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 = 2.8599998 2.8599998 2.8599998 Created orthogonal box = (0.0000000 -49.536650 0.0000000) to (20.223253 49.536650 7.0055402) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8535806 4.2931763 4.6703601 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.536650 0.0000000) to (20.223253 49.536650 7.0055402) create_atoms CPU = 0.006 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8535806 4.2931763 4.6703601 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.536650 0.0000000) to (20.223253 49.536650 7.0055402) create_atoms CPU = 0.004 seconds 601 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 8 37 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 5.4399999999999995 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_857282754307_003#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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 8 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1579.0051 0 -1579.0051 55958.753 86 0 -1823.1249 0 -1823.1249 7512.7566 Loop time of 0.839205 on 1 procs for 86 steps with 1200 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 = -1579.00510541574 -1823.1230307745 -1823.12485030912 Force two-norm initial, final = 521.39948 0.21249397 Force max component initial, final = 158.70063 0.070057783 Final line search alpha, max atom move = 1.0000000 0.070057783 Iterations, force evaluations = 86 161 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78627 | 0.78627 | 0.78627 | 0.0 | 93.69 Neigh | 0.013563 | 0.013563 | 0.013563 | 0.0 | 1.62 Comm | 0.016934 | 0.016934 | 0.016934 | 0.0 | 2.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02244 | | | 2.67 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4171.00 ave 4171 max 4171 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: 69450.0 ave 69450 max 69450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69450 Ave neighs/atom = 57.875000 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 8 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -1823.1249 0 -1823.1249 7512.7566 14036.191 92 0 -1823.415 0 -1823.415 27.96914 14116.465 Loop time of 0.0462435 on 1 procs for 6 steps with 1200 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 = -1823.12485030912 -1823.41494652271 -1823.41497599724 Force two-norm initial, final = 126.46730 0.56327688 Force max component initial, final = 110.51750 0.35155223 Final line search alpha, max atom move = 0.0011130549 0.00039129695 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041863 | 0.041863 | 0.041863 | 0.0 | 90.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077573 | 0.00077573 | 0.00077573 | 0.0 | 1.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003604 | | | 7.79 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3927.00 ave 3927 max 3927 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: 69438.0 ave 69438 max 69438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69438 Ave neighs/atom = 57.865000 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 8 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1823.415 0 -1823.415 27.96914 Loop time of 6.355e-06 on 1 procs for 0 steps with 1200 atoms 204.6% 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 | | 6.355e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3927.00 ave 3927 max 3927 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: 69410.0 ave 69410 max 69410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69410 Ave neighs/atom = 57.841667 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 = 5.44 ghost atom cutoff = 5.44 binsize = 2.72, bins = 8 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.4399999999999995 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) = 4.729 | 4.729 | 4.729 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 -1823.415 -1823.415 20.235075 99.563862 7.0067953 27.96914 27.96914 39.923449 25.582538 18.401434 2.2712744 689.61548 Loop time of 6.796e-06 on 1 procs for 0 steps with 1200 atoms 264.9% 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 | | 6.796e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3927.00 ave 3927 max 3927 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34705.0 ave 34705 max 34705 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69410.0 ave 69410 max 69410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69410 Ave neighs/atom = 57.841667 Neighbor list builds = 0 Dangerous builds = 0 1200 -1823.41497599724 eV 2.2712743911792 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01