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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -69.370413 0.0000000) to (34.685207 69.370413 4.0320734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6246281 5.6246281 4.0320734 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.370413 0.0000000) to (34.685207 69.370413 4.0320734) create_atoms CPU = 0.003 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6246281 5.6246281 4.0320734 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.370413 0.0000000) to (34.685207 69.370413 4.0320734) create_atoms CPU = 0.002 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 37 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 7.687316 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3876.93 0 -3876.93 7386.8378 154 0 -3977.5438 0 -3977.5438 3945.4117 Loop time of 4.68951 on 1 procs for 154 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 = -3876.9300366246 -3977.5403999404 -3977.54383065677 Force two-norm initial, final = 39.840325 0.17624095 Force max component initial, final = 5.6339286 0.039743740 Final line search alpha, max atom move = 1.0000000 0.039743740 Iterations, force evaluations = 154 285 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5366 | 4.5366 | 4.5366 | 0.0 | 96.74 Neigh | 0.05716 | 0.05716 | 0.05716 | 0.0 | 1.22 Comm | 0.052847 | 0.052847 | 0.052847 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04286 | | | 0.91 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8314.00 ave 8314 max 8314 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: 156532.0 ave 156532 max 156532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156532 Ave neighs/atom = 131.98314 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 154 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 154 0 -3977.5438 0 -3977.5438 3945.4117 19403.362 161 0 -3977.8523 0 -3977.8523 -72.692856 19498.319 Loop time of 0.143945 on 1 procs for 7 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 = -3977.54383065676 -3977.84835892662 -3977.85225596822 Force two-norm initial, final = 101.80428 1.6686040 Force max component initial, final = 93.216872 1.3773332 Final line search alpha, max atom move = 0.00014440774 0.00019889757 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13703 | 0.13703 | 0.13703 | 0.0 | 95.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015419 | 0.0015419 | 0.0015419 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005373 | | | 3.73 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8309.00 ave 8309 max 8309 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: 156852.0 ave 156852 max 156852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156852 Ave neighs/atom = 132.25295 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3977.8523 0 -3977.8523 -72.692856 Loop time of 6.335e-06 on 1 procs for 0 steps with 1186 atoms 189.4% 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 | | 6.335e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8324.00 ave 8324 max 8324 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: 156592.0 ave 156592 max 156592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156592 Ave neighs/atom = 132.03373 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.187 | 5.187 | 5.187 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 -3977.8523 -3977.8523 34.601662 139.68429 4.0341556 -72.692856 -72.692856 -48.658335 -56.186347 -113.23389 2.5829653 408.96291 Loop time of 6.866e-06 on 1 procs for 0 steps with 1186 atoms 262.2% 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 | | 6.866e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8324.00 ave 8324 max 8324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78296.0 ave 78296 max 78296 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156592.0 ave 156592 max 156592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156592 Ave neighs/atom = 132.03373 Neighbor list builds = 0 Dangerous builds = 0 1186 -3977.85225596822 eV 2.5829652853654 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05