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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -46.873434 0.0000000) to (38.271998 46.873434 7.7585460) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7184656 4.4947128 5.1723640 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -46.873434 0.0000000) to (38.271998 46.873434 7.7585460) create_atoms CPU = 0.002 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7184656 4.4947128 5.1723640 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -46.873434 0.0000000) to (38.271998 46.873434 7.7585460) create_atoms CPU = 0.001 seconds 877 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 10 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 1743 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_269937397263_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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.554 | 5.554 | 5.554 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11618.308 0 -11618.308 3069.4194 82 0 -11799.881 0 -11799.881 -1178.9747 Loop time of 46.3634 on 1 procs for 82 steps with 1743 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11618.3084163032 -11799.8702792276 -11799.8814549064 Force two-norm initial, final = 68.591744 0.42274968 Force max component initial, final = 9.9526739 0.096327216 Final line search alpha, max atom move = 1.0000000 0.096327216 Iterations, force evaluations = 82 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.259 | 46.259 | 46.259 | 0.0 | 99.77 Neigh | 0.061522 | 0.061522 | 0.061522 | 0.0 | 0.13 Comm | 0.01813 | 0.01813 | 0.01813 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02517 | | | 0.05 Nlocal: 1743.00 ave 1743 max 1743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7170.00 ave 7170 max 7170 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: 234506.0 ave 234506 max 234506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234506 Ave neighs/atom = 134.54159 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -11799.881 0 -11799.881 -1178.9747 27836.732 85 0 -11799.946 0 -11799.946 3.0668837 27822.589 Loop time of 2.30975 on 1 procs for 3 steps with 1743 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 = -11799.8814549064 -11799.945717292 -11799.9458352301 Force two-norm initial, final = 76.364191 0.46903784 Force max component initial, final = 49.269661 0.13300809 Final line search alpha, max atom move = 0.00044741681 5.9510057e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3052 | 2.3052 | 2.3052 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077326 | 0.00077326 | 0.00077326 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003824 | | | 0.17 Nlocal: 1743.00 ave 1743 max 1743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7342.00 ave 7342 max 7342 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: 234452.0 ave 234452 max 234452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234452 Ave neighs/atom = 134.51061 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.695 | 5.695 | 5.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11799.946 0 -11799.946 3.0668837 Loop time of 3.41e-06 on 1 procs for 0 steps with 1743 atoms 176.0% 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 | | 3.41e-06 | | |100.00 Nlocal: 1743.00 ave 1743 max 1743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7343.00 ave 7343 max 7343 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: 234446.0 ave 234446 max 234446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234446 Ave neighs/atom = 134.50717 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.695 | 5.695 | 5.695 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 -11799.946 -11799.946 38.242485 93.864936 7.7508271 3.0668837 3.0668837 3.3013451 -1.7524057 7.6517118 2.3518597 1324.0377 Loop time of 3.746e-06 on 1 procs for 0 steps with 1743 atoms 213.6% 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 | | 3.746e-06 | | |100.00 Nlocal: 1743.00 ave 1743 max 1743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7343.00 ave 7343 max 7343 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117223.0 ave 117223 max 117223 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 234446.0 ave 234446 max 234446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 234446 Ave neighs/atom = 134.50717 Neighbor list builds = 0 Dangerous builds = 0 1743 -11799.9458352301 eV 2.35185973928418 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:50