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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -45.603581 0.0000000) to (26.327209 45.603581 6.0935647) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6415447 5.4285789 6.0935647 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.603581 0.0000000) to (26.327209 45.603581 6.0935647) create_atoms CPU = 0.002 seconds 676 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6415447 5.4285789 6.0935647 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -45.603581 0.0000000) to (26.327209 45.603581 6.0935647) create_atoms CPU = 0.001 seconds 676 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 21 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1332 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_222110751402_000#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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.923 | 5.923 | 5.923 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5770.6374 0 -5770.6374 14423.838 48 0 -5813.8435 0 -5813.8435 -7005.976 Loop time of 1.68493 on 1 procs for 48 steps with 1332 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 = -5770.63742841165 -5813.83848509545 -5813.84348739422 Force two-norm initial, final = 105.67094 0.21335614 Force max component initial, final = 22.190348 0.015800086 Final line search alpha, max atom move = 1.0000000 0.015800086 Iterations, force evaluations = 48 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6722 | 1.6722 | 1.6722 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0071664 | 0.0071664 | 0.0071664 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005564 | | | 0.33 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9220.00 ave 9220 max 9220 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: 327816.0 ave 327816 max 327816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 327816 Ave neighs/atom = 246.10811 Neighbor list builds = 0 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.922 | 5.922 | 5.922 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -5813.8435 0 -5813.8435 -7005.976 14632.05 50 0 -5813.8742 0 -5813.8742 -3954.8629 14605.482 Loop time of 0.106174 on 1 procs for 2 steps with 1332 atoms 87.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5813.84348739454 -5813.87404967735 -5813.87418357769 Force two-norm initial, final = 47.456150 0.21905702 Force max component initial, final = 34.998845 0.019995679 Final line search alpha, max atom move = 0.00060074310 1.2012266e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10442 | 0.10442 | 0.10442 | 0.0 | 98.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035311 | 0.00035311 | 0.00035311 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001402 | | | 1.32 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9168.00 ave 9168 max 9168 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: 328032.0 ave 328032 max 328032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328032 Ave neighs/atom = 246.27027 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.060 | 6.060 | 6.060 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5813.8742 0 -5813.8742 -3954.8629 Loop time of 1.703e-06 on 1 procs for 0 steps with 1332 atoms 176.2% 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 | | 1.703e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9168.00 ave 9168 max 9168 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: 328080.0 ave 328080 max 328080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328080 Ave neighs/atom = 246.30631 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.060 | 6.060 | 6.060 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 -5813.8742 -5813.8742 26.300133 91.207162 6.0887621 -3954.8629 -3954.8629 0.31019513 -11862.707 -2.1917358 2.2481017 612.88729 Loop time of 5.505e-06 on 1 procs for 0 steps with 1332 atoms 236.1% 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 | | 5.505e-06 | | |100.00 Nlocal: 1332.00 ave 1332 max 1332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9168.00 ave 9168 max 9168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164040.0 ave 164040 max 164040 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 328080.0 ave 328080 max 328080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328080 Ave neighs/atom = 246.30631 Neighbor list builds = 0 Dangerous builds = 0 1332 -5813.87418357769 eV 2.24810169184843 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02