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 = 4.0501807 4.0501807 4.0501807 Created orthogonal box = (0.0000000 -59.937202 0.0000000) to (48.938520 59.937202 9.9208762) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0335162 5.7474029 6.6139175 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -59.937202 0.0000000) to (48.938520 59.937202 9.9208762) create_atoms CPU = 0.004 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0335162 5.7474029 6.6139175 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -59.937202 0.0000000) to (48.938520 59.937202 9.9208762) create_atoms CPU = 0.002 seconds 1757 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 29 3 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_131650261510_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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 7.004 | 7.004 | 7.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12399.48 0 -12399.48 8660.8594 87 0 -12530.721 0 -12530.721 6038.8583 Loop time of 3.94582 on 1 procs for 87 steps with 3506 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12399.4796124376 -12530.7089101054 -12530.7211116314 Force two-norm initial, final = 71.244424 0.24273426 Force max component initial, final = 11.560636 0.066603648 Final line search alpha, max atom move = 1.0000000 0.066603648 Iterations, force evaluations = 87 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7976 | 3.7976 | 3.7976 | 0.0 | 96.24 Neigh | 0.10256 | 0.10256 | 0.10256 | 0.0 | 2.60 Comm | 0.018552 | 0.018552 | 0.018552 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02707 | | | 0.69 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11166.0 ave 11166 max 11166 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: 490810.0 ave 490810 max 490810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490810 Ave neighs/atom = 139.99144 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -12530.721 0 -12530.721 6038.8583 58200.581 98 0 -12532.454 0 -12532.454 45.861773 58656.937 Loop time of 0.380939 on 1 procs for 11 steps with 3506 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 = -12530.7211116314 -12532.4474035931 -12532.4538717895 Force two-norm initial, final = 425.14881 2.9536039 Force max component initial, final = 375.11175 1.9608983 Final line search alpha, max atom move = 8.0258835e-05 0.00015737942 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33418 | 0.33418 | 0.33418 | 0.0 | 87.73 Neigh | 0.036184 | 0.036184 | 0.036184 | 0.0 | 9.50 Comm | 0.0016115 | 0.0016115 | 0.0016115 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008961 | | | 2.35 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10781.0 ave 10781 max 10781 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: 490050.0 ave 490050 max 490050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 490050 Ave neighs/atom = 139.77467 Neighbor list builds = 1 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 6.757 | 6.757 | 6.757 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12532.454 0 -12532.454 45.861773 Loop time of 2.41e-06 on 1 procs for 0 steps with 3506 atoms 166.0% 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 | | 2.41e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10815.0 ave 10815 max 10815 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: 489932.0 ave 489932 max 489932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489932 Ave neighs/atom = 139.74102 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 6.757 | 6.757 | 6.757 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 -12532.454 -12532.454 48.851365 121.16029 9.9101988 45.861773 45.861773 38.53408 45.548209 53.503031 2.5123774 2335.5602 Loop time of 2.346e-06 on 1 procs for 0 steps with 3506 atoms 341.0% 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 | | 2.346e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10815.0 ave 10815 max 10815 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 244966.0 ave 244966 max 244966 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 489932.0 ave 489932 max 489932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 489932 Ave neighs/atom = 139.74102 Neighbor list builds = 0 Dangerous builds = 0 3506 -12532.4505282073 eV 2.51237736086328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04