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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -62.513284 0.0000000) to (31.254813 62.513284 3.6580991) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7096293 4.7096293 3.6580991 Created 585 atoms using lattice units in orthogonal box = (0.0000000 -62.513284 0.0000000) to (31.254813 62.513284 3.6580991) create_atoms CPU = 0.001 seconds 585 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7096293 4.7096293 3.6580991 Created 585 atoms using lattice units in orthogonal box = (0.0000000 -62.513284 0.0000000) to (31.254813 62.513284 3.6580991) create_atoms CPU = 0.001 seconds 585 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 = 9 35 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1162 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_634187028437_000#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 = 9 35 2 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4485.4985 0 -4485.4985 5686.4708 152 0 -4516.0176 0 -4516.0176 -3948.4964 Loop time of 2.2625 on 1 procs for 152 steps with 1162 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 = -4485.49850216243 -4516.01313054468 -4516.01759095596 Force two-norm initial, final = 26.141066 0.19722126 Force max component initial, final = 7.0342888 0.038728550 Final line search alpha, max atom move = 1.0000000 0.038728550 Iterations, force evaluations = 152 283 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2152 | 2.2152 | 2.2152 | 0.0 | 97.91 Neigh | 0.017168 | 0.017168 | 0.017168 | 0.0 | 0.76 Comm | 0.015954 | 0.015954 | 0.015954 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01414 | | | 0.63 Nlocal: 1162.00 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7445.00 ave 7445 max 7445 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: 157786.0 ave 157786 max 157786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157786 Ave neighs/atom = 135.78830 Neighbor list builds = 2 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 = 9 35 2 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 : 152 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.040 | 5.040 | 5.040 Mbytes Step Temp E_pair E_mol TotEng Press Volume 152 0 -4516.0176 0 -4516.0176 -3948.4964 14294.688 177 0 -4519.491 0 -4519.491 -5956.6265 14306.04 Loop time of 0.222818 on 1 procs for 25 steps with 1162 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 = -4516.01759095599 -4519.4872554604 -4519.4909647895 Force two-norm initial, final = 207.11796 2.0786530 Force max component initial, final = 170.58706 0.45514480 Final line search alpha, max atom move = 0.00020064351 9.1321851e-05 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21431 | 0.21431 | 0.21431 | 0.0 | 96.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014454 | 0.0014454 | 0.0014454 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007059 | | | 3.17 Nlocal: 1162.00 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7427.00 ave 7427 max 7427 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: 157976.0 ave 157976 max 157976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157976 Ave neighs/atom = 135.95181 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 = 9 35 2 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4519.491 0 -4519.491 -5956.6265 Loop time of 1.776e-06 on 1 procs for 0 steps with 1162 atoms 112.6% 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 | | 1.776e-06 | | |100.00 Nlocal: 1162.00 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 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: 159708.0 ave 159708 max 159708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159708 Ave neighs/atom = 137.44234 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 = 9 35 2 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) = 5.179 | 5.179 | 5.179 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 -4519.491 -4519.491 30.562227 125.02657 3.7439681 -5956.6265 -5956.6265 49.843507 -17876.372 -43.350587 2.2565428 600.35654 Loop time of 1.714e-06 on 1 procs for 0 steps with 1162 atoms 233.4% 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 | | 1.714e-06 | | |100.00 Nlocal: 1162.00 ave 1162 max 1162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7457.00 ave 7457 max 7457 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79854.0 ave 79854 max 79854 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159708.0 ave 159708 max 159708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159708 Ave neighs/atom = 137.44234 Neighbor list builds = 0 Dangerous builds = 0 1162 -4355.15903780227 eV 2.25654282978625 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02