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 -36.901885 0.0000000) to (45.191086 36.901885 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7515927 5.3670352 5.7450679 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -36.901885 0.0000000) to (45.191086 36.901885 8.6176019) create_atoms CPU = 0.002 seconds 1324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7515927 5.3670352 5.7450679 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -36.901885 0.0000000) to (45.191086 36.901885 8.6176019) create_atoms CPU = 0.002 seconds 1324 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 = 11 17 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 50 atoms, new total = 2598 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 = 11 17 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) = 7.355 | 7.355 | 7.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11211.716 0 -11211.716 16548.635 67 0 -11333.775 0 -11333.775 -15439.075 Loop time of 3.74832 on 1 procs for 67 steps with 2598 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 = -11211.7164243433 -11333.7644130085 -11333.7747938605 Force two-norm initial, final = 171.01556 0.33774557 Force max component initial, final = 24.091175 0.057254628 Final line search alpha, max atom move = 1.0000000 0.057254628 Iterations, force evaluations = 67 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6533 | 3.6533 | 3.6533 | 0.0 | 97.47 Neigh | 0.07099 | 0.07099 | 0.07099 | 0.0 | 1.89 Comm | 0.011474 | 0.011474 | 0.011474 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01253 | | | 0.33 Nlocal: 2598.00 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10782.0 ave 10782 max 10782 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: 634214.0 ave 634214 max 634214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 634214 Ave neighs/atom = 244.11624 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 11 17 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.353 | 7.353 | 7.353 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -11333.775 0 -11333.775 -15439.075 28742.051 71 0 -11334.439 0 -11334.439 -5381.4497 28568.204 Loop time of 0.197751 on 1 procs for 4 steps with 2598 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 = -11333.7747938605 -11334.4344388245 -11334.4390024641 Force two-norm initial, final = 306.94815 1.7528403 Force max component initial, final = 231.46337 1.3585451 Final line search alpha, max atom move = 4.7379499e-05 6.4367187e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19494 | 0.19494 | 0.19494 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004388 | 0.0004388 | 0.0004388 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002374 | | | 1.20 Nlocal: 2598.00 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10796.0 ave 10796 max 10796 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: 633834.0 ave 633834 max 633834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 633834 Ave neighs/atom = 243.96998 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 = 11 17 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) = 7.491 | 7.491 | 7.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11334.439 0 -11334.439 -5381.4497 Loop time of 1.804e-06 on 1 procs for 0 steps with 2598 atoms 110.9% 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 | | 1.804e-06 | | |100.00 Nlocal: 2598.00 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10837.0 ave 10837 max 10837 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: 635800.0 ave 635800 max 635800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 635800 Ave neighs/atom = 244.72671 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 = 11 17 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) = 7.491 | 7.491 | 7.491 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 -11334.439 -11334.439 45.042317 73.80377 8.5937689 -5381.4497 -5381.4497 -57.372006 -16162.957 75.979902 2.2203796 1347.6405 Loop time of 2.246e-06 on 1 procs for 0 steps with 2598 atoms 267.1% 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 | | 2.246e-06 | | |100.00 Nlocal: 2598.00 ave 2598 max 2598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10837.0 ave 10837 max 10837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 317900.0 ave 317900 max 317900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 635800.0 ave 635800 max 635800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 635800 Ave neighs/atom = 244.72671 Neighbor list builds = 0 Dangerous builds = 0 2598 -11334.4390024641 eV 2.22037964035678 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04