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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -69.194578 0.0000000) to (39.949508 69.194578 6.7850866) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1460782 6.2097699 6.7850866 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -69.194578 0.0000000) to (39.949508 69.194578 6.7850866) create_atoms CPU = 0.002 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1460782 6.2097699 6.7850866 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -69.194578 0.0000000) to (39.949508 69.194578 6.7850866) create_atoms CPU = 0.002 seconds 1252 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 = 13 43 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2496 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_070797404269_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 = 13 43 3 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) = 5.312 | 5.312 | 5.312 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13803.053 0 -13803.053 45655.041 53 0 -14349.504 0 -14349.504 8130.8598 Loop time of 3.96532 on 1 procs for 53 steps with 2496 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13803.052970137 -14349.491225585 -14349.5043328763 Force two-norm initial, final = 561.39467 0.40448083 Force max component initial, final = 113.52869 0.058852418 Final line search alpha, max atom move = 1.0000000 0.058852418 Iterations, force evaluations = 53 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9423 | 3.9423 | 3.9423 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0099239 | 0.0099239 | 0.0099239 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01313 | | | 0.33 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 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: 194392.0 ave 194392 max 194392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 194392 Ave neighs/atom = 77.881410 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 43 3 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.312 | 5.312 | 5.312 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -14349.504 0 -14349.504 8130.8598 37511.886 59 0 -14350.403 0 -14350.403 -35.808103 37680.18 Loop time of 0.35244 on 1 procs for 6 steps with 2496 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 = -14349.5043328763 -14350.4017527685 -14350.403037563 Force two-norm initial, final = 392.83451 4.1106317 Force max component initial, final = 340.77182 3.8498949 Final line search alpha, max atom move = 6.1798746e-05 0.00023791867 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34829 | 0.34829 | 0.34829 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057954 | 0.00057954 | 0.00057954 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003568 | | | 1.01 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 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: 193456.0 ave 193456 max 193456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193456 Ave neighs/atom = 77.506410 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 = 13 43 3 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) = 5.449 | 5.449 | 5.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14350.403 0 -14350.403 -35.808103 Loop time of 2.094e-06 on 1 procs for 0 steps with 2496 atoms 191.0% 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 | | 2.094e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 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: 193368.0 ave 193368 max 193368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193368 Ave neighs/atom = 77.471154 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 = 13 43 3 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) = 5.449 | 5.449 | 5.449 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 -14350.403 -14350.403 39.997031 139.06071 6.7745551 -35.808103 -35.808103 -163.89382 0.07606308 56.393447 2.4671826 1105.3885 Loop time of 1.928e-06 on 1 procs for 0 steps with 2496 atoms 259.3% 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 | | 1.928e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8364.00 ave 8364 max 8364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 96684.0 ave 96684 max 96684 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 193368.0 ave 193368 max 193368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 193368 Ave neighs/atom = 77.471154 Neighbor list builds = 0 Dangerous builds = 0 2496 -14350.403037563 eV 2.46718258471989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04