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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -59.316937 0.0000000) to (29.656629 59.316937 3.6784521) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0188142 5.0188142 3.6784521 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -59.316937 0.0000000) to (29.656629 59.316937 3.6784521) create_atoms CPU = 0.002 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0188142 5.0188142 3.6784521 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -59.316937 0.0000000) to (29.656629 59.316937 3.6784521) create_atoms CPU = 0.002 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4328.2402 0 -4328.2402 17411.226 59 0 -4378.1341 0 -4378.1341 -196.78596 Loop time of 0.742969 on 1 procs for 59 steps with 1040 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4328.24018740173 -4378.12992157516 -4378.13414625898 Force two-norm initial, final = 44.921822 0.23461235 Force max component initial, final = 9.8393676 0.061002399 Final line search alpha, max atom move = 1.0000000 0.061002399 Iterations, force evaluations = 59 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71401 | 0.71401 | 0.71401 | 0.0 | 96.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014849 | 0.014849 | 0.014849 | 0.0 | 2.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01411 | | | 1.90 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6259.00 ave 6259 max 6259 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: 81048.0 ave 81048 max 81048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81048 Ave neighs/atom = 77.930769 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4378.1341 0 -4378.1341 -196.78596 12941.828 68 0 -4378.3357 0 -4378.3357 -3573.11 12979.625 Loop time of 0.08372 on 1 procs for 9 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 = -4378.13414625898 -4378.33532981489 -4378.33567112339 Force two-norm initial, final = 42.885383 0.48924456 Force max component initial, final = 42.068381 0.13799968 Final line search alpha, max atom move = 0.00082046600 0.00011322405 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076904 | 0.076904 | 0.076904 | 0.0 | 91.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014578 | 0.0014578 | 0.0014578 | 0.0 | 1.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005358 | | | 6.40 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6283.00 ave 6283 max 6283 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: 80824.0 ave 80824 max 80824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80824 Ave neighs/atom = 77.715385 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.751 | 4.751 | 4.751 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4378.3357 0 -4378.3357 -3573.11 Loop time of 6.124e-06 on 1 procs for 0 steps with 1040 atoms 179.6% 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 | | 6.124e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6303.00 ave 6303 max 6303 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: 80836.0 ave 80836 max 80836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80836 Ave neighs/atom = 77.726923 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.751 | 4.751 | 4.751 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 -4378.3357 -4378.3357 29.497891 118.63387 3.7090481 -3573.11 -3573.11 3.7787351 -10705.933 -17.176064 2.3123712 371.08636 Loop time of 6.595e-06 on 1 procs for 0 steps with 1040 atoms 272.9% 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 | | 6.595e-06 | | |100.00 Nlocal: 1040.00 ave 1040 max 1040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6303.00 ave 6303 max 6303 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40418.0 ave 40418 max 40418 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80836.0 ave 80836 max 80836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80836 Ave neighs/atom = 77.726923 Neighbor list builds = 0 Dangerous builds = 0 1040 -4378.33556712339 eV 2.31237119919263 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01