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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -33.536306 0.0000000) to (23.713749 33.536306 4.4419922) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4083989 5.2952062 4.4419922 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -33.536306 0.0000000) to (23.713749 33.536306 4.4419922) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4083989 5.2952062 4.4419922 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -33.536306 0.0000000) to (23.713749 33.536306 4.4419922) create_atoms CPU = 0.001 seconds 229 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 5 12 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 456 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 5 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 4.929 | 4.929 | 4.929 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2771.5123 0 -2771.5123 134549.16 333 0 -3091.9155 0 -3091.9155 5162.5506 Loop time of 5.76703 on 1 procs for 333 steps with 456 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2771.51226985566 -3091.91288637651 -3091.91552493758 Force two-norm initial, final = 455.84983 0.27957749 Force max component initial, final = 124.33028 0.033738368 Final line search alpha, max atom move = 1.0000000 0.033738368 Iterations, force evaluations = 333 614 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5887 | 5.5887 | 5.5887 | 0.0 | 96.91 Neigh | 0.12078 | 0.12078 | 0.12078 | 0.0 | 2.09 Comm | 0.038573 | 0.038573 | 0.038573 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01901 | | | 0.33 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7428.00 ave 7428 max 7428 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: 189034.0 ave 189034 max 189034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189034 Ave neighs/atom = 414.54825 Neighbor list builds = 12 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 5 12 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 333 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.931 | 4.931 | 4.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 333 0 -3091.9155 0 -3091.9155 5162.5506 7065.18 358 0 -3100.8812 0 -3100.8812 -19.98462 7064.9954 Loop time of 0.265419 on 1 procs for 25 steps with 456 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 = -3091.91552493758 -3100.88050640897 -3100.88123621448 Force two-norm initial, final = 593.95280 3.5306564 Force max component initial, final = 498.38072 2.1103838 Final line search alpha, max atom move = 0.00046778422 0.00098720427 Iterations, force evaluations = 25 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24778 | 0.24778 | 0.24778 | 0.0 | 93.35 Neigh | 0.0096293 | 0.0096293 | 0.0096293 | 0.0 | 3.63 Comm | 0.0016937 | 0.0016937 | 0.0016937 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006314 | | | 2.38 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7527.00 ave 7527 max 7527 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: 188172.0 ave 188172 max 188172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188172 Ave neighs/atom = 412.65789 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 5 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3100.8812 0 -3100.8812 -19.98462 Loop time of 1.971e-06 on 1 procs for 0 steps with 456 atoms 152.2% 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 | | 1.971e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7553.00 ave 7553 max 7553 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: 188504.0 ave 188504 max 188504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188504 Ave neighs/atom = 413.38596 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 5 12 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.070 | 5.070 | 5.070 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 -3100.8812 -3100.8812 23.576019 65.904003 4.5470488 -19.98462 -19.98462 -475.80628 225.82807 190.02436 2.6074109 2869.2717 Loop time of 2.581e-06 on 1 procs for 0 steps with 456 atoms 232.5% 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 | | 2.581e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7553.00 ave 7553 max 7553 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94252.0 ave 94252 max 94252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 188504.0 ave 188504 max 188504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 188504 Ave neighs/atom = 413.38596 Neighbor list builds = 0 Dangerous builds = 0 456 -3100.88123621448 eV 2.60741094373753 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06