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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -62.613638 0.0000000) to (25.561911 62.613638 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1348586 5.4265153 5.9032704 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -62.613638 0.0000000) to (25.561911 62.613638 8.8549056) create_atoms CPU = 0.006 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1348586 5.4265153 5.9032704 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -62.613638 0.0000000) to (25.561911 62.613638 8.8549056) create_atoms CPU = 0.005 seconds 1203 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 7 34 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 7 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.082 | 6.082 | 6.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8238.6708 0 -8238.6708 31401.721 96 0 -8470.097 0 -8470.097 1639.2138 Loop time of 5.86989 on 1 procs for 96 steps with 2398 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 = -8238.67082330239 -8470.08910939578 -8470.0970379729 Force two-norm initial, final = 389.66711 0.29300273 Force max component initial, final = 101.66748 0.050710428 Final line search alpha, max atom move = 1.0000000 0.050710428 Iterations, force evaluations = 96 164 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6234 | 5.6234 | 5.6234 | 0.0 | 95.80 Neigh | 0.16729 | 0.16729 | 0.16729 | 0.0 | 2.85 Comm | 0.036321 | 0.036321 | 0.036321 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04288 | | | 0.73 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9205.00 ave 9205 max 9205 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: 338266.0 ave 338266 max 338266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338266 Ave neighs/atom = 141.06172 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 7 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.079 | 6.079 | 6.079 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -8470.097 0 -8470.097 1639.2138 28344.982 100 0 -8470.2583 0 -8470.2583 -183.77375 28381.68 Loop time of 0.243729 on 1 procs for 4 steps with 2398 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8470.09703797304 -8470.25685114117 -8470.25828782309 Force two-norm initial, final = 94.572465 6.8832365 Force max component initial, final = 93.725983 5.6891297 Final line search alpha, max atom move = 9.8656808e-05 0.00056127137 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23599 | 0.23599 | 0.23599 | 0.0 | 96.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001428 | 0.001428 | 0.001428 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006313 | | | 2.59 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8935.00 ave 8935 max 8935 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: 338678.0 ave 338678 max 338678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338678 Ave neighs/atom = 141.23353 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 7 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.217 | 6.217 | 6.217 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8470.2583 0 -8470.2583 -183.77375 Loop time of 6.315e-06 on 1 procs for 0 steps with 2398 atoms 190.0% 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 | | 6.315e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8941.00 ave 8941 max 8941 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: 338588.0 ave 338588 max 338588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338588 Ave neighs/atom = 141.19600 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 7 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.217 | 6.217 | 6.217 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 -8470.2583 -8470.2583 25.532486 125.63646 8.8476782 -183.77375 -183.77375 -217.31294 -13.112914 -320.89538 2.3750133 993.59176 Loop time of 8.47e-06 on 1 procs for 0 steps with 2398 atoms 259.7% 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 | | 8.47e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8941.00 ave 8941 max 8941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169294.0 ave 169294 max 169294 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338588.0 ave 338588 max 338588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338588 Ave neighs/atom = 141.19600 Neighbor list builds = 0 Dangerous builds = 0 2398 -8470.25780604395 eV 2.37501332499882 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07