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 -48.455211 0.0000000) to (22.842005 48.455211 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7182369 6.6507152 5.5400000 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -48.455211 0.0000000) to (22.842005 48.455211 5.5400000) create_atoms CPU = 0.004 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7182369 6.6507152 5.5400000 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -48.455211 0.0000000) to (22.842005 48.455211 5.5400000) create_atoms CPU = 0.003 seconds 412 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 = 8 30 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 = 820 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 = 8 30 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4551.4365 0 -4551.4365 52295.105 35 0 -4713.2324 0 -4713.2324 17209.792 Loop time of 2.00759 on 1 procs for 35 steps with 820 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 = -4551.43651799883 -4713.22782514579 -4713.23241224666 Force two-norm initial, final = 196.11888 0.24464289 Force max component initial, final = 57.591576 0.041966700 Final line search alpha, max atom move = 1.0000000 0.041966700 Iterations, force evaluations = 35 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9947 | 1.9947 | 1.9947 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061758 | 0.0061758 | 0.0061758 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006732 | | | 0.34 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3915.00 ave 3915 max 3915 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: 64152.0 ave 64152 max 64152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64152 Ave neighs/atom = 78.234146 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 = 8 30 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4713.2324 0 -4713.2324 17209.792 12263.501 44 0 -4714.1542 0 -4714.1542 -120.79537 12378.994 Loop time of 0.356984 on 1 procs for 9 steps with 820 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 = -4713.23241224665 -4714.15278521134 -4714.15415380548 Force two-norm initial, final = 248.88286 1.7841425 Force max component initial, final = 212.64765 1.3436081 Final line search alpha, max atom move = 0.00018990122 0.00025515280 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35213 | 0.35213 | 0.35213 | 0.0 | 98.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097535 | 0.00097535 | 0.00097535 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00388 | | | 1.09 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3915.00 ave 3915 max 3915 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: 63464.0 ave 63464 max 63464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63464 Ave neighs/atom = 77.395122 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 = 8 31 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) = 4.689 | 4.689 | 4.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4714.1542 0 -4714.1542 -120.79537 Loop time of 6.495e-06 on 1 procs for 0 steps with 820 atoms 169.4% 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 | | 6.495e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3915.00 ave 3915 max 3915 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: 63400.0 ave 63400 max 63400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63400 Ave neighs/atom = 77.317073 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 = 8 31 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) = 4.689 | 4.689 | 4.689 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 -4714.1542 -4714.1542 22.855807 97.720706 5.5424553 -120.79537 -120.79537 -66.275203 -122.13462 -173.97628 2.5987439 543.47694 Loop time of 6.846e-06 on 1 procs for 0 steps with 820 atoms 248.3% 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 | | 6.846e-06 | | |100.00 Nlocal: 820.000 ave 820 max 820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3915.00 ave 3915 max 3915 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31700.0 ave 31700 max 31700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63400.0 ave 63400 max 63400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63400 Ave neighs/atom = 77.317073 Neighbor list builds = 0 Dangerous builds = 0 820 -4714.15415380548 eV 2.59874385483823 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02