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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -58.227215 0.0000000) to (29.113607 58.227215 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0311149 4.0311149 3.6110986 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.227215 0.0000000) to (29.113607 58.227215 3.6110986) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0311149 4.0311149 3.6110986 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.227215 0.0000000) to (29.113607 58.227215 3.6110986) create_atoms CPU = 0.001 seconds 522 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1040 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_912636107108_001#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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.609 | 4.609 | 4.609 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4130.6365 0 -4130.6365 51848.313 71 0 -4401.4229 0 -4401.4229 4686.1915 Loop time of 4.84421 on 1 procs for 71 steps with 1040 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4130.63645348377 -4401.41895061542 -4401.42292676846 Force two-norm initial, final = 479.94311 0.19809973 Force max component initial, final = 121.31664 0.037072355 Final line search alpha, max atom move = 1.0000000 0.037072355 Iterations, force evaluations = 71 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8194 | 4.8194 | 4.8194 | 0.0 | 99.49 Neigh | 0.0065 | 0.0065 | 0.0065 | 0.0 | 0.13 Comm | 0.0097837 | 0.0097837 | 0.0097837 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008573 | | | 0.18 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 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: 80564.0 ave 80564 max 80564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80564 Ave neighs/atom = 77.465385 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4401.4229 0 -4401.4229 4686.1915 12243.099 84 0 -4401.8442 0 -4401.8442 -56.671463 12276.668 Loop time of 0.526712 on 1 procs for 13 steps with 1040 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 = -4401.42292676846 -4401.84025217677 -4401.8442465318 Force two-norm initial, final = 77.741292 1.6038067 Force max component initial, final = 73.678433 1.4369186 Final line search alpha, max atom move = 0.00026314256 0.00037811443 Iterations, force evaluations = 13 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52218 | 0.52218 | 0.52218 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007403 | 0.0007403 | 0.0007403 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003795 | | | 0.72 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6219.00 ave 6219 max 6219 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: 80584.0 ave 80584 max 80584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80584 Ave neighs/atom = 77.484615 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.749 | 4.749 | 4.749 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4401.8442 0 -4401.8442 -56.671463 Loop time of 2.112e-06 on 1 procs for 0 steps with 1040 atoms 189.4% 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 | | 2.112e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6229.00 ave 6229 max 6229 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: 80596.0 ave 80596 max 80596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80596 Ave neighs/atom = 77.496154 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 ghost atom cutoff = 6 binsize = 3, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.749 | 4.749 | 4.749 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 -4401.8442 -4401.8442 29.029695 115.60836 3.6580428 -56.671463 -56.671463 32.540789 -186.16381 -16.391369 2.2903608 212.34344 Loop time of 2.565e-06 on 1 procs for 0 steps with 1040 atoms 233.9% 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 | | 2.565e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6229.00 ave 6229 max 6229 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40298.0 ave 40298 max 40298 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80596.0 ave 80596 max 80596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80596 Ave neighs/atom = 77.496154 Neighbor list builds = 0 Dangerous builds = 0 1040 -4401.8442465318 eV 2.2903608061149 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05