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 = 3.6150000 3.6150000 3.6150000 Created orthogonal box = (0.0000000 -53.129432 0.0000000) to (18.784091 53.129432 5.1123820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8699495 5.9032703 5.1123820 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.129432 0.0000000) to (18.784091 53.129432 5.1123820) create_atoms CPU = 0.001 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8699495 5.9032703 5.1123820 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.129432 0.0000000) to (18.784091 53.129432 5.1123820) create_atoms CPU = 0.001 seconds 434 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 5 27 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 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_128703483589_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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.007 | 5.007 | 5.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2472.0689 0 -2472.0689 148808.25 98 0 -3041.0838 0 -3041.0838 2827.1639 Loop time of 1.4865 on 1 procs for 98 steps with 862 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2472.06893041895 -3041.08084608074 -3041.08382399934 Force two-norm initial, final = 1699.3390 0.17309408 Force max component initial, final = 454.95826 0.041364129 Final line search alpha, max atom move = 1.0000000 0.041364129 Iterations, force evaluations = 98 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.446 | 1.446 | 1.446 | 0.0 | 97.28 Neigh | 0.021612 | 0.021612 | 0.021612 | 0.0 | 1.45 Comm | 0.010853 | 0.010853 | 0.010853 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008022 | | | 0.54 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6621.00 ave 6621 max 6621 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: 151864.0 ave 151864 max 151864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151864 Ave neighs/atom = 176.17633 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.015 | 5.015 | 5.015 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -3041.0838 0 -3041.0838 2827.1639 10204.193 100 0 -3041.1063 0 -3041.1063 2.7666867 10224.965 Loop time of 0.0404074 on 1 procs for 2 steps with 862 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 = -3041.08382399934 -3041.10454193085 -3041.1063259342 Force two-norm initial, final = 32.377745 1.0949696 Force max component initial, final = 23.229728 0.86128889 Final line search alpha, max atom move = 0.00020126475 0.00017334710 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039221 | 0.039221 | 0.039221 | 0.0 | 97.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026258 | 0.00026258 | 0.00026258 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009233 | | | 2.29 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6929.00 ave 6929 max 6929 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: 151892.0 ave 151892 max 151892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151892 Ave neighs/atom = 176.20882 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.153 | 5.153 | 5.153 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3041.1063 0 -3041.1063 2.7666867 Loop time of 1.483e-06 on 1 procs for 0 steps with 862 atoms 134.9% 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 | | 1.483e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6929.00 ave 6929 max 6929 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: 151788.0 ave 151788 max 151788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151788 Ave neighs/atom = 176.08817 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 = 7.995011 ghost atom cutoff = 7.995011 binsize = 3.9975055, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.995011000293092 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) = 5.153 | 5.153 | 5.153 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 -3041.1063 -3041.1063 18.800823 106.38959 5.1119409 2.7666867 2.7666867 135.07783 -98.306453 -28.471312 2.3401251 489.0346 Loop time of 1.684e-06 on 1 procs for 0 steps with 862 atoms 118.8% 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 | | 1.684e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6929.00 ave 6929 max 6929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75894.0 ave 75894 max 75894 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 151788.0 ave 151788 max 151788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 151788 Ave neighs/atom = 176.08817 Neighbor list builds = 0 Dangerous builds = 0 862 -3041.10615273209 eV 2.34012513614603 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01