074 20.242937 99.649475 7.0086651 202.61225 202.61225 232.0112 235.45677 140.36879 2.2684526 764.72897 Loop time of 2.38e-06 on 1 procs for 0 steps with 1200 atoms 210.1% 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 | | 2.38e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4540.00 ave 4540 max 4540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38590.0 ave 38590 max 38590 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77180.0 ave 77180 max 77180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77180 Ave neighs/atom = 64.316667 Neighbor list builds = 0 Dangerous builds = 0 1200 -5127.10737829568 eV 2.26845256653564 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02