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 = 4.0500047 4.0500047 4.0500047 Created orthogonal box = (0.0000000 -74.678397 0.0000000) to (37.339198 74.678397 4.0500047) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7107009 5.7107009 4.0500047 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -74.678397 0.0000000) to (37.339198 74.678397 4.0500047) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7107009 5.7107009 4.0500047 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.678397 0.0000000) to (37.339198 74.678397 4.0500047) create_atoms CPU = 0.002 seconds 682 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1362 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_651801486679_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4519.8876 0 -4519.8876 3856.6678 110 0 -4570.5931 0 -4570.5931 2298.3051 Loop time of 4.55044 on 1 procs for 110 steps with 1362 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 = -4519.88760635375 -4570.58871029058 -4570.59307346438 Force two-norm initial, final = 23.388765 0.16832476 Force max component initial, final = 3.6032802 0.034865074 Final line search alpha, max atom move = 1.0000000 0.034865074 Iterations, force evaluations = 110 200 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3939 | 4.3939 | 4.3939 | 0.0 | 96.56 Neigh | 0.073135 | 0.073135 | 0.073135 | 0.0 | 1.61 Comm | 0.048731 | 0.048731 | 0.048731 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03462 | | | 0.76 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9979.00 ave 9979 max 9979 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: 190584.0 ave 190584 max 190584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190584 Ave neighs/atom = 139.92952 Neighbor list builds = 3 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.122 | 5.122 | 5.122 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -4570.5931 0 -4570.5931 2298.3051 22586.321 115 0 -4570.7131 0 -4570.7131 -28.058051 22652.185 Loop time of 0.157048 on 1 procs for 5 steps with 1362 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 = -4570.59307346439 -4570.71251176505 -4570.71307885484 Force two-norm initial, final = 66.943661 1.3691034 Force max component initial, final = 61.945929 1.2760829 Final line search alpha, max atom move = 0.00018592773 0.00023725920 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15057 | 0.15057 | 0.15057 | 0.0 | 95.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016019 | 0.0016019 | 0.0016019 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004879 | | | 3.11 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10662.0 ave 10662 max 10662 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: 190596.0 ave 190596 max 190596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190596 Ave neighs/atom = 139.93833 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.260 | 5.260 | 5.260 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4570.7131 0 -4570.7131 -28.058051 Loop time of 6.846e-06 on 1 procs for 0 steps with 1362 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 | | 6.846e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10646.0 ave 10646 max 10646 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: 190464.0 ave 190464 max 190464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190464 Ave neighs/atom = 139.84141 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 10 37 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.260 | 5.260 | 5.260 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 -4570.7131 -4570.7131 37.307224 149.98247 4.0483371 -28.058051 -28.058051 -19.959394 26.004716 -90.219474 2.5818091 198.93454 Loop time of 7.186e-06 on 1 procs for 0 steps with 1362 atoms 306.2% 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 | | 7.186e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10646.0 ave 10646 max 10646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95232.0 ave 95232 max 95232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 190464.0 ave 190464 max 190464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 190464 Ave neighs/atom = 139.84141 Neighbor list builds = 0 Dangerous builds = 0 1362 -4570.71307899679 eV 2.58180912641766 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05