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 = 3.6149602 3.6149602 3.6149602 Created orthogonal box = (0.0000000 -36.865505 0.0000000) to (31.926464 36.865505 6.2612947) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7303909 5.6716161 6.2612947 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -36.865505 0.0000000) to (31.926464 36.865505 6.2612947) create_atoms CPU = 0.004 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7303909 5.6716161 6.2612947 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.865505 0.0000000) to (31.926464 36.865505 6.2612947) create_atoms CPU = 0.004 seconds 629 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, 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 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1250 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_950828638160_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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 5.474 | 5.474 | 5.474 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4156.4358 0 -4156.4358 54637.036 75 0 -4404.0048 0 -4404.0048 17875.117 Loop time of 3.84454 on 1 procs for 75 steps with 1250 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 = -4156.43581314116 -4404.00079063034 -4404.00478556357 Force two-norm initial, final = 263.88830 0.20877065 Force max component initial, final = 50.765172 0.055011151 Final line search alpha, max atom move = 1.0000000 0.055011151 Iterations, force evaluations = 75 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7278 | 3.7278 | 3.7278 | 0.0 | 96.96 Neigh | 0.06982 | 0.06982 | 0.06982 | 0.0 | 1.82 Comm | 0.025216 | 0.025216 | 0.025216 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02167 | | | 0.56 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7340.00 ave 7340 max 7340 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: 253256.0 ave 253256 max 253256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253256 Ave neighs/atom = 202.60480 Neighbor list builds = 2 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.474 | 5.474 | 5.474 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4404.0048 0 -4404.0048 17875.117 14738.902 88 0 -4405.5795 0 -4405.5795 84.110954 14922.456 Loop time of 0.411889 on 1 procs for 13 steps with 1250 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 = -4404.00478556356 -4405.57923333167 -4405.57948726804 Force two-norm initial, final = 309.74905 1.4913058 Force max component initial, final = 262.31378 0.95599663 Final line search alpha, max atom move = 0.00049777351 0.00047586979 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40068 | 0.40068 | 0.40068 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002348 | 0.002348 | 0.002348 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008865 | | | 2.15 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 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: 253582.0 ave 253582 max 253582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 253582 Ave neighs/atom = 202.86560 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 5.612 | 5.612 | 5.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4405.5795 0 -4405.5795 84.110954 Loop time of 6.475e-06 on 1 procs for 0 steps with 1250 atoms 185.3% 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 | | 6.475e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7328.00 ave 7328 max 7328 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: 249422.0 ave 249422 max 249422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249422 Ave neighs/atom = 199.53760 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 = 8.3953378 ghost atom cutoff = 8.3953378 binsize = 4.1976689, bins = 8 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.395337773223552 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) = 5.612 | 5.612 | 5.612 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 -4405.5795 -4405.5795 31.948827 74.623236 6.2590918 84.110954 84.110954 72.017466 103.88439 76.431004 2.3315752 948.25194 Loop time of 6.846e-06 on 1 procs for 0 steps with 1250 atoms 306.7% 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 | | 6.846e-06 | | |100.00 Nlocal: 1250.00 ave 1250 max 1250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7328.00 ave 7328 max 7328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124711.0 ave 124711 max 124711 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 249422.0 ave 249422 max 249422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 249422 Ave neighs/atom = 199.53760 Neighbor list builds = 0 Dangerous builds = 0 1250 -4405.57948726804 eV 2.33157524316705 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04