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 = 3.1409628 3.1409628 3.1409628 Created orthogonal box = (0.0000000 -57.916493 0.0000000) to (28.958246 57.916493 3.1409628) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4289083 4.4289083 3.1409628 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -57.916493 0.0000000) to (28.958246 57.916493 3.1409628) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4289083 4.4289083 3.1409628 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -57.916493 0.0000000) to (28.958246 57.916493 3.1409628) create_atoms CPU = 0.000 seconds 341 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 21 1 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 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 677 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_666830945336_004#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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.393 | 5.393 | 5.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3241.8287 0 -3241.8287 208462.5 159 0 -4562.3998 0 -4562.3998 -6225.7298 Loop time of 6.37205 on 1 procs for 159 steps with 677 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3241.82871381189 -4562.39527425504 -4562.39978979076 Force two-norm initial, final = 2980.8222 0.39925558 Force max component initial, final = 1397.1119 0.088515599 Final line search alpha, max atom move = 0.43961078 0.038912411 Iterations, force evaluations = 159 290 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2354 | 6.2354 | 6.2354 | 0.0 | 97.86 Neigh | 0.068033 | 0.068033 | 0.068033 | 0.0 | 1.07 Comm | 0.046656 | 0.046656 | 0.046656 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02191 | | | 0.34 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10923.0 ave 10923 max 10923 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: 274406.0 ave 274406 max 274406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 274406 Ave neighs/atom = 405.32644 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 159 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.393 | 5.393 | 5.393 Mbytes Step Temp E_pair E_mol TotEng Press Volume 159 0 -4562.3998 0 -4562.3998 -6225.7298 10535.795 212 0 -4571.5173 0 -4571.5173 283.61993 10503.231 Loop time of 1.62531 on 1 procs for 53 steps with 677 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4562.39978979075 -4571.51645440663 -4571.51733031435 Force two-norm initial, final = 249.71421 7.0979791 Force max component initial, final = 225.63396 5.4819613 Final line search alpha, max atom move = 0.00023862958 0.0013081581 Iterations, force evaluations = 53 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5131 | 1.5131 | 1.5131 | 0.0 | 93.10 Neigh | 0.061647 | 0.061647 | 0.061647 | 0.0 | 3.79 Comm | 0.010879 | 0.010879 | 0.010879 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03967 | | | 2.44 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12247.0 ave 12247 max 12247 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: 276388.0 ave 276388 max 276388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 276388 Ave neighs/atom = 408.25406 Neighbor list builds = 2 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.545 | 5.545 | 5.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4571.5173 0 -4571.5173 283.61993 Loop time of 3.282e-06 on 1 procs for 0 steps with 677 atoms 152.3% 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 | | 3.282e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12211.0 ave 12211 max 12211 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: 278006.0 ave 278006 max 278006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278006 Ave neighs/atom = 410.64402 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 = 11.54372 ghost atom cutoff = 11.54372 binsize = 5.77186, bins = 6 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.54372 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) = 5.545 | 5.545 | 5.545 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 -4571.5173 -4571.5173 29.69788 118.50389 2.9844538 283.61993 283.61993 857.58385 -289.98163 283.25757 2.5621301 196.82703 Loop time of 3.382e-06 on 1 procs for 0 steps with 677 atoms 207.0% 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 | | 3.382e-06 | | |100.00 Nlocal: 677.000 ave 677 max 677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12211.0 ave 12211 max 12211 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139003.0 ave 139003 max 139003 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 278006.0 ave 278006 max 278006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 278006 Ave neighs/atom = 410.64402 Neighbor list builds = 0 Dangerous builds = 0 677 -4571.51733031435 eV 2.5621300699651 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08