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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3852318 5.1298605 5.9032705 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) create_atoms CPU = 0.006 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3852318 5.1298605 5.9032705 Created 1758 atoms using lattice units in orthogonal box = (0.0000000 -53.497117 0.0000000) to (43.680213 53.497117 8.8549058) create_atoms CPU = 0.006 seconds 1758 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 = 12 28 3 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 4 atoms, new total = 3504 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 = 12 28 3 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) = 7.394 | 7.394 | 7.394 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12000.692 0 -12000.692 13142.595 83 0 -12360.21 0 -12360.21 5907.4329 Loop time of 8.2239 on 1 procs for 83 steps with 3504 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 = -12000.6920533808 -12360.1977501992 -12360.2096421109 Force two-norm initial, final = 113.00321 0.32137927 Force max component initial, final = 9.6719992 0.055081161 Final line search alpha, max atom move = 1.0000000 0.055081161 Iterations, force evaluations = 83 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9668 | 7.9668 | 7.9668 | 0.0 | 96.87 Neigh | 0.16137 | 0.16137 | 0.16137 | 0.0 | 1.96 Comm | 0.042109 | 0.042109 | 0.042109 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0536 | | | 0.65 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11412.0 ave 11412 max 11412 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: 581770.0 ave 581770 max 581770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581770 Ave neighs/atom = 166.03025 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 12 28 3 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.394 | 7.394 | 7.394 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -12360.21 0 -12360.21 5907.4329 41383.676 89 0 -12360.796 0 -12360.796 118.77028 41556.811 Loop time of 0.402685 on 1 procs for 6 steps with 3504 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12360.2096421109 -12360.7952481945 -12360.7959111217 Force two-norm initial, final = 289.87295 5.9556544 Force max component initial, final = 249.35111 4.4708966 Final line search alpha, max atom move = 0.00014100079 0.00063039997 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39186 | 0.39186 | 0.39186 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020354 | 0.0020354 | 0.0020354 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008788 | | | 2.18 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11385.0 ave 11385 max 11385 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: 603322.0 ave 603322 max 603322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 603322 Ave neighs/atom = 172.18094 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 = 12 28 3 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) = 7.532 | 7.532 | 7.532 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12360.796 0 -12360.796 118.77028 Loop time of 6.144e-06 on 1 procs for 0 steps with 3504 atoms 211.6% 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 | | 6.144e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11331.0 ave 11331 max 11331 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: 601016.0 ave 601016 max 601016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 601016 Ave neighs/atom = 171.52283 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 = 12 28 3 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) = 7.532 | 7.532 | 7.532 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 -12360.796 -12360.796 43.653376 107.53095 8.8530085 118.77028 118.77028 37.346891 173.2351 145.72886 2.2843655 1471.1385 Loop time of 6.856e-06 on 1 procs for 0 steps with 3504 atoms 262.5% 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 | | 6.856e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11331.0 ave 11331 max 11331 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 300508.0 ave 300508 max 300508 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 601016.0 ave 601016 max 601016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 601016 Ave neighs/atom = 171.52283 Neighbor list builds = 0 Dangerous builds = 0 3504 -12360.7959111217 eV 2.28436550090522 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09