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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -50.029149 0.0000000) to (13.616210 50.029149 8.9139016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8355184 5.5587943 5.9426011 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -50.029149 0.0000000) to (13.616210 50.029149 8.9139016) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8355184 5.5587943 5.9426011 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -50.029149 0.0000000) to (13.616210 50.029149 8.9139016) create_atoms CPU = 0.001 seconds 507 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1008 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_600021860456_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.932 | 5.932 | 5.932 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2678.0231 0 -2678.0231 139625.8 77 0 -3296.0791 0 -3296.0791 5504.3101 Loop time of 2.57463 on 1 procs for 77 steps with 1008 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2678.02307734181 -3296.07592988904 -3296.07913535621 Force two-norm initial, final = 1251.9352 0.16328670 Force max component initial, final = 224.39148 0.010007651 Final line search alpha, max atom move = 1.0000000 0.010007651 Iterations, force evaluations = 77 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5093 | 2.5093 | 2.5093 | 0.0 | 97.46 Neigh | 0.040446 | 0.040446 | 0.040446 | 0.0 | 1.57 Comm | 0.014808 | 0.014808 | 0.014808 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01011 | | | 0.39 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7928.00 ave 7928 max 7928 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: 320088.0 ave 320088 max 320088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320088 Ave neighs/atom = 317.54762 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.931 | 5.931 | 5.931 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3296.0791 0 -3296.0791 5504.3101 12144.431 83 0 -3296.2454 0 -3296.2454 3.6048528 12190.782 Loop time of 0.152587 on 1 procs for 6 steps with 1008 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3296.07913535623 -3296.24538412796 -3296.24543826221 Force two-norm initial, final = 82.748791 0.26977077 Force max component initial, final = 74.168202 0.14624038 Final line search alpha, max atom move = 0.00072326230 0.00010577015 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14954 | 0.14954 | 0.14954 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056707 | 0.00056707 | 0.00056707 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002479 | | | 1.62 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7908.00 ave 7908 max 7908 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: 320216.0 ave 320216 max 320216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320216 Ave neighs/atom = 317.67460 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.069 | 6.069 | 6.069 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3296.2454 0 -3296.2454 3.6048528 Loop time of 2.031e-06 on 1 procs for 0 steps with 1008 atoms 196.9% 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 | | 2.031e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7909.00 ave 7909 max 7909 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: 320006.0 ave 320006 max 320006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320006 Ave neighs/atom = 317.46627 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.069 | 6.069 | 6.069 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 -3296.2454 -3296.2454 13.615615 100.53896 8.905533 3.6048528 3.6048528 -12.04613 3.6590541 19.201634 2.2789079 380.03414 Loop time of 2.172e-06 on 1 procs for 0 steps with 1008 atoms 276.2% 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 | | 2.172e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7909.00 ave 7909 max 7909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160003.0 ave 160003 max 160003 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320006.0 ave 320006 max 320006 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320006 Ave neighs/atom = 317.46627 Neighbor list builds = 0 Dangerous builds = 0 1008 -3296.24543826221 eV 2.27890787575301 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03