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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -29.240296 0.0000000) to (25.320356 29.240296 4.9657304) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5446793 4.4980660 4.9657304 Created 316 atoms using lattice units in orthogonal box = (0.0000000 -29.240296 0.0000000) to (25.320356 29.240296 4.9657304) create_atoms CPU = 0.002 seconds 316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5446793 4.4980660 4.9657304 Created 315 atoms using lattice units in orthogonal box = (0.0000000 -29.240296 0.0000000) to (25.320356 29.240296 4.9657304) create_atoms CPU = 0.002 seconds 315 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 16 2 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 625 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.903 | 4.903 | 4.903 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2141.8896 0 -2141.8896 253960.83 158 0 -2521.358 0 -2521.358 -69675.086 Loop time of 3.37298 on 1 procs for 158 steps with 625 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 = -2141.88960473193 -2521.35599699325 -2521.357985664 Force two-norm initial, final = 566.84939 0.17209380 Force max component initial, final = 127.63468 0.032178205 Final line search alpha, max atom move = 1.0000000 0.032178205 Iterations, force evaluations = 158 302 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2839 | 3.2839 | 3.2839 | 0.0 | 97.36 Neigh | 0.028385 | 0.028385 | 0.028385 | 0.0 | 0.84 Comm | 0.033288 | 0.033288 | 0.033288 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02736 | | | 0.81 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4515.00 ave 4515 max 4515 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: 97494.0 ave 97494 max 97494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97494 Ave neighs/atom = 155.99040 Neighbor list builds = 2 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 158 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 158 0 -2521.358 0 -2521.358 -69675.086 7353.0024 234 0 -2531.6235 0 -2531.6235 -21039.867 6911.0095 Loop time of 1.07892 on 1 procs for 76 steps with 625 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 = -2521.357985664 -2531.62264643641 -2531.62354643745 Force two-norm initial, final = 417.55003 3.8975413 Force max component initial, final = 329.25787 3.1644461 Final line search alpha, max atom move = 0.00057977536 0.0018346679 Iterations, force evaluations = 76 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0227 | 1.0227 | 1.0227 | 0.0 | 94.79 Neigh | 0.01439 | 0.01439 | 0.01439 | 0.0 | 1.33 Comm | 0.0092694 | 0.0092694 | 0.0092694 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03259 | | | 3.02 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4660.00 ave 4660 max 4660 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: 102216.0 ave 102216 max 102216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102216 Ave neighs/atom = 163.54560 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2531.6235 0 -2531.6235 -21039.867 Loop time of 6.656e-06 on 1 procs for 0 steps with 625 atoms 180.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4658.00 ave 4658 max 4658 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: 102224.0 ave 102224 max 102224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102224 Ave neighs/atom = 163.55840 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.043 | 5.043 | 5.043 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 -2531.6235 -2531.6235 24.327041 58.480592 4.8578091 -21039.867 -21039.867 -71.895704 -62330.037 -717.66848 2.2841125 2848.6939 Loop time of 7.297e-06 on 1 procs for 0 steps with 625 atoms 246.7% 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 | | 7.297e-06 | | |100.00 Nlocal: 625.000 ave 625 max 625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4658.00 ave 4658 max 4658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51112.0 ave 51112 max 51112 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102224.0 ave 102224 max 102224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102224 Ave neighs/atom = 163.55840 Neighbor list builds = 0 Dangerous builds = 0 625 -2531.62354643745 eV 2.28411253968278 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04