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 -63.649754 0.0000000) to (22.503586 63.649754 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1373417 6.7507315 5.5400000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -63.649754 0.0000000) to (22.503586 63.649754 5.5400000) create_atoms CPU = 0.006 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1373417 6.7507315 5.5400000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -63.649754 0.0000000) to (22.503586 63.649754 5.5400000) create_atoms CPU = 0.005 seconds 530 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 = 7 40 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 = 1058 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_020840179467_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 = 7 40 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) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5918.5005 0 -5918.5005 36801.099 54 0 -6088.0227 0 -6088.0227 9332.9471 Loop time of 4.29546 on 1 procs for 54 steps with 1058 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 = -5918.50048052945 -6088.01749893364 -6088.02272188117 Force two-norm initial, final = 247.06750 0.29599061 Force max component initial, final = 58.757642 0.053863681 Final line search alpha, max atom move = 1.0000000 0.053863681 Iterations, force evaluations = 54 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2695 | 4.2695 | 4.2695 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012603 | 0.012603 | 0.012603 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01333 | | | 0.31 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4901.00 ave 4901 max 4901 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: 82508.0 ave 82508 max 82508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82508 Ave neighs/atom = 77.984877 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 = 7 40 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.620 | 4.620 | 4.620 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -6088.0227 0 -6088.0227 9332.9471 15870.413 60 0 -6088.4574 0 -6088.4574 23.627327 15953.497 Loop time of 0.383966 on 1 procs for 6 steps with 1058 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 = -6088.02272188117 -6088.45727435182 -6088.45736211612 Force two-norm initial, final = 187.72387 0.90695334 Force max component initial, final = 172.02436 0.64927541 Final line search alpha, max atom move = 0.00040725439 0.00026442026 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.37897 | 0.37897 | 0.37897 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095906 | 0.00095906 | 0.00095906 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004032 | | | 1.05 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4922.00 ave 4922 max 4922 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: 82052.0 ave 82052 max 82052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82052 Ave neighs/atom = 77.553875 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 = 7 40 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) = 4.758 | 4.758 | 4.758 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6088.4574 0 -6088.4574 23.627327 Loop time of 6.565e-06 on 1 procs for 0 steps with 1058 atoms 198.0% 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 | | 6.565e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4922.00 ave 4922 max 4922 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: 82016.0 ave 82016 max 82016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82016 Ave neighs/atom = 77.519849 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 = 7 40 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) = 4.758 | 4.758 | 4.758 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 -6088.4574 -6088.4574 22.511188 127.9332 5.5395465 23.627327 23.627327 -33.638699 39.320639 65.200041 2.5669648 427.5644 Loop time of 8.289e-06 on 1 procs for 0 steps with 1058 atoms 241.3% 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 | | 8.289e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4922.00 ave 4922 max 4922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41008.0 ave 41008 max 41008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82016.0 ave 82016 max 82016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82016 Ave neighs/atom = 77.519849 Neighbor list builds = 0 Dangerous builds = 0 1058 -6088.45736211612 eV 2.56696477867844 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05