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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -51.865306 0.0000000) to (36.674310 51.865306 5.7275649) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2614675 6.9575411 5.7275649 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -51.865306 0.0000000) to (36.674310 51.865306 5.7275649) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2614675 6.9575411 5.7275649 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -51.865306 0.0000000) to (36.674310 51.865306 5.7275649) create_atoms CPU = 0.004 seconds 660 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_664470114311_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4352.9028 0 -4352.9028 4855.8173 66 0 -4399.322 0 -4399.322 3398.6775 Loop time of 3.29297 on 1 procs for 66 steps with 1312 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 = -4352.90279675362 -4399.31799061365 -4399.3219967311 Force two-norm initial, final = 37.041514 0.14737659 Force max component initial, final = 8.5555279 0.0092618685 Final line search alpha, max atom move = 1.0000000 0.0092618685 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2156 | 3.2156 | 3.2156 | 0.0 | 97.65 Neigh | 0.033222 | 0.033222 | 0.033222 | 0.0 | 1.01 Comm | 0.024113 | 0.024113 | 0.024113 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02005 | | | 0.61 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8306.00 ave 8306 max 8306 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: 227512.0 ave 227512 max 227512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227512 Ave neighs/atom = 173.40854 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -4399.322 0 -4399.322 3398.6775 21789.081 74 0 -4399.6176 0 -4399.6176 1.7415602 21882.385 Loop time of 0.292356 on 1 procs for 8 steps with 1312 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 = -4399.32199673111 -4399.61756312576 -4399.61759418175 Force two-norm initial, final = 99.301892 0.24870922 Force max component initial, final = 93.904546 0.11350565 Final line search alpha, max atom move = 0.00098662283 0.00011198726 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28373 | 0.28373 | 0.28373 | 0.0 | 97.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018911 | 0.0018911 | 0.0018911 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006731 | | | 2.30 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8300.00 ave 8300 max 8300 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: 227792.0 ave 227792 max 227792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227792 Ave neighs/atom = 173.62195 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.611 | 5.611 | 5.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4399.6176 0 -4399.6176 1.7415602 Loop time of 6.465e-06 on 1 procs for 0 steps with 1312 atoms 185.6% 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 | | 6.465e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8300.00 ave 8300 max 8300 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: 227456.0 ave 227456 max 227456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227456 Ave neighs/atom = 173.36585 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.611 | 5.611 | 5.611 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 -4399.6176 -4399.6176 36.604192 104.44883 5.7234809 1.7415602 1.7415602 -3.2074306 0.1274219 8.3046893 2.6451598 771.27866 Loop time of 7.347e-06 on 1 procs for 0 steps with 1312 atoms 258.6% 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 | | 7.347e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8300.00 ave 8300 max 8300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113728.0 ave 113728 max 113728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227456.0 ave 227456 max 227456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227456 Ave neighs/atom = 173.36585 Neighbor list builds = 0 Dangerous builds = 0 1312 -4391.64140223289 eV 2.64515978117606 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04