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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -40.648946 0.0000000) to (28.743145 40.648946 5.6919909) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0723197 6.3763052 5.6919909 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -40.648946 0.0000000) to (28.743145 40.648946 5.6919909) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0723197 6.3763052 5.6919909 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.648946 0.0000000) to (28.743145 40.648946 5.6919909) create_atoms CPU = 0.002 seconds 410 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 20 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 812 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_149316865608_005#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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1991.4253 0 -1991.4253 26216.988 133 0 -2140.8988 0 -2140.8988 2498.8486 Loop time of 3.78431 on 1 procs for 133 steps with 812 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 = -1991.42534296627 -2140.8968807682 -2140.89876879072 Force two-norm initial, final = 246.68074 0.12099731 Force max component initial, final = 56.233380 0.021393168 Final line search alpha, max atom move = 1.0000000 0.021393168 Iterations, force evaluations = 133 249 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6692 | 3.6692 | 3.6692 | 0.0 | 96.96 Neigh | 0.052719 | 0.052719 | 0.052719 | 0.0 | 1.39 Comm | 0.033527 | 0.033527 | 0.033527 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02888 | | | 0.76 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5372.00 ave 5372 max 5372 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: 113540.0 ave 113540 max 113540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113540 Ave neighs/atom = 139.82759 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -2140.8988 0 -2140.8988 2498.8486 13300.8 140 0 -2141.0239 0 -2141.0239 6.7241553 13342.043 Loop time of 0.148252 on 1 procs for 7 steps with 812 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 = -2140.89876879072 -2141.0238395321 -2141.02388561898 Force two-norm initial, final = 47.856616 0.34039986 Force max component initial, final = 46.342102 0.23987596 Final line search alpha, max atom move = 0.00091922781 0.00022050065 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14306 | 0.14306 | 0.14306 | 0.0 | 96.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011543 | 0.0011543 | 0.0011543 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00404 | | | 2.73 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5372.00 ave 5372 max 5372 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: 113512.0 ave 113512 max 113512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113512 Ave neighs/atom = 139.79310 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.095 | 5.095 | 5.095 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2141.0239 0 -2141.0239 6.7241553 Loop time of 6.225e-06 on 1 procs for 0 steps with 812 atoms 176.7% 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 | | 6.225e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5372.00 ave 5372 max 5372 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: 113420.0 ave 113420 max 113420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113420 Ave neighs/atom = 139.67980 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.095 | 5.095 | 5.095 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 -2141.0239 -2141.0239 28.713133 81.778297 5.6820323 6.7241553 6.7241553 -13.73095 5.1483581 28.755058 2.6331346 837.66502 Loop time of 7.107e-06 on 1 procs for 0 steps with 812 atoms 267.3% 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 | | 7.107e-06 | | |100.00 Nlocal: 812.000 ave 812 max 812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5372.00 ave 5372 max 5372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56710.0 ave 56710 max 56710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113420.0 ave 113420 max 113420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113420 Ave neighs/atom = 139.67980 Neighbor list builds = 0 Dangerous builds = 0 812 -2116.0676639776 eV 2.63313456956927 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04