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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -39.600342 0.0000000) to (8.0833859 39.600342 8.8549056) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8500316 5.2800456 5.9032704 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.600342 0.0000000) to (8.0833859 39.600342 8.8549056) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8500316 5.2800456 5.9032704 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.600342 0.0000000) to (8.0833859 39.600342 8.8549056) create_atoms CPU = 0.001 seconds 242 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 3 25 3 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 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_179025990738_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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1642.237 0 -1642.237 2017.0047 109 0 -1666.3074 0 -1666.3074 2119.46 Loop time of 0.593313 on 1 procs for 109 steps with 476 atoms 86.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1642.2369649944 -1666.30578688084 -1666.307422823 Force two-norm initial, final = 32.208762 0.12081102 Force max component initial, final = 10.979571 0.030123345 Final line search alpha, max atom move = 1.0000000 0.030123345 Iterations, force evaluations = 109 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57089 | 0.57089 | 0.57089 | 0.0 | 96.22 Neigh | 0.011256 | 0.011256 | 0.011256 | 0.0 | 1.90 Comm | 0.0058777 | 0.0058777 | 0.0058777 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005286 | | | 0.89 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3014.00 ave 3014 max 3014 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: 40736.0 ave 40736 max 40736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40736 Ave neighs/atom = 85.579832 Neighbor list builds = 3 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 3 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.464 | 4.464 | 4.464 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -1666.3074 0 -1666.3074 2119.46 5668.9964 112 0 -1666.3202 0 -1666.3202 -69.509747 5677.2274 Loop time of 0.0143782 on 1 procs for 3 steps with 476 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 = -1666.307422823 -1666.32012439307 -1666.32024307507 Force two-norm initial, final = 15.301432 0.75569748 Force max component initial, final = 13.434502 0.72322980 Final line search alpha, max atom move = 0.00060300950 0.00043611444 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.013541 | 0.013541 | 0.013541 | 0.0 | 94.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014957 | 0.00014957 | 0.00014957 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006879 | | | 4.78 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2870.00 ave 2870 max 2870 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: 40740.0 ave 40740 max 40740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40740 Ave neighs/atom = 85.588235 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1666.3202 0 -1666.3202 -69.509747 Loop time of 1.848e-06 on 1 procs for 0 steps with 476 atoms 162.3% 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 | | 1.848e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2870.00 ave 2870 max 2870 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: 40728.0 ave 40728 max 40728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40728 Ave neighs/atom = 85.563025 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 = 6.4274528 ghost atom cutoff = 6.4274528 binsize = 3.2137264, bins = 3 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4274528135 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) = 4.602 | 4.602 | 4.602 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 -1666.3202 -1666.3202 8.0852459 79.355088 8.8484719 -69.509747 -69.509747 -204.15043 -35.292329 30.91352 2.3520118 262.87253 Loop time of 1.987e-06 on 1 procs for 0 steps with 476 atoms 151.0% 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 | | 1.987e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2870.00 ave 2870 max 2870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20364.0 ave 20364 max 20364 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40728.0 ave 40728 max 40728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40728 Ave neighs/atom = 85.563025 Neighbor list builds = 0 Dangerous builds = 0 476 -1666.32024307507 eV 2.3520117791618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00