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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0915243 5.2645489 5.1100000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0915243 5.2645489 5.1100000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) create_atoms CPU = 0.002 seconds 916 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.166 | 5.166 | 5.166 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6000.3526 0 -6000.3526 66169.729 54 0 -6455.7335 0 -6455.7335 6915.2947 Loop time of 8.76807 on 1 procs for 54 steps with 1828 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6000.35264074144 -6455.72855601367 -6455.73349755907 Force two-norm initial, final = 466.30096 0.20840370 Force max component initial, final = 88.282970 0.029757179 Final line search alpha, max atom move = 1.0000000 0.029757179 Iterations, force evaluations = 54 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7072 | 8.7072 | 8.7072 | 0.0 | 99.31 Neigh | 0.025522 | 0.025522 | 0.025522 | 0.0 | 0.29 Comm | 0.018357 | 0.018357 | 0.018357 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01696 | | | 0.19 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 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: 158608.0 ave 158608 max 158608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158608 Ave neighs/atom = 86.765864 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.165 | 5.165 | 5.165 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -6455.7335 0 -6455.7335 6915.2947 21512.088 59 0 -6456.0102 0 -6456.0102 2.3595318 21616.366 Loop time of 0.882347 on 1 procs for 5 steps with 1828 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6455.73349755907 -6456.00935660292 -6456.01020024644 Force two-norm initial, final = 165.11448 1.1780470 Force max component initial, final = 120.99970 0.82236127 Final line search alpha, max atom move = 9.6391630e-05 7.9268743e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87494 | 0.87494 | 0.87494 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012524 | 0.0012524 | 0.0012524 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00615 | | | 0.70 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 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: 158480.0 ave 158480 max 158480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158480 Ave neighs/atom = 86.695842 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.303 | 5.303 | 5.303 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6456.0102 0 -6456.0102 2.3595318 Loop time of 4.043e-06 on 1 procs for 0 steps with 1828 atoms 173.1% 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 | | 4.043e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 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: 158392.0 ave 158392 max 158392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158392 Ave neighs/atom = 86.647702 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.303 | 5.303 | 5.303 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 -6456.0102 -6456.0102 38.623114 109.53891 5.1093657 2.3595318 2.3595318 -59.280656 5.4144865 60.944764 2.3799004 851.46813 Loop time of 4.391e-06 on 1 procs for 0 steps with 1828 atoms 205.0% 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 | | 4.391e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7734.00 ave 7734 max 7734 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79196.0 ave 79196 max 79196 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158392.0 ave 158392 max 158392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158392 Ave neighs/atom = 86.647702 Neighbor list builds = 0 Dangerous builds = 0 1828 -6456.01020024644 eV 2.37990039608695 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10