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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -29.203572 0.0000000) to (25.291035 29.203572 4.9599800) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5394165 4.4928572 4.9599800 Created 311 atoms using lattice units in orthogonal box = (0.0000000 -29.203572 0.0000000) to (25.291035 29.203572 4.9599800) create_atoms CPU = 0.001 seconds 311 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5394165 4.4928572 4.9599800 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -29.203572 0.0000000) to (25.291035 29.203572 4.9599800) create_atoms CPU = 0.001 seconds 316 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 = 8 18 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 624 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_924736622203_001#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 = 8 18 2 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) = 4.500 | 4.500 | 4.500 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2436.304 0 -2436.304 84223.25 159 0 -2659.7478 0 -2659.7478 9166.8029 Loop time of 16.5415 on 1 procs for 159 steps with 624 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 = -2436.30395888764 -2659.74522957127 -2659.74784805189 Force two-norm initial, final = 335.31209 0.16495808 Force max component initial, final = 90.931500 0.034947658 Final line search alpha, max atom move = 1.0000000 0.034947658 Iterations, force evaluations = 159 307 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.501 | 16.501 | 16.501 | 0.0 | 99.75 Neigh | 0.01415 | 0.01415 | 0.01415 | 0.0 | 0.09 Comm | 0.01399 | 0.01399 | 0.01399 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01268 | | | 0.08 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3600.00 ave 3600 max 3600 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: 67522.0 ave 67522 max 67522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67522 Ave neighs/atom = 108.20833 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 18 2 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 : 159 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 159 0 -2659.7478 0 -2659.7478 9166.8029 7326.769 162 0 -2659.8643 0 -2659.8643 -309.88505 7366.9956 Loop time of 0.275303 on 1 procs for 3 steps with 624 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 = -2659.74784805189 -2659.86281940083 -2659.86427072816 Force two-norm initial, final = 73.386370 2.7490976 Force max component initial, final = 47.704832 2.3690568 Final line search alpha, max atom move = 0.00025611795 0.00060675796 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27419 | 0.27419 | 0.27419 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001825 | 0.0001825 | 0.0001825 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009269 | | | 0.34 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3598.00 ave 3598 max 3598 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: 67540.0 ave 67540 max 67540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67540 Ave neighs/atom = 108.23718 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 = 8 19 2 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2659.8643 0 -2659.8643 -309.88505 Loop time of 2.273e-06 on 1 procs for 0 steps with 624 atoms 220.0% 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 | | 2.273e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3597.00 ave 3597 max 3597 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: 67356.0 ave 67356 max 67356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67356 Ave neighs/atom = 107.94231 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 = 8 19 2 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) = 4.639 | 4.639 | 4.639 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 -2659.8643 -2659.8643 25.316639 58.531906 4.9715486 -309.88505 -309.88505 -515.74481 -155.49605 -258.41427 2.3383146 671.09426 Loop time of 2.659e-06 on 1 procs for 0 steps with 624 atoms 300.9% 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 | | 2.659e-06 | | |100.00 Nlocal: 624.000 ave 624 max 624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3597.00 ave 3597 max 3597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33678.0 ave 33678 max 33678 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67356.0 ave 67356 max 67356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67356 Ave neighs/atom = 107.94231 Neighbor list builds = 0 Dangerous builds = 0 624 -2659.86427072815 eV 2.33831457157669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17