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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -53.208600 0.0000000) to (18.812081 53.208600 5.1200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8772062 5.9120667 5.1200000 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.208600 0.0000000) to (18.812081 53.208600 5.1200000) create_atoms CPU = 0.004 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8772062 5.9120667 5.1200000 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.208600 0.0000000) to (18.812081 53.208600 5.1200000) create_atoms CPU = 0.003 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 36 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 864 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_390178379548_001#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 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2856.3308 0 -2856.3308 49487.421 76 0 -3048.674 0 -3048.674 7381.0294 Loop time of 5.06599 on 1 procs for 76 steps with 864 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2856.33075535287 -3048.67125998573 -3048.67401311137 Force two-norm initial, final = 224.10783 0.15447362 Force max component initial, final = 42.978999 0.036590483 Final line search alpha, max atom move = 1.0000000 0.036590483 Iterations, force evaluations = 76 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0205 | 5.0205 | 5.0205 | 0.0 | 99.10 Neigh | 0.01133 | 0.01133 | 0.01133 | 0.0 | 0.22 Comm | 0.01758 | 0.01758 | 0.01758 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01661 | | | 0.33 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4693.00 ave 4693 max 4693 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: 66904.0 ave 66904 max 66904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66904 Ave neighs/atom = 77.435185 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 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.581 | 4.581 | 4.581 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -3048.674 0 -3048.674 7381.0294 10249.876 83 0 -3048.9536 0 -3048.9536 -252.59229 10304.219 Loop time of 0.296206 on 1 procs for 7 steps with 864 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 = -3048.67401311138 -3048.95291229625 -3048.95359107026 Force two-norm initial, final = 99.981916 3.1006588 Force max component initial, final = 92.190268 2.6461403 Final line search alpha, max atom move = 0.00038111361 0.0010084801 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29209 | 0.29209 | 0.29209 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086707 | 0.00086707 | 0.00086707 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003246 | | | 1.10 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4229.00 ave 4229 max 4229 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: 66916.0 ave 66916 max 66916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66916 Ave neighs/atom = 77.449074 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 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.719 | 4.719 | 4.719 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3048.9536 0 -3048.9536 -252.59229 Loop time of 6.785e-06 on 1 procs for 0 steps with 864 atoms 191.6% 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 | | 6.785e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4277.00 ave 4277 max 4277 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: 66896.0 ave 66896 max 66896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66896 Ave neighs/atom = 77.425926 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 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.719 | 4.719 | 4.719 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 -3048.9536 -3048.9536 18.814889 107.08825 5.1141279 -252.59229 -252.59229 -411.50296 -202.82795 -143.44596 2.3536379 438.94122 Loop time of 6.936e-06 on 1 procs for 0 steps with 864 atoms 302.8% 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 | | 6.936e-06 | | |100.00 Nlocal: 864.000 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4277.00 ave 4277 max 4277 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33448.0 ave 33448 max 33448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66896.0 ave 66896 max 66896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66896 Ave neighs/atom = 77.425926 Neighbor list builds = 0 Dangerous builds = 0 864 -3048.95359107026 eV 2.35363791213175 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05