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 = 4.0497635 4.0497635 4.0497635 Created orthogonal box = (0.0000000 -71.533086 0.0000000) to (41.299647 71.533086 7.0143962) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3537918 6.4196360 7.0143962 Created 1248 atoms using lattice units in orthogonal box = (0.0000000 -71.533086 0.0000000) to (41.299647 71.533086 7.0143962) create_atoms CPU = 0.003 seconds 1248 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3537918 6.4196360 7.0143962 Created 1252 atoms using lattice units in orthogonal box = (0.0000000 -71.533086 0.0000000) to (41.299647 71.533086 7.0143962) create_atoms CPU = 0.003 seconds 1252 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 10 33 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 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2496 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_942551040047_005#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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7944.2206 0 -7944.2206 23599.235 80 0 -8267.0165 0 -8267.0165 2802.1733 Loop time of 3.01396 on 1 procs for 80 steps with 2496 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7944.22061956774 -8267.00827711452 -8267.01646588831 Force two-norm initial, final = 377.55911 0.19340207 Force max component initial, final = 93.308683 0.029675808 Final line search alpha, max atom move = 1.0000000 0.029675808 Iterations, force evaluations = 80 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8408 | 2.8408 | 2.8408 | 0.0 | 94.25 Neigh | 0.13523 | 0.13523 | 0.13523 | 0.0 | 4.49 Comm | 0.019745 | 0.019745 | 0.019745 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0182 | | | 0.60 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12017.0 ave 12017 max 12017 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: 433824.0 ave 433824 max 433824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 433824 Ave neighs/atom = 173.80769 Neighbor list builds = 5 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -8267.0165 0 -8267.0165 2802.1733 41445.138 85 0 -8267.2313 0 -8267.2313 -6.5942167 41595.627 Loop time of 0.185633 on 1 procs for 5 steps with 2496 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 = -8267.01646588829 -8267.22977390078 -8267.23129144188 Force two-norm initial, final = 135.48367 1.7634709 Force max component initial, final = 113.59624 1.3771469 Final line search alpha, max atom move = 5.0755810e-05 6.9898204e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18017 | 0.18017 | 0.18017 | 0.0 | 97.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085079 | 0.00085079 | 0.00085079 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004614 | | | 2.49 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11994.0 ave 11994 max 11994 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: 433472.0 ave 433472 max 433472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 433472 Ave neighs/atom = 173.66667 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 6.668 | 6.668 | 6.668 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8267.2313 0 -8267.2313 -6.5942167 Loop time of 2.152e-06 on 1 procs for 0 steps with 2496 atoms 185.9% 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 | | 2.152e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11999.0 ave 11999 max 11999 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: 432936.0 ave 432936 max 432936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432936 Ave neighs/atom = 173.45192 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.682500000000001 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) = 6.668 | 6.668 | 6.668 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 -8267.2313 -8267.2313 41.295788 143.65537 7.0116468 -6.5942167 -6.5942167 -53.03986 -7.5655161 40.822726 2.5948594 1265.7147 Loop time of 2.689e-06 on 1 procs for 0 steps with 2496 atoms 223.1% 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 | | 2.689e-06 | | |100.00 Nlocal: 2496.00 ave 2496 max 2496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11999.0 ave 11999 max 11999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 216468.0 ave 216468 max 216468 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 432936.0 ave 432936 max 432936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432936 Ave neighs/atom = 173.45192 Neighbor list builds = 0 Dangerous builds = 0 2496 -8267.23129144186 eV 2.59485936389057 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03