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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -39.278800 0.0000000) to (27.771705 39.278800 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3594518 6.2013350 5.2021169 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.278800 0.0000000) to (27.771705 39.278800 5.2021169) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3594518 6.2013350 5.2021169 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.278800 0.0000000) to (27.771705 39.278800 5.2021169) create_atoms CPU = 0.001 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 26 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 892 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3729.2922 0 -3729.2922 -3793.8365 69 0 -3747.2345 0 -3747.2345 -26067.495 Loop time of 0.304351 on 1 procs for 69 steps with 892 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 = -3729.29216695139 -3747.23170501922 -3747.23445419835 Force two-norm initial, final = 10.628498 0.15883137 Force max component initial, final = 3.4893608 0.030709289 Final line search alpha, max atom move = 1.0000000 0.030709289 Iterations, force evaluations = 69 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29163 | 0.29163 | 0.29163 | 0.0 | 95.82 Neigh | 0.0047612 | 0.0047612 | 0.0047612 | 0.0 | 1.56 Comm | 0.0038051 | 0.0038051 | 0.0038051 | 0.0 | 1.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004159 | | | 1.37 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 68640.0 ave 68640 max 68640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68640 Ave neighs/atom = 76.950673 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3747.2345 0 -3747.2345 -26067.495 11349.346 98 0 -3751.0103 0 -3751.0103 -2332.6842 11099.842 Loop time of 0.0775375 on 1 procs for 29 steps with 892 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 = -3747.23445419835 -3751.00967699059 -3751.01029893579 Force two-norm initial, final = 299.85844 1.1514206 Force max component initial, final = 286.97509 0.37851689 Final line search alpha, max atom move = 0.00059543331 0.00022538156 Iterations, force evaluations = 29 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071744 | 0.071744 | 0.071744 | 0.0 | 92.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090194 | 0.00090194 | 0.00090194 | 0.0 | 1.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004892 | | | 6.31 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3959.00 ave 3959 max 3959 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: 68544.0 ave 68544 max 68544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68544 Ave neighs/atom = 76.843049 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.700 | 4.700 | 4.700 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3751.0103 0 -3751.0103 -2332.6842 Loop time of 1.579e-06 on 1 procs for 0 steps with 892 atoms 126.7% 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 | | 1.579e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3973.00 ave 3973 max 3973 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: 68760.0 ave 68760 max 68760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68760 Ave neighs/atom = 77.085202 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.700 | 4.700 | 4.700 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 -3751.0103 -3751.0103 26.984569 78.5576 5.2361621 -2332.6842 -2332.6842 53.087441 -7006.9204 -44.219498 2.3363227 997.75452 Loop time of 1.575e-06 on 1 procs for 0 steps with 892 atoms 190.5% 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 | | 1.575e-06 | | |100.00 Nlocal: 892.000 ave 892 max 892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3973.00 ave 3973 max 3973 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34380.0 ave 34380 max 34380 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68760.0 ave 68760 max 68760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68760 Ave neighs/atom = 77.085202 Neighbor list builds = 0 Dangerous builds = 0 892 -3751.01020973579 eV 2.33632266482448 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00