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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -66.229332 0.0000000) to (46.828349 66.229332 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9893059 6.4248412 5.7209934 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -66.229332 0.0000000) to (46.828349 66.229332 5.7209934) create_atoms CPU = 0.003 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9893059 6.4248412 5.7209934 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -66.229332 0.0000000) to (46.828349 66.229332 5.7209934) create_atoms CPU = 0.003 seconds 1079 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 2143 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7141.6941 0 -7141.6941 5579.0819 22 0 -7185.4269 0 -7185.4269 2114.1553 Loop time of 2.21439 on 1 procs for 22 steps with 2143 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7141.69405813572 -7185.41990661472 -7185.42686522773 Force two-norm initial, final = 34.710960 0.19283378 Force max component initial, final = 4.7146673 0.030296985 Final line search alpha, max atom move = 1.0000000 0.030296985 Iterations, force evaluations = 22 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1967 | 2.1967 | 2.1967 | 0.0 | 99.20 Neigh | 0.0096252 | 0.0096252 | 0.0096252 | 0.0 | 0.43 Comm | 0.0028724 | 0.0028724 | 0.0028724 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005144 | | | 0.23 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6758.00 ave 6758 max 6758 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: 116482.0 ave 116482 max 116482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116482 Ave neighs/atom = 54.354643 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 15 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -7185.4269 0 -7185.4269 2114.1553 35486.296 24 0 -7185.4472 0 -7185.4472 1056.9653 35536.801 Loop time of 0.32019 on 1 procs for 2 steps with 2143 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 = -7185.42686522773 -7185.44658060474 -7185.44719418374 Force two-norm initial, final = 37.843832 0.19917305 Force max component initial, final = 31.047846 0.029020399 Final line search alpha, max atom move = 0.00032718924 9.4951621e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31841 | 0.31841 | 0.31841 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025926 | 0.00025926 | 0.00025926 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00152 | | | 0.47 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6758.00 ave 6758 max 6758 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: 116078.0 ave 116078 max 116078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116078 Ave neighs/atom = 54.166122 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.343 | 5.343 | 5.343 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7185.4472 0 -7185.4472 1056.9653 Loop time of 2.127e-06 on 1 procs for 0 steps with 2143 atoms 188.1% 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 | | 2.127e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6758.00 ave 6758 max 6758 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: 116068.0 ave 116068 max 116068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116068 Ave neighs/atom = 54.161456 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.343 | 5.343 | 5.343 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 -7185.4472 -7185.4472 46.877825 132.45866 5.723089 1056.9653 1056.9653 -0.75205383 3172.3792 -0.731372 2.6065987 944.22567 Loop time of 3.792e-06 on 1 procs for 0 steps with 2143 atoms 211.0% 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 | | 3.792e-06 | | |100.00 Nlocal: 2143.00 ave 2143 max 2143 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6758.00 ave 6758 max 6758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58034.0 ave 58034 max 58034 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116068.0 ave 116068 max 116068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116068 Ave neighs/atom = 54.161456 Neighbor list builds = 0 Dangerous builds = 0 2143 -7185.44719418374 eV 2.60659865725527 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03