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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -53.662401 0.0000000) to (32.858898 53.662401 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9743451 6.0975404 6.6048870 Created 1065 atoms using lattice units in orthogonal box = (0.0000000 -53.662401 0.0000000) to (32.858898 53.662401 9.9073306) create_atoms CPU = 0.002 seconds 1065 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9743451 6.0975404 6.6048870 Created 1065 atoms using lattice units in orthogonal box = (0.0000000 -53.662401 0.0000000) to (32.858898 53.662401 9.9073306) create_atoms CPU = 0.001 seconds 1065 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 66 atoms, new total = 2064 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_353977746962_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6883.6151 0 -6883.6151 -4131.2226 55 0 -6919.7966 0 -6919.7966 -15646.773 Loop time of 7.04298 on 1 procs for 55 steps with 2064 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6883.61510176383 -6919.79006472673 -6919.79660739816 Force two-norm initial, final = 7.7671081 0.18312530 Force max component initial, final = 1.6088277 0.0098778539 Final line search alpha, max atom move = 1.0000000 0.0098778539 Iterations, force evaluations = 55 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0102 | 7.0102 | 7.0102 | 0.0 | 99.53 Neigh | 0.010993 | 0.010993 | 0.010993 | 0.0 | 0.16 Comm | 0.0075408 | 0.0075408 | 0.0075408 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01423 | | | 0.20 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5208.00 ave 5208 max 5208 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: 153678.0 ave 153678 max 153678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153678 Ave neighs/atom = 74.456395 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.067 | 5.067 | 5.067 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -6919.7966 0 -6919.7966 -15646.773 34938.941 64 0 -6921.9579 0 -6921.9579 -4235.498 34412.15 Loop time of 0.699762 on 1 procs for 9 steps with 2064 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 = -6919.79660739817 -6921.95772619951 -6921.95786922993 Force two-norm initial, final = 398.91672 0.32918251 Force max component initial, final = 288.25733 0.056983857 Final line search alpha, max atom move = 0.00070859551 4.0378505e-05 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69582 | 0.69582 | 0.69582 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049107 | 0.00049107 | 0.00049107 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00345 | | | 0.49 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5197.00 ave 5197 max 5197 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: 152162.0 ave 152162 max 152162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152162 Ave neighs/atom = 73.721899 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.205 | 5.205 | 5.205 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6921.9579 0 -6921.9579 -4235.498 Loop time of 1.86e-06 on 1 procs for 0 steps with 2064 atoms 161.3% 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 | | 1.86e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5232.00 ave 5232 max 5232 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: 154042.0 ave 154042 max 154042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154042 Ave neighs/atom = 74.632752 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.205 | 5.205 | 5.205 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 -6921.9579 -6921.9579 32.59784 107.3248 9.8360989 -4235.498 -4235.498 0.87129657 -12704.731 -2.6340052 2.7481771 824.17108 Loop time of 2.156e-06 on 1 procs for 0 steps with 2064 atoms 185.5% 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 | | 2.156e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5232.00 ave 5232 max 5232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77021.0 ave 77021 max 77021 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154042.0 ave 154042 max 154042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154042 Ave neighs/atom = 74.632752 Neighbor list builds = 0 Dangerous builds = 0 2064 -6921.95786922993 eV 2.74817709409469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08