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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -41.390126 0.0000000) to (6.3365430 41.390126 8.9612251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3365430 5.1737657 5.9741501 Created 192 atoms using lattice units in orthogonal box = (0.0000000 -41.390126 0.0000000) to (6.3365430 41.390126 8.9612251) create_atoms CPU = 0.001 seconds 192 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3365430 5.1737657 5.9741501 Created 198 atoms using lattice units in orthogonal box = (0.0000000 -41.390126 0.0000000) to (6.3365430 41.390126 8.9612251) create_atoms CPU = 0.000 seconds 198 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 390 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_249706810527_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1192.056 0 -1192.056 259674.43 156 0 -1522.6858 0 -1522.6858 -5312.6833 Loop time of 0.991901 on 1 procs for 156 steps with 390 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1192.0560347078 -1522.68431395414 -1522.68581421193 Force two-norm initial, final = 581.13832 0.12604502 Force max component initial, final = 154.99690 0.012151587 Final line search alpha, max atom move = 1.0000000 0.012151587 Iterations, force evaluations = 156 303 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96293 | 0.96293 | 0.96293 | 0.0 | 97.08 Neigh | 0.011758 | 0.011758 | 0.011758 | 0.0 | 1.19 Comm | 0.010041 | 0.010041 | 0.010041 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00717 | | | 0.72 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3553.00 ave 3553 max 3553 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: 55032.0 ave 55032 max 55032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55032 Ave neighs/atom = 141.10769 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 156 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.511 | 4.511 | 4.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 156 0 -1522.6858 0 -1522.6858 -5312.6833 4700.5266 208 0 -1527.5889 0 -1527.5889 371.8208 4697.6673 Loop time of 0.185653 on 1 procs for 52 steps with 390 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 = -1522.68581421194 -1527.58826555983 -1527.58890602875 Force two-norm initial, final = 172.09177 2.3703928 Force max component initial, final = 134.42814 1.3274092 Final line search alpha, max atom move = 0.00056559162 0.00075077152 Iterations, force evaluations = 52 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16935 | 0.16935 | 0.16935 | 0.0 | 91.22 Neigh | 0.0072908 | 0.0072908 | 0.0072908 | 0.0 | 3.93 Comm | 0.0017834 | 0.0017834 | 0.0017834 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00723 | | | 3.89 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567.00 ave 3567 max 3567 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: 55380.0 ave 55380 max 55380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55380 Ave neighs/atom = 142.00000 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1527.5889 0 -1527.5889 371.8208 Loop time of 3.239e-06 on 1 procs for 0 steps with 390 atoms 154.4% 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 | | 3.239e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3535.00 ave 3535 max 3535 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: 54564.0 ave 54564 max 54564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54564 Ave neighs/atom = 139.90769 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 2 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.648 | 4.648 | 4.648 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 -1527.5889 -1527.5889 6.3232221 79.760971 9.3143679 371.8208 371.8208 403.00921 436.211 276.24219 2.354186 74.223334 Loop time of 2.747e-06 on 1 procs for 0 steps with 390 atoms 218.4% 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 | | 2.747e-06 | | |100.00 Nlocal: 390.000 ave 390 max 390 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3535.00 ave 3535 max 3535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27282.0 ave 27282 max 27282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54564.0 ave 54564 max 54564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54564 Ave neighs/atom = 139.90769 Neighbor list builds = 0 Dangerous builds = 0 390 -1527.58890602875 eV 2.35418599599384 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01