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 = 3.3024436 3.3024436 3.3024436 Created orthogonal box = (0.0000000 -58.332784 0.0000000) to (33.678448 58.332784 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1812997 5.2349934 5.7200000 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -58.332784 0.0000000) to (33.678448 58.332784 5.7200000) create_atoms CPU = 0.002 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1812997 5.2349934 5.7200000 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -58.332784 0.0000000) to (33.678448 58.332784 5.7200000) create_atoms CPU = 0.002 seconds 626 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 36 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 1 atoms, new total = 1248 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.636 | 4.636 | 4.636 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8935.159 0 -8935.159 36686.931 52 0 -9286.5364 0 -9286.5364 6093.6056 Loop time of 3.09492 on 1 procs for 52 steps with 1248 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8935.15904049353 -9286.52877125987 -9286.53636354149 Force two-norm initial, final = 325.48381 0.29556433 Force max component initial, final = 50.578528 0.032343533 Final line search alpha, max atom move = 1.0000000 0.032343533 Iterations, force evaluations = 52 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0756 | 3.0756 | 3.0756 | 0.0 | 99.37 Neigh | 0.0059947 | 0.0059947 | 0.0059947 | 0.0 | 0.19 Comm | 0.0059962 | 0.0059962 | 0.0059962 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007375 | | | 0.24 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4881.00 ave 4881 max 4881 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: 75164.0 ave 75164 max 75164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75164 Ave neighs/atom = 60.227564 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -9286.5364 0 -9286.5364 6093.6056 22474.539 55 0 -9286.6861 0 -9286.6861 -3.0923791 22544.543 Loop time of 0.211606 on 1 procs for 3 steps with 1248 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9286.53636354149 -9286.68342377865 -9286.68610582585 Force two-norm initial, final = 151.56996 0.84876318 Force max component initial, final = 102.42882 0.66560764 Final line search alpha, max atom move = 6.8627286e-05 4.5678846e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2098 | 0.2098 | 0.2098 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002699 | 0.0002699 | 0.0002699 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001533 | | | 0.72 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884.00 ave 4884 max 4884 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: 75492.0 ave 75492 max 75492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75492 Ave neighs/atom = 60.490385 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.774 | 4.774 | 4.774 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9286.6861 0 -9286.6861 -3.0923791 Loop time of 2.339e-06 on 1 procs for 0 steps with 1248 atoms 171.0% 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 | | 2.339e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884.00 ave 4884 max 4884 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: 74228.0 ave 74228 max 74228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74228 Ave neighs/atom = 59.477564 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.774 | 4.774 | 4.774 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 -9286.6861 -9286.6861 33.684965 116.85416 5.7274482 -3.0923791 -3.0923791 9.0564836 29.030814 -47.364435 2.6646025 986.73636 Loop time of 2.375e-06 on 1 procs for 0 steps with 1248 atoms 210.5% 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 | | 2.375e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884.00 ave 4884 max 4884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37114.0 ave 37114 max 37114 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74228.0 ave 74228 max 74228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74228 Ave neighs/atom = 59.477564 Neighbor list builds = 0 Dangerous builds = 0 1248 -9286.68610582585 eV 2.66460251267575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03