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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -51.315520 0.0000000) to (18.142776 51.315520 4.4664427) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9480299 5.4425552 4.4664427 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -51.315520 0.0000000) to (18.142776 51.315520 4.4664427) create_atoms CPU = 0.001 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9480299 5.4425552 4.4664427 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.315520 0.0000000) to (18.142776 51.315520 4.4664427) create_atoms CPU = 0.001 seconds 265 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 527 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_228581001644_004#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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2825.3456 0 -2825.3456 143230.7 470 0 -3354.2121 0 -3354.2121 7804.0038 Loop time of 2.63593 on 1 procs for 470 steps with 527 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 = -2825.34563680674 -3354.20915765044 -3354.21212951953 Force two-norm initial, final = 1104.4146 0.30083676 Force max component initial, final = 360.07935 0.049751083 Final line search alpha, max atom move = 0.83840780 0.041711697 Iterations, force evaluations = 470 883 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5106 | 2.5106 | 2.5106 | 0.0 | 95.24 Neigh | 0.071428 | 0.071428 | 0.071428 | 0.0 | 2.71 Comm | 0.032375 | 0.032375 | 0.032375 | 0.0 | 1.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02156 | | | 0.82 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4764.00 ave 4764 max 4764 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: 83100.0 ave 83100 max 83100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 83100 Ave neighs/atom = 157.68501 Neighbor list builds = 15 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 470 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 470 0 -3354.2121 0 -3354.2121 7804.0038 8316.5699 521 0 -3370.1783 0 -3370.1783 578.95248 8312.2358 Loop time of 0.176637 on 1 procs for 51 steps with 527 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 = -3354.21212951953 -3370.17554884846 -3370.17826211868 Force two-norm initial, final = 672.97323 7.3567425 Force max component initial, final = 490.39869 3.6998163 Final line search alpha, max atom move = 0.00011520834 0.00042624969 Iterations, force evaluations = 51 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.161 | 0.161 | 0.161 | 0.0 | 91.15 Neigh | 0.0046787 | 0.0046787 | 0.0046787 | 0.0 | 2.65 Comm | 0.00213 | 0.00213 | 0.00213 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008832 | | | 5.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4885.00 ave 4885 max 4885 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: 82868.0 ave 82868 max 82868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82868 Ave neighs/atom = 157.24478 Neighbor list builds = 1 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3370.1783 0 -3370.1783 578.95248 Loop time of 1.648e-06 on 1 procs for 0 steps with 527 atoms 182.0% 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 | | 1.648e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4907.00 ave 4907 max 4907 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: 82590.0 ave 82590 max 82590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82590 Ave neighs/atom = 156.71727 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.655 | 4.655 | 4.655 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 -3370.1783 -3370.1783 17.495068 104.04985 4.5662612 578.95248 578.95248 405.23833 722.99518 608.62392 2.6075556 2470.5149 Loop time of 1.45e-06 on 1 procs for 0 steps with 527 atoms 206.9% 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 | | 1.45e-06 | | |100.00 Nlocal: 527.000 ave 527 max 527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4907.00 ave 4907 max 4907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41295.0 ave 41295 max 41295 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82590.0 ave 82590 max 82590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82590 Ave neighs/atom = 156.71727 Neighbor list builds = 0 Dangerous builds = 0 527 -3370.17826211867 eV 2.60755560396109 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03