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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -62.169446 0.0000000) to (31.082916 62.169446 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0404729 5.0404729 3.6133156 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.169446 0.0000000) to (31.082916 62.169446 3.6133156) create_atoms CPU = 0.003 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0404729 5.0404729 3.6133156 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.169446 0.0000000) to (31.082916 62.169446 3.6133156) create_atoms CPU = 0.002 seconds 594 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1178 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4122.6789 0 -4122.6789 9733.0045 71 0 -4159.6321 0 -4159.6321 -2331.6214 Loop time of 5.46814 on 1 procs for 71 steps with 1178 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 = -4122.67890175267 -4159.62848585802 -4159.63210239271 Force two-norm initial, final = 45.218451 0.17239475 Force max component initial, final = 15.839584 0.041309554 Final line search alpha, max atom move = 1.0000000 0.041309554 Iterations, force evaluations = 71 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4308 | 5.4308 | 5.4308 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018242 | 0.018242 | 0.018242 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01911 | | | 0.35 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5882.00 ave 5882 max 5882 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: 63696.0 ave 63696 max 63696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63696 Ave neighs/atom = 54.071307 Neighbor list builds = 0 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.628 | 4.628 | 4.628 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4159.6321 0 -4159.6321 -2331.6214 13964.798 73 0 -4159.6524 0 -4159.6524 68.029859 13940.947 Loop time of 0.212292 on 1 procs for 2 steps with 1178 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 = -4159.63210239271 -4159.65228661754 -4159.6524234389 Force two-norm initial, final = 33.809534 0.18310629 Force max component initial, final = 25.034584 0.047106117 Final line search alpha, max atom move = 0.00099877717 4.7048514e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20955 | 0.20955 | 0.20955 | 0.0 | 98.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061516 | 0.00061516 | 0.00061516 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002131 | | | 1.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5850.00 ave 5850 max 5850 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: 67944.0 ave 67944 max 67944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67944 Ave neighs/atom = 57.677419 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.766 | 4.766 | 4.766 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4159.6524 0 -4159.6524 68.029859 Loop time of 6.385e-06 on 1 procs for 0 steps with 1178 atoms 187.9% 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 | | 6.385e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 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: 68668.0 ave 68668 max 68668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68668 Ave neighs/atom = 58.292020 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.766 | 4.766 | 4.766 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 -4159.6524 -4159.6524 31.059622 124.33889 3.6098496 68.029859 68.029859 -4.2066636 207.17801 1.1182354 2.3060426 322.78646 Loop time of 6.976e-06 on 1 procs for 0 steps with 1178 atoms 229.4% 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 | | 6.976e-06 | | |100.00 Nlocal: 1178.00 ave 1178 max 1178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5858.00 ave 5858 max 5858 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34334.0 ave 34334 max 34334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68668.0 ave 68668 max 68668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68668 Ave neighs/atom = 58.292020 Neighbor list builds = 0 Dangerous builds = 0 1178 -4159.6524234389 eV 2.30604256350347 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06