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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -74.194304 0.0000000) to (42.836101 74.194304 6.4094117) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7541032 5.9060143 6.4094117 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -74.194304 0.0000000) to (42.836101 74.194304 6.4094117) create_atoms CPU = 0.004 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7541032 5.9060143 6.4094117 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -74.194304 0.0000000) to (42.836101 74.194304 6.4094117) create_atoms CPU = 0.004 seconds 1610 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 39 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 3216 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 6.665 | 6.665 | 6.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11719.994 0 -11719.994 68203.419 362 0 -12926.914 0 -12926.914 -63575.898 Loop time of 21.5628 on 1 procs for 362 steps with 3216 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 = -11719.9939114393 -12926.9020353265 -12926.9142699773 Force two-norm initial, final = 1579.3011 0.35170865 Force max component initial, final = 478.17734 0.080291353 Final line search alpha, max atom move = 1.0000000 0.080291353 Iterations, force evaluations = 362 689 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.049 | 21.049 | 21.049 | 0.0 | 97.62 Neigh | 0.2408 | 0.2408 | 0.2408 | 0.0 | 1.12 Comm | 0.14437 | 0.14437 | 0.14437 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1287 | | | 0.60 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13420.0 ave 13420 max 13420 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: 501788.0 ave 501788 max 501788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 501788 Ave neighs/atom = 156.02861 Neighbor list builds = 7 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 362 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.80 | 10.80 | 10.80 Mbytes Step Temp E_pair E_mol TotEng Press Volume 362 0 -12926.914 0 -12926.914 -63575.898 40740.717 396 0 -12973.758 0 -12973.758 5.4125151 38698.49 Loop time of 1.44467 on 1 procs for 34 steps with 3216 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 = -12926.9142699772 -12973.7478488723 -12973.7575081331 Force two-norm initial, final = 2838.6312 6.5353847 Force max component initial, final = 1924.1363 1.3639309 Final line search alpha, max atom move = 5.6448116e-05 7.6991328e-05 Iterations, force evaluations = 34 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2998 | 1.2998 | 1.2998 | 0.0 | 89.97 Neigh | 0.10927 | 0.10927 | 0.10927 | 0.0 | 7.56 Comm | 0.0060444 | 0.0060444 | 0.0060444 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0296 | | | 2.05 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13628.0 ave 13628 max 13628 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: 518438.0 ave 518438 max 518438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518438 Ave neighs/atom = 161.20585 Neighbor list builds = 3 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 10.32 | 10.32 | 10.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12973.758 0 -12973.758 5.4125151 Loop time of 2.044e-06 on 1 procs for 0 steps with 3216 atoms 146.8% 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 | | 2.044e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13628.0 ave 13628 max 13628 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: 518584.0 ave 518584 max 518584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518584 Ave neighs/atom = 161.25124 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 10.32 | 10.32 | 10.32 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 -12973.758 -12973.758 41.533027 145.50102 6.4037503 5.4125151 5.4125151 29.99442 -55.369956 41.613082 2.248091 7124.7927 Loop time of 2.588e-06 on 1 procs for 0 steps with 3216 atoms 270.5% 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 | | 2.588e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13628.0 ave 13628 max 13628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 259292.0 ave 259292 max 259292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 518584.0 ave 518584 max 518584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 518584 Ave neighs/atom = 161.25124 Neighbor list builds = 0 Dangerous builds = 0 3216 -12973.7575081331 eV 2.24809098442564 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24