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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -74.490203 0.0000000) to (37.245101 74.490203 4.0397985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6963096 5.6963096 4.0397985 Created 679 atoms using lattice units in orthogonal box = (0.0000000 -74.490203 0.0000000) to (37.245101 74.490203 4.0397985) create_atoms CPU = 0.003 seconds 679 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6963096 5.6963096 4.0397985 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -74.490203 0.0000000) to (37.245101 74.490203 4.0397985) create_atoms CPU = 0.002 seconds 681 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 26 1 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1360 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 10.65 | 10.65 | 10.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3774.108 0 -3774.108 13794.407 104 0 -3919.6065 0 -3919.6065 1019.546 Loop time of 13.715 on 1 procs for 104 steps with 1360 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 = -3774.10801852282 -3919.60308745305 -3919.60650260688 Force two-norm initial, final = 148.26060 0.18216739 Force max component initial, final = 32.905762 0.025168025 Final line search alpha, max atom move = 1.0000000 0.025168025 Iterations, force evaluations = 104 179 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.425 | 13.425 | 13.425 | 0.0 | 97.89 Neigh | 0.18511 | 0.18511 | 0.18511 | 0.0 | 1.35 Comm | 0.067646 | 0.067646 | 0.067646 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03697 | | | 0.27 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15723.0 ave 15723 max 15723 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: 551910.0 ave 551910 max 551910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551910 Ave neighs/atom = 405.81618 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 10.64 | 10.64 | 10.64 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -3919.6065 0 -3919.6065 1019.546 22415.995 109 0 -3919.6791 0 -3919.6791 -37.688574 22446.713 Loop time of 0.640993 on 1 procs for 5 steps with 1360 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 = -3919.60650260689 -3919.67684189664 -3919.67914867882 Force two-norm initial, final = 38.096091 2.4000191 Force max component initial, final = 30.928151 2.1762393 Final line search alpha, max atom move = 7.2620932e-05 0.00015804053 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62938 | 0.62938 | 0.62938 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029285 | 0.0029285 | 0.0029285 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008683 | | | 1.35 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15369.0 ave 15369 max 15369 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: 553196.0 ave 553196 max 553196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 553196 Ave neighs/atom = 406.76176 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 10.15 | 10.15 | 10.15 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3919.6791 0 -3919.6791 -37.688574 Loop time of 7.407e-06 on 1 procs for 0 steps with 1360 atoms 175.5% 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 | | 7.407e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15369.0 ave 15369 max 15369 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: 548474.0 ave 548474 max 548474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 548474 Ave neighs/atom = 403.28971 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 10.15 | 10.15 | 10.15 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 -3919.6791 -3919.6791 37.153711 148.88241 4.0579544 -37.688574 -37.688574 66.078547 -155.23102 -23.913252 2.5424769 167.90743 Loop time of 9.412e-06 on 1 procs for 0 steps with 1360 atoms 212.5% 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 | | 9.412e-06 | | |100.00 Nlocal: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15369.0 ave 15369 max 15369 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 274237.0 ave 274237 max 274237 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 548474.0 ave 548474 max 548474 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 548474 Ave neighs/atom = 403.28971 Neighbor list builds = 0 Dangerous builds = 0 1360 -3919.67914867882 eV 2.54247691686023 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15