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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -37.587095 0.0000000) to (21.698887 37.587095 6.0968610) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7102335 5.2748878 6.0968610 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.587095 0.0000000) to (21.698887 37.587095 6.0968610) create_atoms CPU = 0.003 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7102335 5.2748878 6.0968610 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.587095 0.0000000) to (21.698887 37.587095 6.0968610) create_atoms CPU = 0.002 seconds 458 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 18 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.410 | 5.410 | 5.410 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3959.6826 0 -3959.6826 6204.0193 33 0 -3981.3013 0 -3981.3013 -10231.852 Loop time of 1.25591 on 1 procs for 33 steps with 900 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 = -3959.68258712143 -3981.29753143387 -3981.30133057364 Force two-norm initial, final = 38.929456 0.20079996 Force max component initial, final = 11.155292 0.016062853 Final line search alpha, max atom move = 1.0000000 0.016062853 Iterations, force evaluations = 33 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2115 | 1.2115 | 1.2115 | 0.0 | 96.47 Neigh | 0.027242 | 0.027242 | 0.027242 | 0.0 | 2.17 Comm | 0.0096102 | 0.0096102 | 0.0096102 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007513 | | | 0.60 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6888.00 ave 6888 max 6888 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: 199772.0 ave 199772 max 199772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199772 Ave neighs/atom = 221.96889 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.413 | 5.413 | 5.413 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -3981.3013 0 -3981.3013 -10231.852 9945.1772 36 0 -3981.3759 0 -3981.3759 -4331.256 9911.5132 Loop time of 0.129182 on 1 procs for 3 steps with 900 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3981.30133057369 -3981.37580862494 -3981.37590102781 Force two-norm initial, final = 62.051254 0.22068796 Force max component initial, final = 44.147547 0.038119353 Final line search alpha, max atom move = 0.00087564140 3.3378884e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1256 | 0.1256 | 0.1256 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091256 | 0.00091256 | 0.00091256 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002667 | | | 2.06 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6916.00 ave 6916 max 6916 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: 199592.0 ave 199592 max 199592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199592 Ave neighs/atom = 221.76889 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.551 | 5.551 | 5.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3981.3759 0 -3981.3759 -4331.256 Loop time of 6.165e-06 on 1 procs for 0 steps with 900 atoms 178.4% 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 | | 6.165e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6920.00 ave 6920 max 6920 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: 199692.0 ave 199692 max 199692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199692 Ave neighs/atom = 221.88000 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 6 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.551 | 5.551 | 5.551 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 -3981.3759 -3981.3759 21.659351 75.174191 6.0873149 -4331.256 -4331.256 0.3732957 -12987.989 -6.1522701 2.261216 496.56112 Loop time of 3.1022e-05 on 1 procs for 0 steps with 900 atoms 0.0% 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 | | 3.102e-05 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6920.00 ave 6920 max 6920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99846.0 ave 99846 max 99846 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 199692.0 ave 199692 max 199692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199692 Ave neighs/atom = 221.88000 Neighbor list builds = 0 Dangerous builds = 0 900 -3956.84063940781 eV 2.26121595497052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02