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 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2299022 4.3171259 4.6763329 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) create_atoms CPU = 0.003 seconds 529 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2299022 4.3171259 4.6763329 Created 529 atoms using lattice units in orthogonal box = (0.0000000 -37.993571 0.0000000) to (23.264462 37.993571 7.0144993) create_atoms CPU = 0.002 seconds 529 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 1051 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4368.0772 0 -4368.0772 29891.364 62 0 -4485.5965 0 -4485.5965 958.4335 Loop time of 6.60723 on 1 procs for 62 steps with 1051 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 = -4368.07721944804 -4485.59228267526 -4485.59648148132 Force two-norm initial, final = 145.21316 0.22803479 Force max component initial, final = 31.250420 0.052721524 Final line search alpha, max atom move = 1.0000000 0.052721524 Iterations, force evaluations = 62 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5709 | 6.5709 | 6.5709 | 0.0 | 99.45 Neigh | 0.01177 | 0.01177 | 0.01177 | 0.0 | 0.18 Comm | 0.010173 | 0.010173 | 0.010173 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0144 | | | 0.22 Nlocal: 1051.00 ave 1051 max 1051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3671.00 ave 3671 max 3671 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: 61116.0 ave 61116 max 61116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61116 Ave neighs/atom = 58.150333 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -4485.5965 0 -4485.5965 958.4335 12400.232 64 0 -4485.6041 0 -4485.6041 2680.8247 12387.854 Loop time of 0.282219 on 1 procs for 2 steps with 1051 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4485.59648148132 -4485.60405512328 -4485.60406325749 Force two-norm initial, final = 21.609060 0.46682273 Force max component initial, final = 16.016826 0.39779477 Final line search alpha, max atom move = 0.0083541188 0.0033232248 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28018 | 0.28018 | 0.28018 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038702 | 0.00038702 | 0.00038702 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001653 | | | 0.59 Nlocal: 1051.00 ave 1051 max 1051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3705.00 ave 3705 max 3705 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: 61120.0 ave 61120 max 61120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61120 Ave neighs/atom = 58.154139 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4485.6041 0 -4485.6041 2680.8247 Loop time of 6.605e-06 on 1 procs for 0 steps with 1051 atoms 166.5% 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 | | 6.605e-06 | | |100.00 Nlocal: 1051.00 ave 1051 max 1051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3705.00 ave 3705 max 3705 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: 61124.0 ave 61124 max 61124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61124 Ave neighs/atom = 58.157945 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.686 | 4.686 | 4.686 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 -4485.6041 -4485.6041 23.253909 75.987143 7.0106776 2680.8247 2680.8247 -10.376214 8001.4298 51.420544 2.2586449 826.73432 Loop time of 6.886e-06 on 1 procs for 0 steps with 1051 atoms 290.4% 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 | | 6.886e-06 | | |100.00 Nlocal: 1051.00 ave 1051 max 1051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3705.00 ave 3705 max 3705 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30562.0 ave 30562 max 30562 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61124.0 ave 61124 max 61124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61124 Ave neighs/atom = 58.157945 Neighbor list builds = 0 Dangerous builds = 0 1051 -4485.60406325749 eV 2.25864487430556 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07