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 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4751049 5.3644854 5.7481359 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) create_atoms CPU = 0.003 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4751049 5.3644854 5.7481359 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -55.433015 0.0000000) to (33.945651 55.433015 8.6222039) create_atoms CPU = 0.002 seconds 1492 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 27 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2978 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.416 | 7.416 | 7.416 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12852.886 0 -12852.886 35376.878 75 0 -13215.705 0 -13215.705 7408.1209 Loop time of 4.60609 on 1 procs for 75 steps with 2978 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12852.8861170925 -13215.6926557162 -13215.7052843303 Force two-norm initial, final = 316.47750 0.40340292 Force max component initial, final = 46.904597 0.058901157 Final line search alpha, max atom move = 0.98883853 0.058243734 Iterations, force evaluations = 75 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5247 | 4.5247 | 4.5247 | 0.0 | 98.23 Neigh | 0.038048 | 0.038048 | 0.038048 | 0.0 | 0.83 Comm | 0.019546 | 0.019546 | 0.019546 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02383 | | | 0.52 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12241.0 ave 12241 max 12241 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: 667430.0 ave 667430 max 667430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667430 Ave neighs/atom = 224.12021 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.419 | 7.419 | 7.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -13215.705 0 -13215.705 7408.1209 32448.971 79 0 -13216.103 0 -13216.103 -69.044895 32585.008 Loop time of 0.23812 on 1 procs for 4 steps with 2978 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13215.7052843301 -13216.1024496677 -13216.102690232 Force two-norm initial, final = 273.00371 2.8822028 Force max component initial, final = 198.46540 2.6134284 Final line search alpha, max atom move = 0.00022972851 0.00060037901 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23262 | 0.23262 | 0.23262 | 0.0 | 97.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007814 | 0.0007814 | 0.0007814 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004723 | | | 1.98 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12430.0 ave 12430 max 12430 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: 667722.0 ave 667722 max 667722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667722 Ave neighs/atom = 224.21827 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.557 | 7.557 | 7.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13216.103 0 -13216.103 -69.044895 Loop time of 2.333e-06 on 1 procs for 0 steps with 2978 atoms 171.5% 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 | | 2.333e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12412.0 ave 12412 max 12412 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: 667254.0 ave 667254 max 667254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667254 Ave neighs/atom = 224.06111 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.557 | 7.557 | 7.557 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 -13216.103 -13216.103 34.002484 111.16856 8.620356 -69.044895 -69.044895 -128.71514 -33.181263 -45.238279 2.2297927 1088.6225 Loop time of 2.902e-06 on 1 procs for 0 steps with 2978 atoms 275.7% 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 | | 2.902e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12412.0 ave 12412 max 12412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 333627.0 ave 333627 max 333627 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 667254.0 ave 667254 max 667254 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 667254 Ave neighs/atom = 224.06111 Neighbor list builds = 0 Dangerous builds = 0 2978 -13216.102690232 eV 2.22979273716736 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05