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 -37.120105 0.0000000) to (21.429649 37.120105 4.9600000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5920677 4.4187192 4.9600000 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -37.120105 0.0000000) to (21.429649 37.120105 4.9600000) create_atoms CPU = 0.003 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5920677 4.4187192 4.9600000 Created 339 atoms using lattice units in orthogonal box = (0.0000000 -37.120105 0.0000000) to (21.429649 37.120105 4.9600000) create_atoms CPU = 0.002 seconds 339 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 = 8 27 2 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 = 672 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 27 2 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2817.3068 0 -2817.3068 31556.755 19 0 -2868.1375 0 -2868.1375 6991.0177 Loop time of 1.35269 on 1 procs for 19 steps with 672 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 = -2817.30675848436 -2868.13497385378 -2868.13746173288 Force two-norm initial, final = 65.970726 0.18207291 Force max component initial, final = 12.541338 0.051053933 Final line search alpha, max atom move = 1.0000000 0.051053933 Iterations, force evaluations = 19 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3461 | 1.3461 | 1.3461 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032037 | 0.0032037 | 0.0032037 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003352 | | | 0.25 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 39214.0 ave 39214 max 39214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39214 Ave neighs/atom = 58.354167 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 27 2 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 : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -2868.1375 0 -2868.1375 6991.0177 7891.0707 22 0 -2868.1864 0 -2868.1864 1768.6898 7914.7057 Loop time of 0.232302 on 1 procs for 3 steps with 672 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 = -2868.13746173288 -2868.18620139962 -2868.18637645692 Force two-norm initial, final = 44.493457 0.19450910 Force max component initial, final = 36.870584 0.054007734 Final line search alpha, max atom move = 0.00061728119 3.3337958e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23018 | 0.23018 | 0.23018 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045715 | 0.00045715 | 0.00045715 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001669 | | | 0.72 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3250.00 ave 3250 max 3250 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: 39192.0 ave 39192 max 39192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39192 Ave neighs/atom = 58.321429 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 = 8 27 2 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) = 4.646 | 4.646 | 4.646 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2868.1864 0 -2868.1864 1768.6898 Loop time of 6.505e-06 on 1 procs for 0 steps with 672 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3236.00 ave 3236 max 3236 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: 39190.0 ave 39190 max 39190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39190 Ave neighs/atom = 58.318452 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 = 8 27 2 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) = 4.646 | 4.646 | 4.646 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 -2868.1864 -2868.1864 21.45159 74.24021 4.9697678 1768.6898 1768.6898 2.3071963 5307.1826 -3.4204245 2.3178349 501.62277 Loop time of 6.906e-06 on 1 procs for 0 steps with 672 atoms 246.2% 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 | | 6.906e-06 | | |100.00 Nlocal: 672.000 ave 672 max 672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3236.00 ave 3236 max 3236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19595.0 ave 19595 max 19595 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39190.0 ave 39190 max 39190 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39190 Ave neighs/atom = 58.318452 Neighbor list builds = 0 Dangerous builds = 0 672 -2868.18637645692 eV 2.31783486292935 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02