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 = 3.3116877 3.3116877 3.3116877 Created orthogonal box = (0.0000000 -40.559725 0.0000000) to (4.6834336 40.559725 5.7360113) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6834336 5.4079633 5.7360113 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -40.559725 0.0000000) to (4.6834336 40.559725 5.7360113) create_atoms CPU = 0.002 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6834336 5.4079633 5.7360113 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -40.559725 0.0000000) to (4.6834336 40.559725 5.7360113) create_atoms CPU = 0.002 seconds 122 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 22 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 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 242 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_255315407910_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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.503 | 4.503 | 4.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -598.69967 0 -598.69967 399713.06 103 0 -938.89196 0 -938.89196 104025.1 Loop time of 1.31586 on 1 procs for 103 steps with 242 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 = -598.699670475773 -938.891160929218 -938.891957277846 Force two-norm initial, final = 871.41030 0.17169256 Force max component initial, final = 435.26296 0.019398960 Final line search alpha, max atom move = 1.0000000 0.019398960 Iterations, force evaluations = 103 193 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2797 | 1.2797 | 1.2797 | 0.0 | 97.25 Neigh | 0.0061745 | 0.0061745 | 0.0061745 | 0.0 | 0.47 Comm | 0.018532 | 0.018532 | 0.018532 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01144 | | | 0.87 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3672.00 ave 3672 max 3672 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: 47828.0 ave 47828 max 47828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47828 Ave neighs/atom = 197.63636 Neighbor list builds = 1 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -938.89196 0 -938.89196 104025.1 2179.2114 654 0 -965.28021 0 -965.28021 -399.3813 2943.2586 Loop time of 3.87778 on 1 procs for 551 steps with 242 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 = -938.891957277839 -965.279322127566 -965.280207338371 Force two-norm initial, final = 255.78007 1.7550392 Force max component initial, final = 201.21242 0.90863083 Final line search alpha, max atom move = 0.00046462409 0.00042217177 Iterations, force evaluations = 551 622 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6203 | 3.6203 | 3.6203 | 0.0 | 93.36 Neigh | 0.045847 | 0.045847 | 0.045847 | 0.0 | 1.18 Comm | 0.052507 | 0.052507 | 0.052507 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1592 | | | 4.10 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 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: 35020.0 ave 35020 max 35020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35020 Ave neighs/atom = 144.71074 Neighbor list builds = 8 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -965.28021 0 -965.28021 -399.3813 Loop time of 6.094e-06 on 1 procs for 0 steps with 242 atoms 196.9% 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 | | 6.094e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3506.00 ave 3506 max 3506 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: 34032.0 ave 34032 max 34032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34032 Ave neighs/atom = 140.62810 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 = 7.5 ghost atom cutoff = 7.5 binsize = 3.75, bins = 2 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5 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) = 4.640 | 4.640 | 4.640 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 -965.28021 -965.28021 5.1725809 89.738482 6.340776 -399.3813 -399.3813 -148.19499 -503.18252 -546.7664 2.4380643 12.929118 Loop time of 7.216e-06 on 1 procs for 0 steps with 242 atoms 263.3% 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 | | 7.216e-06 | | |100.00 Nlocal: 242.000 ave 242 max 242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17016.0 ave 17016 max 17016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34032.0 ave 34032 max 34032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34032 Ave neighs/atom = 140.62810 Neighbor list builds = 0 Dangerous builds = 0 242 -965.280207338371 eV 2.4380643345235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06