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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -47.479476 0.0000000) to (33.570499 47.479476 5.1194532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2456743 6.0724932 5.1194532 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.479476 0.0000000) to (33.570499 47.479476 5.1194532) create_atoms CPU = 0.003 seconds 694 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2456743 6.0724932 5.1194532 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -47.479476 0.0000000) to (33.570499 47.479476 5.1194532) create_atoms CPU = 0.003 seconds 694 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1374 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_803527979660_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4788.2239 0 -4788.2239 6589.6319 41 0 -4851.6383 0 -4851.6383 1999.8512 Loop time of 1.6791 on 1 procs for 41 steps with 1374 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4788.22386454818 -4851.63447712454 -4851.63834396432 Force two-norm initial, final = 33.211688 0.22312137 Force max component initial, final = 5.9628916 0.047011184 Final line search alpha, max atom move = 1.0000000 0.047011184 Iterations, force evaluations = 41 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6344 | 1.6344 | 1.6344 | 0.0 | 97.34 Neigh | 0.026749 | 0.026749 | 0.026749 | 0.0 | 1.59 Comm | 0.0094106 | 0.0094106 | 0.0094106 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008523 | | | 0.51 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8026.00 ave 8026 max 8026 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: 238956.0 ave 238956 max 238956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238956 Ave neighs/atom = 173.91266 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.493 | 5.493 | 5.493 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -4851.6383 0 -4851.6383 1999.8512 16319.892 43 0 -4851.647 0 -4851.647 1132.1797 16330.258 Loop time of 0.121825 on 1 procs for 2 steps with 1374 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 = -4851.63834396432 -4851.645785961 -4851.64702735295 Force two-norm initial, final = 19.645066 0.22345389 Force max component initial, final = 19.538454 0.042601489 Final line search alpha, max atom move = 0.00015794689 6.7287726e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11877 | 0.11877 | 0.11877 | 0.0 | 97.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059734 | 0.00059734 | 0.00059734 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002459 | | | 2.02 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8034.00 ave 8034 max 8034 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: 239132.0 ave 239132 max 239132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239132 Ave neighs/atom = 174.04076 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.631 | 5.631 | 5.631 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4851.647 0 -4851.647 1132.1797 Loop time of 3.09e-06 on 1 procs for 0 steps with 1374 atoms 161.8% 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 | | 3.09e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8026.00 ave 8026 max 8026 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: 239084.0 ave 239084 max 239084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239084 Ave neighs/atom = 174.00582 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.631 | 5.631 | 5.631 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 -4851.647 -4851.647 33.6013 94.958951 5.1180091 1132.1797 1132.1797 0.37577406 3395.8715 0.29187263 2.4250912 894.55614 Loop time of 3.359e-06 on 1 procs for 0 steps with 1374 atoms 178.6% 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 | | 3.359e-06 | | |100.00 Nlocal: 1374.00 ave 1374 max 1374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8026.00 ave 8026 max 8026 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119542.0 ave 119542 max 119542 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 239084.0 ave 239084 max 239084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 239084 Ave neighs/atom = 174.00582 Neighbor list builds = 0 Dangerous builds = 0 1374 -4851.64702735295 eV 2.42509120427823 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02