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 = 3.5927866 3.5927866 3.5927866 Created orthogonal box = (0.0000000 -42.510424 0.0000000) to (52.064423 42.510424 8.8004938) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9502198 5.4656259 5.8669959 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -42.510424 0.0000000) to (52.064423 42.510424 8.8004938) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9502198 5.4656259 5.8669959 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -42.510424 0.0000000) to (52.064423 42.510424 8.8004938) create_atoms CPU = 0.003 seconds 1686 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 15 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 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 3318 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_396616545191_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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.533 | 6.533 | 6.533 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11486.819 0 -11486.819 9783.8414 138 0 -11601.88 0 -11601.88 -9540.4223 Loop time of 16.994 on 1 procs for 138 steps with 3318 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 = -11486.8186971996 -11601.8688849611 -11601.8798948993 Force two-norm initial, final = 100.83043 0.36291518 Force max component initial, final = 14.164439 0.067430074 Final line search alpha, max atom move = 0.89249887 0.060181265 Iterations, force evaluations = 138 244 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.536 | 16.536 | 16.536 | 0.0 | 97.30 Neigh | 0.33338 | 0.33338 | 0.33338 | 0.0 | 1.96 Comm | 0.048673 | 0.048673 | 0.048673 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.076 | | | 0.45 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9263.00 ave 9263 max 9263 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: 437370.0 ave 437370 max 437370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437370 Ave neighs/atom = 131.81736 Neighbor list builds = 6 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 138 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press Volume 138 0 -11601.88 0 -11601.88 -9540.4223 38955.926 144 0 -11602.888 0 -11602.888 -2.6694413 38672.624 Loop time of 0.678779 on 1 procs for 6 steps with 3318 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 = -11601.8798948993 -11602.8848906144 -11602.8875618132 Force two-norm initial, final = 413.48212 0.79074911 Force max component initial, final = 302.51798 0.43541012 Final line search alpha, max atom move = 4.5821146e-05 1.9950991e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66794 | 0.66794 | 0.66794 | 0.0 | 98.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014004 | 0.0014004 | 0.0014004 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009443 | | | 1.39 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9261.00 ave 9261 max 9261 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: 437386.0 ave 437386 max 437386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437386 Ave neighs/atom = 131.82218 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.667 | 6.667 | 6.667 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11602.888 0 -11602.888 -2.6694413 Loop time of 3.811e-06 on 1 procs for 0 steps with 3318 atoms 157.4% 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 | | 3.811e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9266.00 ave 9266 max 9266 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: 437978.0 ave 437978 max 437978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437978 Ave neighs/atom = 132.00060 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 = 6.9840864 ghost atom cutoff = 6.9840864 binsize = 3.4920432, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.9840864150596245 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) = 6.667 | 6.667 | 6.667 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 -11602.888 -11602.888 51.947816 84.615693 8.7980299 -2.6694413 -2.6694413 17.998299 -9.5118793 -16.494744 2.3196865 1930.6607 Loop time of 4.192e-06 on 1 procs for 0 steps with 3318 atoms 214.7% 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 | | 4.192e-06 | | |100.00 Nlocal: 3318.00 ave 3318 max 3318 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9266.00 ave 9266 max 9266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 218989.0 ave 218989 max 218989 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 437978.0 ave 437978 max 437978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 437978 Ave neighs/atom = 132.00060 Neighbor list builds = 0 Dangerous builds = 0 3318 -11602.8875618132 eV 2.31968648083015 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18