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 = 3.5937292 3.5937292 3.5937292 Created orthogonal box = (0.0000000 -43.423195 0.0000000) to (53.182335 43.423195 8.8028028) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0996760 5.3535446 5.8685352 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -43.423195 0.0000000) to (53.182335 43.423195 8.8028028) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0996760 5.3535446 5.8685352 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -43.423195 0.0000000) to (53.182335 43.423195 8.8028028) create_atoms CPU = 0.002 seconds 1755 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 3480 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.526 | 6.526 | 6.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11240.94 0 -11240.94 177985.76 108 0 -14823.518 0 -14823.518 -6516.702 Loop time of 33.1935 on 1 procs for 108 steps with 3480 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11240.939582811 -14823.5028466285 -14823.5175839555 Force two-norm initial, final = 3662.8053 0.48260704 Force max component initial, final = 692.05142 0.080968492 Final line search alpha, max atom move = 1.0000000 0.080968492 Iterations, force evaluations = 108 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.039 | 33.039 | 33.039 | 0.0 | 99.54 Neigh | 0.099702 | 0.099702 | 0.099702 | 0.0 | 0.30 Comm | 0.022121 | 0.022121 | 0.022121 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03233 | | | 0.10 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9737.00 ave 9737 max 9737 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: 460174.0 ave 460174 max 460174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460174 Ave neighs/atom = 132.23391 Neighbor list builds = 3 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.526 | 6.526 | 6.526 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -14823.518 0 -14823.518 -6516.702 40657.451 113 0 -14824.073 0 -14824.073 12.081378 40492.572 Loop time of 1.39189 on 1 procs for 5 steps with 3480 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 = -14823.5175839555 -14824.0667650578 -14824.0727044483 Force two-norm initial, final = 310.83572 4.3984966 Force max component initial, final = 256.71024 3.6882155 Final line search alpha, max atom move = 2.5079531e-05 9.2498716e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3874 | 1.3874 | 1.3874 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061642 | 0.00061642 | 0.00061642 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003913 | | | 0.28 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9709.00 ave 9709 max 9709 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: 461694.0 ave 461694 max 461694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461694 Ave neighs/atom = 132.67069 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.664 | 6.664 | 6.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14824.073 0 -14824.073 12.081378 Loop time of 2.13e-06 on 1 procs for 0 steps with 3480 atoms 187.8% 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 | | 2.13e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9727.00 ave 9727 max 9727 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: 461968.0 ave 461968 max 461968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461968 Ave neighs/atom = 132.74943 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 ghost atom cutoff = 7 binsize = 3.5, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.664 | 6.664 | 6.664 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 -14824.073 -14824.073 53.143514 86.483877 8.8102847 12.081378 12.081378 145.82573 -19.999315 -89.58228 2.3131259 1416.3959 Loop time of 2.443e-06 on 1 procs for 0 steps with 3480 atoms 245.6% 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 | | 2.443e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9727.00 ave 9727 max 9727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 230984.0 ave 230984 max 230984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 461968.0 ave 461968 max 461968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 461968 Ave neighs/atom = 132.74943 Neighbor list builds = 0 Dangerous builds = 0 3480 -14824.0727044483 eV 2.31312586565661 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35