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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2455555 6.0221927 5.1100000 Created 1295 atoms using lattice units in orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) create_atoms CPU = 0.010 seconds 1295 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2455555 6.0221927 5.1100000 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -65.039682 0.0000000) to (45.990000 65.039682 5.1100000) create_atoms CPU = 0.009 seconds 1299 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 17 46 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2594 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 17 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.314 | 5.314 | 5.314 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8463.5739 0 -8463.5739 62696.108 83 0 -9160.4822 0 -9160.4822 4968.7832 Loop time of 13.5288 on 1 procs for 83 steps with 2594 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 = -8463.57393051187 -9160.47322604515 -9160.4821537977 Force two-norm initial, final = 562.36359 0.31772250 Force max component initial, final = 91.740467 0.057548443 Final line search alpha, max atom move = 1.0000000 0.057548443 Iterations, force evaluations = 83 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.403 | 13.403 | 13.403 | 0.0 | 99.07 Neigh | 0.054796 | 0.054796 | 0.054796 | 0.0 | 0.41 Comm | 0.031984 | 0.031984 | 0.031984 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03862 | | | 0.29 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8827.00 ave 8827 max 8827 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: 155240.0 ave 155240 max 155240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155240 Ave neighs/atom = 59.845798 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 17 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.312 | 5.312 | 5.312 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -9160.4822 0 -9160.4822 4968.7832 30569.808 86 0 -9160.6799 0 -9160.6799 -0.96863307 30676.661 Loop time of 0.579388 on 1 procs for 3 steps with 2594 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 = -9160.48215379769 -9160.67110745921 -9160.679913748 Force two-norm initial, final = 169.24832 1.0512354 Force max component initial, final = 124.37225 0.79942837 Final line search alpha, max atom move = 5.0624061e-05 4.0470310e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57369 | 0.57369 | 0.57369 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001227 | 0.001227 | 0.001227 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004468 | | | 0.77 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8638.00 ave 8638 max 8638 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: 157782.0 ave 157782 max 157782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157782 Ave neighs/atom = 60.825752 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 17 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9160.6799 0 -9160.6799 -0.96863307 Loop time of 6.064e-06 on 1 procs for 0 steps with 2594 atoms 181.4% 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 | | 6.064e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8638.00 ave 8638 max 8638 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: 152046.0 ave 152046 max 152046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152046 Ave neighs/atom = 58.614495 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 17 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 5.450 | 5.450 | 5.450 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 -9160.6799 -9160.6799 46.043059 130.37873 5.1101914 -0.96863307 -0.96863307 41.800606 -20.97224 -23.734266 2.3641825 1336.3895 Loop time of 6.606e-06 on 1 procs for 0 steps with 2594 atoms 287.6% 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 | | 6.606e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8638.00 ave 8638 max 8638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76023.0 ave 76023 max 76023 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152046.0 ave 152046 max 152046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152046 Ave neighs/atom = 58.614495 Neighbor list builds = 0 Dangerous builds = 0 2594 -9160.679913748 eV 2.36418248441277 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15