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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -72.430572 0.0000000) to (44.354486 72.430572 8.9609594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1294304 5.1736123 5.9739729 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -72.430572 0.0000000) to (44.354486 72.430572 8.9609594) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1294304 5.1736123 5.9739729 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -72.430572 0.0000000) to (44.354486 72.430572 8.9609594) create_atoms CPU = 0.003 seconds 2357 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 37 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 4703 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -17072.01 0 -17072.01 69839.938 917 0 -19117.624 0 -19117.624 -75999.881 Loop time of 68.6407 on 1 procs for 917 steps with 4703 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 = -17072.0099263766 -19117.6064822393 -19117.6237343121 Force two-norm initial, final = 1728.4780 0.42638673 Force max component initial, final = 294.15625 0.034511031 Final line search alpha, max atom move = 1.0000000 0.034511031 Iterations, force evaluations = 917 1742 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 66.625 | 66.625 | 66.625 | 0.0 | 97.06 Neigh | 1.3173 | 1.3173 | 1.3173 | 0.0 | 1.92 Comm | 0.29566 | 0.29566 | 0.29566 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.4029 | | | 0.59 Nlocal: 4703.00 ave 4703 max 4703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14981.0 ave 14981 max 14981 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: 797360.0 ave 797360 max 797360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 797360 Ave neighs/atom = 169.54284 Neighbor list builds = 25 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 917 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.34 | 12.34 | 12.34 Mbytes Step Temp E_pair E_mol TotEng Press Volume 917 0 -19117.624 0 -19117.624 -75999.881 57576.329 970 0 -19280.642 0 -19280.642 -2.8361125 55203.479 Loop time of 2.14258 on 1 procs for 53 steps with 4703 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 = -19117.6237343119 -19280.6283553038 -19280.6415202554 Force two-norm initial, final = 5823.4447 5.9469967 Force max component initial, final = 4203.4906 0.87629458 Final line search alpha, max atom move = 3.2395695e-05 2.8388172e-05 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8313 | 1.8313 | 1.8313 | 0.0 | 85.47 Neigh | 0.25738 | 0.25738 | 0.25738 | 0.0 | 12.01 Comm | 0.0083839 | 0.0083839 | 0.0083839 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04555 | | | 2.13 Nlocal: 4703.00 ave 4703 max 4703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14972.0 ave 14972 max 14972 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: 810662.0 ave 810662 max 810662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 810662 Ave neighs/atom = 172.37125 Neighbor list builds = 5 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 11.85 | 11.85 | 11.85 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19280.642 0 -19280.642 -2.8361125 Loop time of 2.216e-06 on 1 procs for 0 steps with 4703 atoms 225.6% 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 | | 2.216e-06 | | |100.00 Nlocal: 4703.00 ave 4703 max 4703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14876.0 ave 14876 max 14876 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: 801054.0 ave 801054 max 801054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 801054 Ave neighs/atom = 170.32830 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 11.85 | 11.85 | 11.85 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 -19280.642 -19280.642 42.75177 138.95271 9.2927728 -2.8361125 -2.8361125 11.901369 5.9648304 -26.374537 2.226517 7948.4987 Loop time of 2.691e-06 on 1 procs for 0 steps with 4703 atoms 260.1% 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 | | 2.691e-06 | | |100.00 Nlocal: 4703.00 ave 4703 max 4703 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14876.0 ave 14876 max 14876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 400527.0 ave 400527 max 400527 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 801054.0 ave 801054 max 801054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 801054 Ave neighs/atom = 170.32830 Neighbor list builds = 0 Dangerous builds = 0 4703 -19280.6415202554 eV 2.22651703439552 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:11