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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -38.559668 0.0000000) to (7.8709593 38.559668 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7225756 5.1412891 5.7481360 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -38.559668 0.0000000) to (7.8709593 38.559668 8.6222040) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7225756 5.1412891 5.7481360 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.559668 0.0000000) to (7.8709593 38.559668 8.6222040) create_atoms CPU = 0.001 seconds 242 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 2 19 3 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2104.6188 0 -2104.6188 9512.6325 35 0 -2125.3975 0 -2125.3975 12967.13 Loop time of 0.452325 on 1 procs for 35 steps with 480 atoms 94.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2104.61883493406 -2125.39548845806 -2125.39753527298 Force two-norm initial, final = 21.443486 0.13421976 Force max component initial, final = 4.3654056 0.012054811 Final line search alpha, max atom move = 1.0000000 0.012054811 Iterations, force evaluations = 35 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44611 | 0.44611 | 0.44611 | 0.0 | 98.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003603 | 0.003603 | 0.003603 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002614 | | | 0.58 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5148.00 ave 5148 max 5148 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: 108112.0 ave 108112 max 108112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108112 Ave neighs/atom = 225.23333 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -2125.3975 0 -2125.3975 12967.13 5233.7051 45 0 -2125.7028 0 -2125.7028 33.785313 5271.8527 Loop time of 0.0837807 on 1 procs for 10 steps with 480 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 = -2125.39753527298 -2125.70275690355 -2125.70278129377 Force two-norm initial, final = 83.517554 0.39128377 Force max component initial, final = 74.461022 0.23904758 Final line search alpha, max atom move = 0.0015177142 0.00036280590 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.080616 | 0.080616 | 0.080616 | 0.0 | 96.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005284 | 0.0005284 | 0.0005284 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002636 | | | 3.15 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836.00 ave 4836 max 4836 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: 107492.0 ave 107492 max 107492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107492 Ave neighs/atom = 223.94167 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.131 | 5.131 | 5.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2125.7028 0 -2125.7028 33.785313 Loop time of 2.418e-06 on 1 procs for 0 steps with 480 atoms 165.4% 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 | | 2.418e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4794.00 ave 4794 max 4794 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: 107320.0 ave 107320 max 107320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107320 Ave neighs/atom = 223.58333 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.131 | 5.131 | 5.131 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 -2125.7028 -2125.7028 7.8658836 77.795263 8.6151451 33.785313 33.785313 12.93315 15.832966 72.589824 2.1949282 286.76447 Loop time of 2.739e-06 on 1 procs for 0 steps with 480 atoms 219.1% 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 | | 2.739e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4794.00 ave 4794 max 4794 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53660.0 ave 53660 max 53660 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 107320.0 ave 107320 max 107320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107320 Ave neighs/atom = 223.58333 Neighbor list builds = 0 Dangerous builds = 0 480 -2125.70278129377 eV 2.19492816061828 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00