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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -54.949016 0.0000000) to (38.854822 54.949016 5.1464469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1349719 6.2661159 5.1464469 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.949016 0.0000000) to (38.854822 54.949016 5.1464469) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1349719 6.2661159 5.1464469 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.949016 0.0000000) to (38.854822 54.949016 5.1464469) create_atoms CPU = 0.002 seconds 916 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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_945691923444_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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.984 | 5.984 | 5.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4623.9225 0 -4623.9225 146134.6 54 0 -5973.1406 0 -5973.1406 4623.6198 Loop time of 1.55426 on 1 procs for 54 steps with 1824 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4623.92247173338 -5973.13554214144 -5973.14055240331 Force two-norm initial, final = 2504.5843 0.18093025 Force max component initial, final = 614.52632 0.0093101217 Final line search alpha, max atom move = 1.0000000 0.0093101217 Iterations, force evaluations = 54 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4926 | 1.4926 | 1.4926 | 0.0 | 96.03 Neigh | 0.041377 | 0.041377 | 0.041377 | 0.0 | 2.66 Comm | 0.011061 | 0.011061 | 0.011061 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009197 | | | 0.59 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10705.0 ave 10705 max 10705 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: 320840.0 ave 320840 max 320840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320840 Ave neighs/atom = 175.89912 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.986 | 5.986 | 5.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -5973.1406 0 -5973.1406 4623.6198 21975.681 59 0 -5973.3566 0 -5973.3566 -8.8550114 22046.795 Loop time of 0.1326 on 1 procs for 5 steps with 1824 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 = -5973.1405524033 -5973.35583487583 -5973.35660867677 Force two-norm initial, final = 130.97761 1.0937852 Force max component initial, final = 121.31306 0.73601044 Final line search alpha, max atom move = 0.00011427284 8.4106002e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12889 | 0.12889 | 0.12889 | 0.0 | 97.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063904 | 0.00063904 | 0.00063904 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00307 | | | 2.32 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10697.0 ave 10697 max 10697 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: 320656.0 ave 320656 max 320656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320656 Ave neighs/atom = 175.79825 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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.124 | 6.124 | 6.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5973.3566 0 -5973.3566 -8.8550114 Loop time of 1.643e-06 on 1 procs for 0 steps with 1824 atoms 121.7% 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 | | 1.643e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10657.0 ave 10657 max 10657 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: 320288.0 ave 320288 max 320288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320288 Ave neighs/atom = 175.59649 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 ghost atom cutoff = 8 binsize = 4, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.124 | 6.124 | 6.124 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 -5973.3566 -5973.3566 38.86124 110.30163 5.1433594 -8.8550114 -8.8550114 50.803171 -23.913215 -53.45499 2.3672139 642.77969 Loop time of 1.906e-06 on 1 procs for 0 steps with 1824 atoms 209.9% 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 | | 1.906e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10657.0 ave 10657 max 10657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160144.0 ave 160144 max 160144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320288.0 ave 320288 max 320288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320288 Ave neighs/atom = 175.59649 Neighbor list builds = 0 Dangerous builds = 0 1824 -5973.35660867677 eV 2.36721392585229 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02