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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -80.555440 0.0000000) to (46.508705 80.555440 7.2931469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8619401 6.1627113 7.2931469 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -80.555440 0.0000000) to (46.508705 80.555440 7.2931469) create_atoms CPU = 0.008 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8619401 6.1627113 7.2931469 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -80.555440 0.0000000) to (46.508705 80.555440 7.2931469) create_atoms CPU = 0.007 seconds 1465 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 36 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2928 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9966.8654 0 -9966.8654 72706.02 127 0 -10903.459 0 -10903.459 1484.5643 Loop time of 17.2282 on 1 procs for 127 steps with 2928 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 = -9966.86535574819 -10903.4501866261 -10903.4591826338 Force two-norm initial, final = 2864.9130 0.17782918 Force max component initial, final = 878.18577 0.026063501 Final line search alpha, max atom move = 1.0000000 0.026063501 Iterations, force evaluations = 127 202 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.532 | 16.532 | 16.532 | 0.0 | 95.96 Neigh | 0.54711 | 0.54711 | 0.54711 | 0.0 | 3.18 Comm | 0.073363 | 0.073363 | 0.073363 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07597 | | | 0.44 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12888.0 ave 12888 max 12888 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: 507002.0 ave 507002 max 507002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507002 Ave neighs/atom = 173.15642 Neighbor list builds = 8 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 127 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.88 | 10.88 | 10.88 Mbytes Step Temp E_pair E_mol TotEng Press Volume 127 0 -10903.459 0 -10903.459 1484.5643 54647.975 131 0 -10903.604 0 -10903.604 94.943105 54837.084 Loop time of 0.545321 on 1 procs for 4 steps with 2928 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 = -10903.4591826338 -10903.5967476779 -10903.6037214173 Force two-norm initial, final = 92.262563 5.6805094 Force max component initial, final = 72.782608 3.8965411 Final line search alpha, max atom move = 0.00013674138 0.00053281842 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.53666 | 0.53666 | 0.53666 | 0.0 | 98.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018378 | 0.0018378 | 0.0018378 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006826 | | | 1.25 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12829.0 ave 12829 max 12829 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: 507300.0 ave 507300 max 507300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507300 Ave neighs/atom = 173.25820 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 10.39 | 10.39 | 10.39 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10903.604 0 -10903.604 94.943105 Loop time of 3.4309e-05 on 1 procs for 0 steps with 2928 atoms 35.0% 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 | | 3.431e-05 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12798.0 ave 12798 max 12798 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: 506292.0 ave 506292 max 506292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506292 Ave neighs/atom = 172.91393 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 10.39 | 10.39 | 10.39 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 -10903.604 -10903.604 46.460361 161.7406 7.2974769 94.943105 94.943105 85.288969 114.29032 85.250028 2.6933942 1873.3891 Loop time of 8.279e-06 on 1 procs for 0 steps with 2928 atoms 241.6% 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 | | 8.279e-06 | | |100.00 Nlocal: 2928.00 ave 2928 max 2928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12798.0 ave 12798 max 12798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 253146.0 ave 253146 max 253146 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 506292.0 ave 506292 max 506292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506292 Ave neighs/atom = 172.91393 Neighbor list builds = 0 Dangerous builds = 0 2928 -10903.6037214173 eV 2.69339416245594 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19