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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -53.496006 0.0000000) to (43.679306 53.496006 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3851199 5.1297540 5.9031479 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.496006 0.0000000) to (43.679306 53.496006 8.8547219) create_atoms CPU = 0.007 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3851199 5.1297540 5.9031479 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.496006 0.0000000) to (43.679306 53.496006 8.8547219) create_atoms CPU = 0.006 seconds 1758 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 3504 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.011 | 7.011 | 7.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10306.956 0 -10306.956 141534.53 83 0 -12359.989 0 -12359.989 6098.0286 Loop time of 7.77643 on 1 procs for 83 steps with 3504 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 = -10306.9560948678 -12359.9784102 -12359.989260918 Force two-norm initial, final = 2791.9129 0.37809782 Force max component initial, final = 394.83562 0.075805715 Final line search alpha, max atom move = 1.0000000 0.075805715 Iterations, force evaluations = 83 156 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5242 | 7.5242 | 7.5242 | 0.0 | 96.76 Neigh | 0.15482 | 0.15482 | 0.15482 | 0.0 | 1.99 Comm | 0.0431 | 0.0431 | 0.0431 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05432 | | | 0.70 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11125.0 ave 11125 max 11125 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: 507128.0 ave 507128 max 507128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507128 Ave neighs/atom = 144.72831 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.009 | 7.009 | 7.009 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -12359.989 0 -12359.989 6098.0286 41381.098 89 0 -12360.661 0 -12360.661 -301.19621 41571.015 Loop time of 0.379782 on 1 procs for 6 steps with 3504 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 = -12359.989260918 -12360.6566379649 -12360.6607095089 Force two-norm initial, final = 304.08828 15.625690 Force max component initial, final = 267.05863 13.473630 Final line search alpha, max atom move = 5.8005265e-05 0.00078154150 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36923 | 0.36923 | 0.36923 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020169 | 0.0020169 | 0.0020169 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008538 | | | 2.25 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11014.0 ave 11014 max 11014 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: 496112.0 ave 496112 max 496112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 496112 Ave neighs/atom = 141.58447 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.147 | 7.147 | 7.147 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12360.661 0 -12360.661 -301.19621 Loop time of 6.655e-06 on 1 procs for 0 steps with 3504 atoms 210.4% 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 | | 6.655e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11016.0 ave 11016 max 11016 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: 494788.0 ave 494788 max 494788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494788 Ave neighs/atom = 141.20662 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.147 | 7.147 | 7.147 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 -12360.661 -12360.661 43.650079 107.56884 8.8535839 -301.19621 -301.19621 -518.93583 -95.817286 -288.83551 2.3005761 1586.7096 Loop time of 6.896e-06 on 1 procs for 0 steps with 3504 atoms 275.5% 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 | | 6.896e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11016.0 ave 11016 max 11016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 247394.0 ave 247394 max 247394 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 494788.0 ave 494788 max 494788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 494788 Ave neighs/atom = 141.20662 Neighbor list builds = 0 Dangerous builds = 0 3504 -12360.6782295089 eV 2.30057613963217 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09