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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4288349 5.2783032 4.4499064 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -41.266734 0.0000000) to (29.179987 41.266734 4.4499064) create_atoms CPU = 0.001 seconds 345 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 688 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_831380044253_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4013.5362 0 -4013.5362 223108.05 73 0 -4661.7607 0 -4661.7607 7877.816 Loop time of 2.62281 on 1 procs for 73 steps with 688 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 = -4013.53620932558 -4661.75655362967 -4661.76068881437 Force two-norm initial, final = 570.32916 0.39162312 Force max component initial, final = 151.81601 0.14105236 Final line search alpha, max atom move = 0.49949806 0.070455378 Iterations, force evaluations = 73 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6056 | 2.6056 | 2.6056 | 0.0 | 99.35 Neigh | 0.0073281 | 0.0073281 | 0.0073281 | 0.0 | 0.28 Comm | 0.0050404 | 0.0050404 | 0.0050404 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004807 | | | 0.18 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3908.00 ave 3908 max 3908 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: 44132.0 ave 44132 max 44132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44132 Ave neighs/atom = 64.145349 Neighbor list builds = 2 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.507 | 4.507 | 4.507 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -4661.7607 0 -4661.7607 7877.816 10716.823 76 0 -4661.8574 0 -4661.8574 -3.0651048 10748.819 Loop time of 0.111915 on 1 procs for 3 steps with 688 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 = -4661.76068881437 -4661.85313462503 -4661.8573552321 Force two-norm initial, final = 94.489528 0.44571098 Force max component initial, final = 70.215369 0.17815823 Final line search alpha, max atom move = 7.9348572e-05 1.4136601e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11098 | 0.11098 | 0.11098 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017416 | 0.00017416 | 0.00017416 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007578 | | | 0.68 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3908.00 ave 3908 max 3908 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: 44138.0 ave 44138 max 44138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44138 Ave neighs/atom = 64.154070 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.645 | 4.645 | 4.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4661.8574 0 -4661.8574 -3.0651048 Loop time of 1.634e-06 on 1 procs for 0 steps with 688 atoms 183.6% 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 | | 1.634e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3908.00 ave 3908 max 3908 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: 44116.0 ave 44116 max 44116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44116 Ave neighs/atom = 64.122093 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.645 | 4.645 | 4.645 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 -4661.8574 -4661.8574 29.208114 82.704174 4.4496906 -3.0651048 -3.0651048 -26.581158 7.3459283 10.039916 2.4650875 475.59842 Loop time of 1.533e-06 on 1 procs for 0 steps with 688 atoms 195.7% 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 | | 1.533e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3908.00 ave 3908 max 3908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22058.0 ave 22058 max 22058 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44116.0 ave 44116 max 44116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44116 Ave neighs/atom = 64.122093 Neighbor list builds = 0 Dangerous builds = 0 688 -4661.8573552321 eV 2.46508746430323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02