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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9099749 5.5148277 5.9032704 Created 1316 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) create_atoms CPU = 0.005 seconds 1316 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9099749 5.5148277 5.9032704 Created 1322 atoms using lattice units in orthogonal box = (0.0000000 -37.914441 0.0000000) to (46.435517 37.914441 8.8549056) create_atoms CPU = 0.005 seconds 1322 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 13 21 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2638 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.072 | 6.072 | 6.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8830.4992 0 -8830.4992 55163.986 63 0 -9295.9023 0 -9295.9023 5844.044 Loop time of 4.48663 on 1 procs for 63 steps with 2638 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 = -8830.49923300058 -9295.89359818718 -9295.90229616917 Force two-norm initial, final = 536.47100 0.31573810 Force max component initial, final = 128.48579 0.036861911 Final line search alpha, max atom move = 1.0000000 0.036861911 Iterations, force evaluations = 63 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2493 | 4.2493 | 4.2493 | 0.0 | 94.71 Neigh | 0.18041 | 0.18041 | 0.18041 | 0.0 | 4.02 Comm | 0.024522 | 0.024522 | 0.024522 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03236 | | | 0.72 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8847.00 ave 8847 max 8847 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: 372428.0 ave 372428 max 372428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372428 Ave neighs/atom = 141.17817 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.072 | 6.072 | 6.072 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -9295.9023 0 -9295.9023 5844.044 31179.48 69 0 -9296.4123 0 -9296.4123 -141.11452 31313.128 Loop time of 0.305542 on 1 procs for 6 steps with 2638 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 = -9295.90229616916 -9296.41115732352 -9296.41229890284 Force two-norm initial, final = 225.80784 6.4491802 Force max component initial, final = 200.27427 5.0754329 Final line search alpha, max atom move = 9.7335904e-05 0.00049402185 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29724 | 0.29724 | 0.29724 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001504 | 0.001504 | 0.001504 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006799 | | | 2.23 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8839.00 ave 8839 max 8839 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: 372628.0 ave 372628 max 372628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372628 Ave neighs/atom = 141.25398 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.210 | 6.210 | 6.210 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9296.4123 0 -9296.4123 -141.11452 Loop time of 6.776e-06 on 1 procs for 0 steps with 2638 atoms 191.9% 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 | | 6.776e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 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: 372020.0 ave 372020 max 372020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372020 Ave neighs/atom = 141.02350 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.210 | 6.210 | 6.210 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 -9296.4123 -9296.4123 46.45584 76.224239 8.8428659 -141.11452 -141.11452 -199.25742 35.251829 -259.33796 2.3208691 1500.914 Loop time of 7.437e-06 on 1 procs for 0 steps with 2638 atoms 255.5% 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 | | 7.437e-06 | | |100.00 Nlocal: 2638.00 ave 2638 max 2638 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 186010.0 ave 186010 max 186010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 372020.0 ave 372020 max 372020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 372020 Ave neighs/atom = 141.02350 Neighbor list builds = 0 Dangerous builds = 0 2638 -9296.4117689056 eV 2.3208690942675 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05