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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -54.525673 0.0000000) to (38.555473 54.525673 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0877063 5.2612491 5.1067972 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.525673 0.0000000) to (38.555473 54.525673 5.1067972) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0877063 5.2612491 5.1067972 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.525673 0.0000000) to (38.555473 54.525673 5.1067972) 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 22 1 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1820 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6874.2427 0 -6874.2427 49615.177 229 0 -7539.4983 0 -7539.4983 447.48235 Loop time of 13.593 on 1 procs for 229 steps with 1820 atoms 91.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6874.24265320151 -7539.49100487561 -7539.4983271169 Force two-norm initial, final = 825.67653 0.37327133 Force max component initial, final = 200.70204 0.076785410 Final line search alpha, max atom move = 0.84812194 0.065123391 Iterations, force evaluations = 229 415 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.178 | 13.178 | 13.178 | 0.0 | 96.95 Neigh | 0.22942 | 0.22942 | 0.22942 | 0.0 | 1.69 Comm | 0.11636 | 0.11636 | 0.11636 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06891 | | | 0.51 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15348.0 ave 15348 max 15348 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: 691044.0 ave 691044 max 691044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 691044 Ave neighs/atom = 379.69451 Neighbor list builds = 6 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 229 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.49 | 11.49 | 11.49 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -7539.4983 0 -7539.4983 447.48235 21471.663 235 0 -7539.9351 0 -7539.9351 -5.7561285 21476.877 Loop time of 0.23827 on 1 procs for 6 steps with 1820 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 = -7539.49832711686 -7539.93470559054 -7539.9351217697 Force two-norm initial, final = 142.67560 0.73449685 Force max component initial, final = 120.17096 0.39789323 Final line search alpha, max atom move = 0.00029472168 0.00011726776 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2326 | 0.2326 | 0.2326 | 0.0 | 97.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097006 | 0.00097006 | 0.00097006 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004696 | | | 1.97 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15026.0 ave 15026 max 15026 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: 691988.0 ave 691988 max 691988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 691988 Ave neighs/atom = 380.21319 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.00 | 11.00 | 11.00 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7539.9351 0 -7539.9351 -5.7561285 Loop time of 2.176e-06 on 1 procs for 0 steps with 1820 atoms 183.8% 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 | | 2.176e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15101.0 ave 15101 max 15101 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: 691376.0 ave 691376 max 691376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 691376 Ave neighs/atom = 379.87692 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.00 | 11.00 | 11.00 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 -7539.9351 -7539.9351 38.45584 109.6135 5.0950068 -5.7561285 -5.7561285 -29.606157 -3.6436591 15.981431 2.3584262 954.04387 Loop time of 2.601e-06 on 1 procs for 0 steps with 1820 atoms 269.1% 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 | | 2.601e-06 | | |100.00 Nlocal: 1820.00 ave 1820 max 1820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15101.0 ave 15101 max 15101 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 345688.0 ave 345688 max 345688 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 691376.0 ave 691376 max 691376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 691376 Ave neighs/atom = 379.87692 Neighbor list builds = 0 Dangerous builds = 0 1820 -7539.9351217697 eV 2.35842623238188 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14