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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -68.246907 0.0000000) to (39.402370 68.246907 6.1787847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8134645 5.2210749 6.1787847 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -68.246907 0.0000000) to (39.402370 68.246907 6.1787847) create_atoms CPU = 0.008 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8134645 5.2210749 6.1787847 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -68.246907 0.0000000) to (39.402370 68.246907 6.1787847) create_atoms CPU = 0.007 seconds 1466 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 49 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2930 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.391 | 5.391 | 5.391 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11867.251 0 -11867.251 40480.836 84 0 -12363.878 0 -12363.878 39420.472 Loop time of 27.7354 on 1 procs for 84 steps with 2930 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 = -11867.2511513056 -12363.868325216 -12363.8783960439 Force two-norm initial, final = 562.65280 0.39500936 Force max component initial, final = 144.00892 0.048345461 Final line search alpha, max atom move = 0.99053829 0.047888030 Iterations, force evaluations = 84 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 27.561 | 27.561 | 27.561 | 0.0 | 99.37 Neigh | 0.096723 | 0.096723 | 0.096723 | 0.0 | 0.35 Comm | 0.03191 | 0.03191 | 0.03191 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04524 | | | 0.16 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9101.00 ave 9101 max 9101 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: 166456.0 ave 166456 max 166456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166456 Ave neighs/atom = 56.810922 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 84 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.389 | 5.389 | 5.389 Mbytes Step Temp E_pair E_mol TotEng Press Volume 84 0 -12363.878 0 -12363.878 39420.472 33230.615 89 0 -12368.242 0 -12368.242 -20.31469 33593.06 Loop time of 1.72006 on 1 procs for 5 steps with 2930 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 = -12363.8783960439 -12368.2387746571 -12368.2424176475 Force two-norm initial, final = 1417.6199 2.2977211 Force max component initial, final = 869.90607 0.79852619 Final line search alpha, max atom move = 7.2501266e-05 5.7894159e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7078 | 1.7078 | 1.7078 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020124 | 0.0020124 | 0.0020124 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01023 | | | 0.59 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9077.00 ave 9077 max 9077 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: 167076.0 ave 167076 max 167076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 167076 Ave neighs/atom = 57.022526 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.526 | 5.526 | 5.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12368.242 0 -12368.242 -20.31469 Loop time of 8.35e-06 on 1 procs for 0 steps with 2930 atoms 167.7% 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 | | 8.35e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9016.00 ave 9016 max 9016 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: 163908.0 ave 163908 max 163908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163908 Ave neighs/atom = 55.941297 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 15 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.526 | 5.526 | 5.526 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 -12368.242 -12368.242 39.548803 137.04671 6.1979436 -20.31469 -20.31469 -15.471108 -38.238918 -7.2340456 2.2809241 1386.9166 Loop time of 7.307e-06 on 1 procs for 0 steps with 2930 atoms 287.4% 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 | | 7.307e-06 | | |100.00 Nlocal: 2930.00 ave 2930 max 2930 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9016.00 ave 9016 max 9016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81954.0 ave 81954 max 81954 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163908.0 ave 163908 max 163908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163908 Ave neighs/atom = 55.941297 Neighbor list builds = 0 Dangerous builds = 0 2930 -12368.2424176475 eV 2.28092412459921 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30