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 = 4.0501996 4.0501996 4.0501996 Created orthogonal box = (0.0000000 -69.682269 0.0000000) to (34.841135 69.682269 4.0501996) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6499137 5.6499137 4.0501996 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.682269 0.0000000) to (34.841135 69.682269 4.0501996) create_atoms CPU = 0.006 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6499137 5.6499137 4.0501996 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.682269 0.0000000) to (34.841135 69.682269 4.0501996) create_atoms CPU = 0.004 seconds 594 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 9 34 1 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 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_060567868558_000#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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4186.3205 0 -4186.3205 9352.7462 69 0 -4240.621 0 -4240.621 5646.3938 Loop time of 2.87133 on 1 procs for 69 steps with 1186 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 = -4186.32047478842 -4240.61710365873 -4240.62097273779 Force two-norm initial, final = 53.621547 0.12354311 Force max component initial, final = 9.9920214 0.021557266 Final line search alpha, max atom move = 1.0000000 0.021557266 Iterations, force evaluations = 69 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7823 | 2.7823 | 2.7823 | 0.0 | 96.90 Neigh | 0.044588 | 0.044588 | 0.044588 | 0.0 | 1.55 Comm | 0.025509 | 0.025509 | 0.025509 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01888 | | | 0.66 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8629.00 ave 8629 max 8629 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: 166208.0 ave 166208 max 166208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166208 Ave neighs/atom = 140.14165 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -4240.621 0 -4240.621 5646.3938 19666.225 79 0 -4241.1354 0 -4241.1354 25.619013 19811.594 Loop time of 0.272077 on 1 procs for 10 steps with 1186 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 = -4240.62097273779 -4241.13152935809 -4241.13536990296 Force two-norm initial, final = 134.62390 0.79685051 Force max component initial, final = 119.02017 0.72027942 Final line search alpha, max atom move = 0.00017017461 0.00012257327 Iterations, force evaluations = 10 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2402 | 0.2402 | 0.2402 | 0.0 | 88.28 Neigh | 0.022212 | 0.022212 | 0.022212 | 0.0 | 8.16 Comm | 0.0025507 | 0.0025507 | 0.0025507 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007116 | | | 2.62 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8624.00 ave 8624 max 8624 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: 165920.0 ave 165920 max 165920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165920 Ave neighs/atom = 139.89882 Neighbor list builds = 1 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.210 | 5.210 | 5.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4241.1354 0 -4241.1354 25.619013 Loop time of 6.605e-06 on 1 procs for 0 steps with 1186 atoms 181.7% 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 | | 6.605e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8624.00 ave 8624 max 8624 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: 165888.0 ave 165888 max 165888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165888 Ave neighs/atom = 139.87184 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 5.210 | 5.210 | 5.210 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 -4241.1354 -4241.1354 34.826582 140.75818 4.0414285 25.619013 25.619013 58.225136 22.569221 -3.9373176 2.5491635 416.43868 Loop time of 6.976e-06 on 1 procs for 0 steps with 1186 atoms 258.0% 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 | | 6.976e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8624.00 ave 8624 max 8624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82944.0 ave 82944 max 82944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 165888.0 ave 165888 max 165888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165888 Ave neighs/atom = 139.87184 Neighbor list builds = 0 Dangerous builds = 0 1186 -4241.13536990296 eV 2.54916347296172 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03