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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4542474 4.4542474 3.5213917 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) create_atoms CPU = 0.002 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4542474 4.4542474 3.5213917 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.545995 0.0000000) to (11.135618 44.545995 3.5213917) create_atoms CPU = 0.001 seconds 162 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 = 4 28 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 8 atoms, new total = 316 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_876687166519_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 = 4 28 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) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1383.9849 0 -1383.9849 12748.215 55 0 -1399.2642 0 -1399.2642 -10574.253 Loop time of 4.32957 on 1 procs for 55 steps with 316 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 = -1383.9849455293 -1399.26309603947 -1399.2641836273 Force two-norm initial, final = 36.684053 0.10273911 Force max component initial, final = 13.720037 0.016858629 Final line search alpha, max atom move = 1.0000000 0.016858629 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.31 | 4.31 | 4.31 | 0.0 | 99.55 Neigh | 0.0045779 | 0.0045779 | 0.0045779 | 0.0 | 0.11 Comm | 0.0084058 | 0.0084058 | 0.0084058 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006628 | | | 0.15 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3164.00 ave 3164 max 3164 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: 27540.0 ave 27540 max 27540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27540 Ave neighs/atom = 87.151899 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 28 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1399.2642 0 -1399.2642 -10574.253 3493.5531 59 0 -1399.3176 0 -1399.3176 -1772.617 3476.6923 Loop time of 0.312573 on 1 procs for 4 steps with 316 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 = -1399.2641836273 -1399.31708451589 -1399.31761245695 Force two-norm initial, final = 30.643760 0.14001187 Force max component initial, final = 22.894913 0.041189254 Final line search alpha, max atom move = 0.00075707175 3.1183220e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31032 | 0.31032 | 0.31032 | 0.0 | 99.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052263 | 0.00052263 | 0.00052263 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001726 | | | 0.55 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3154.00 ave 3154 max 3154 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: 27380.0 ave 27380 max 27380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27380 Ave neighs/atom = 86.645570 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 = 4 28 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1399.3176 0 -1399.3176 -1772.617 Loop time of 6.886e-06 on 1 procs for 0 steps with 316 atoms 174.3% 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 | | 6.886e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3154.00 ave 3154 max 3154 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: 27436.0 ave 27436 max 27436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27436 Ave neighs/atom = 86.822785 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 = 4 28 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) = 4.580 | 4.580 | 4.580 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 -1399.3176 -1399.3176 11.117213 89.09199 3.5101985 -1772.617 -1772.617 -6.6575816 -5313.3673 2.1739504 2.2963179 159.07771 Loop time of 6.966e-06 on 1 procs for 0 steps with 316 atoms 272.8% 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 | | 6.966e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3154.00 ave 3154 max 3154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13718.0 ave 13718 max 13718 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27436.0 ave 27436 max 27436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27436 Ave neighs/atom = 86.822785 Neighbor list builds = 0 Dangerous builds = 0 316 -1399.31761245695 eV 2.29631785248229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05