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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -37.516677 0.0000000) to (32.487210 37.516677 6.3712660) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8310376 5.7712306 6.3712660 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -37.516677 0.0000000) to (32.487210 37.516677 6.3712660) create_atoms CPU = 0.004 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8310376 5.7712306 6.3712660 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -37.516677 0.0000000) to (32.487210 37.516677 6.3712660) create_atoms CPU = 0.003 seconds 628 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 25 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 1228 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5115.5483 0 -5115.5483 3007.2203 123 0 -5158.371 0 -5158.371 -25369.589 Loop time of 1.86229 on 1 procs for 123 steps with 1228 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 = -5115.54831568906 -5158.36626962923 -5158.37104424953 Force two-norm initial, final = 35.625639 0.23514091 Force max component initial, final = 7.5171112 0.091242412 Final line search alpha, max atom move = 1.0000000 0.091242412 Iterations, force evaluations = 123 221 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7609 | 1.7609 | 1.7609 | 0.0 | 94.55 Neigh | 0.045883 | 0.045883 | 0.045883 | 0.0 | 2.46 Comm | 0.024053 | 0.024053 | 0.024053 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03147 | | | 1.69 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4656.00 ave 4656 max 4656 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: 94154.0 ave 94154 max 94154 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94154 Ave neighs/atom = 76.672638 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 123 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.638 | 4.638 | 4.638 Mbytes Step Temp E_pair E_mol TotEng Press Volume 123 0 -5158.371 0 -5158.371 -25369.589 15530.753 139 0 -5160.9312 0 -5160.9312 -5534.4463 15253.55 Loop time of 0.156679 on 1 procs for 16 steps with 1228 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5158.37104424952 -5160.93093958673 -5160.93119020406 Force two-norm initial, final = 341.27047 1.3262389 Force max component initial, final = 308.93959 0.71095397 Final line search alpha, max atom move = 0.00033017605 0.00023473997 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14651 | 0.14651 | 0.14651 | 0.0 | 93.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017861 | 0.0017861 | 0.0017861 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008384 | | | 5.35 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4650.00 ave 4650 max 4650 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: 93660.0 ave 93660 max 93660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93660 Ave neighs/atom = 76.270358 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.776 | 4.776 | 4.776 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5160.9312 0 -5160.9312 -5534.4463 Loop time of 6.024e-06 on 1 procs for 0 steps with 1228 atoms 166.0% 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 | | 6.024e-06 | | |100.00 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4679.00 ave 4679 max 4679 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: 94192.0 ave 94192 max 94192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94192 Ave neighs/atom = 76.703583 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.776 | 4.776 | 4.776 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 -5160.9312 -5160.9312 32.001038 75.033354 6.3526144 -5534.4463 -5534.4463 -73.558451 -16506.097 -23.683419 2.2785621 1226.319 Loop time of 6.926e-06 on 1 procs for 0 steps with 1228 atoms 274.3% 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 | | 6.926e-06 | | |100.00 Nlocal: 1228.00 ave 1228 max 1228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47096.0 ave 47096 max 47096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94192.0 ave 94192 max 94192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94192 Ave neighs/atom = 76.703583 Neighbor list builds = 0 Dangerous builds = 0 1228 -5160.93106740406 eV 2.27856209706004 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02