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 = 0.004 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 = 0.003 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 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 6.8 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_694335101831_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.117 | 6.117 | 6.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8463.5975 0 -8463.5975 62723.593 104 0 -9160.7214 0 -9160.7214 4917.6743 Loop time of 15.2467 on 1 procs for 104 steps with 2594 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 = -8463.59749174077 -9160.71331059707 -9160.72137997646 Force two-norm initial, final = 562.36207 0.30353703 Force max component initial, final = 91.740463 0.062885912 Final line search alpha, max atom move = 1.0000000 0.062885912 Iterations, force evaluations = 104 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.148 | 15.148 | 15.148 | 0.0 | 99.35 Neigh | 0.03973 | 0.03973 | 0.03973 | 0.0 | 0.26 Comm | 0.030728 | 0.030728 | 0.030728 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02831 | | | 0.19 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10903.0 ave 10903 max 10903 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: 337328.0 ave 337328 max 337328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337328 Ave neighs/atom = 130.04163 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.110 | 6.110 | 6.110 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -9160.7214 0 -9160.7214 4917.6743 30569.808 107 0 -9160.9028 0 -9160.9028 -2.4881751 30675.641 Loop time of 0.486537 on 1 procs for 3 steps with 2594 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 = -9160.72137997648 -9160.89753824622 -9160.90278512824 Force two-norm initial, final = 165.59405 0.94391204 Force max component initial, final = 117.06925 0.67743288 Final line search alpha, max atom move = 6.9144332e-05 4.6840644e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48345 | 0.48345 | 0.48345 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052582 | 0.00052582 | 0.00052582 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002565 | | | 0.53 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10392.0 ave 10392 max 10392 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: 337884.0 ave 337884 max 337884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337884 Ave neighs/atom = 130.25598 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.248 | 6.248 | 6.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9160.9028 0 -9160.9028 -2.4881751 Loop time of 1.974e-06 on 1 procs for 0 steps with 2594 atoms 202.6% 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 | | 1.974e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10385.0 ave 10385 max 10385 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: 336212.0 ave 336212 max 336212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336212 Ave neighs/atom = 129.61141 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.248 | 6.248 | 6.248 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 -9160.9028 -9160.9028 46.041578 130.34552 5.1114879 -2.4881751 -2.4881751 35.421731 -19.504579 -23.381677 2.3639211 1334.5377 Loop time of 1.998e-06 on 1 procs for 0 steps with 2594 atoms 200.2% 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 | | 1.998e-06 | | |100.00 Nlocal: 2594.00 ave 2594 max 2594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10385.0 ave 10385 max 10385 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 168106.0 ave 168106 max 168106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 336212.0 ave 336212 max 336212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 336212 Ave neighs/atom = 129.61141 Neighbor list builds = 0 Dangerous builds = 0 2594 -9160.90278512824 eV 2.36392108728341 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16