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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -45.961781 0.0000000) to (32.499887 45.961781 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0184976 6.2417233 5.1068645 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -45.961781 0.0000000) to (32.499887 45.961781 5.1068645) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0184976 6.2417233 5.1068645 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.961781 0.0000000) to (32.499887 45.961781 5.1068645) create_atoms CPU = 0.001 seconds 650 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1296 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5108.1227 0 -5108.1227 59787.681 443 0 -5499.9501 0 -5499.9501 6599.9023 Loop time of 86.4793 on 1 procs for 443 steps with 1296 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 = -5108.12270108227 -5499.94515732008 -5499.95008650558 Force two-norm initial, final = 557.78992 0.22281227 Force max component initial, final = 125.28339 0.025806743 Final line search alpha, max atom move = 1.0000000 0.025806743 Iterations, force evaluations = 443 864 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 86.248 | 86.248 | 86.248 | 0.0 | 99.73 Neigh | 0.091659 | 0.091659 | 0.091659 | 0.0 | 0.11 Comm | 0.074305 | 0.074305 | 0.074305 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06579 | | | 0.08 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6423.00 ave 6423 max 6423 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: 149130.0 ave 149130 max 149130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149130 Ave neighs/atom = 115.06944 Neighbor list builds = 9 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 443 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 443 0 -5499.9501 0 -5499.9501 6599.9023 15256.785 474 0 -5511.9137 0 -5511.9137 -6.4323027 15291.533 Loop time of 3.76863 on 1 procs for 31 steps with 1296 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 = -5499.95008650559 -5511.90989267186 -5511.91372699664 Force two-norm initial, final = 643.62781 2.1408731 Force max component initial, final = 557.95317 0.49891919 Final line search alpha, max atom move = 0.00011056364 5.5162321e-05 Iterations, force evaluations = 31 32 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7464 | 3.7464 | 3.7464 | 0.0 | 99.41 Neigh | 0.010011 | 0.010011 | 0.010011 | 0.0 | 0.27 Comm | 0.0019955 | 0.0019955 | 0.0019955 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01025 | | | 0.27 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6500.00 ave 6500 max 6500 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: 146708.0 ave 146708 max 146708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146708 Ave neighs/atom = 113.20062 Neighbor list builds = 1 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.189 | 5.189 | 5.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5511.9137 0 -5511.9137 -6.4323027 Loop time of 2.026e-06 on 1 procs for 0 steps with 1296 atoms 148.1% 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 | | 2.026e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6477.00 ave 6477 max 6477 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: 146614.0 ave 146614 max 146614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146614 Ave neighs/atom = 113.12809 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.189 | 5.189 | 5.189 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 -5511.9137 -5511.9137 33.493834 91.302804 5.0003688 -6.4323027 -6.4323027 -41.142027 -29.339239 51.184357 2.357437 2609.4603 Loop time of 2.117e-06 on 1 procs for 0 steps with 1296 atoms 188.9% 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 | | 2.117e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6477.00 ave 6477 max 6477 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73307.0 ave 73307 max 73307 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146614.0 ave 146614 max 146614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146614 Ave neighs/atom = 113.12809 Neighbor list builds = 0 Dangerous builds = 0 1296 -5511.91372699663 eV 2.35743700069241 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:30