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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -48.707195 0.0000000) to (59.653887 48.707195 9.8739816) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7202357 6.0049966 6.5826544 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -48.707195 0.0000000) to (59.653887 48.707195 9.8739816) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7202357 6.0049966 6.5826544 Created 1753 atoms using lattice units in orthogonal box = (0.0000000 -48.707195 0.0000000) to (59.653887 48.707195 9.8739816) create_atoms CPU = 0.002 seconds 1753 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3500 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_699137396381_005#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.526 | 6.526 | 6.526 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11458.302 0 -11458.302 11170.151 66 0 -11734.316 0 -11734.316 1870.8511 Loop time of 2.28153 on 1 procs for 66 steps with 3500 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 = -11458.3017120248 -11734.3050777593 -11734.3163332405 Force two-norm initial, final = 80.783824 0.29568938 Force max component initial, final = 6.7105983 0.038871781 Final line search alpha, max atom move = 1.0000000 0.038871781 Iterations, force evaluations = 66 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2181 | 2.2181 | 2.2181 | 0.0 | 97.22 Neigh | 0.030631 | 0.030631 | 0.030631 | 0.0 | 1.34 Comm | 0.01236 | 0.01236 | 0.01236 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02047 | | | 0.90 Nlocal: 3500.00 ave 3500 max 3500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9652.00 ave 9652 max 9652 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: 457454.0 ave 457454 max 457454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457454 Ave neighs/atom = 130.70114 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.525 | 6.525 | 6.525 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -11734.316 0 -11734.316 1870.8511 57379.158 70 0 -11734.537 0 -11734.537 -175.32752 57538.09 Loop time of 0.120508 on 1 procs for 4 steps with 3500 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 = -11734.3163332405 -11734.5327043445 -11734.5370745808 Force two-norm initial, final = 138.96169 12.740572 Force max component initial, final = 122.75143 9.9895022 Final line search alpha, max atom move = 5.8403069e-05 0.00058341758 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11644 | 0.11644 | 0.11644 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052415 | 0.00052415 | 0.00052415 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003545 | | | 2.94 Nlocal: 3500.00 ave 3500 max 3500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9625.00 ave 9625 max 9625 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: 459590.0 ave 459590 max 459590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459590 Ave neighs/atom = 131.31143 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.662 | 6.662 | 6.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11734.537 0 -11734.537 -175.32752 Loop time of 2.331e-06 on 1 procs for 0 steps with 3500 atoms 171.6% 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 | | 2.331e-06 | | |100.00 Nlocal: 3500.00 ave 3500 max 3500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9583.00 ave 9583 max 9583 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: 458834.0 ave 458834 max 458834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458834 Ave neighs/atom = 131.09543 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 6.662 | 6.662 | 6.662 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 -11734.537 -11734.537 59.692823 97.744725 9.8614322 -175.32752 -175.32752 -218.06255 -30.110936 -277.80908 2.5925562 2200.5424 Loop time of 2.658e-06 on 1 procs for 0 steps with 3500 atoms 263.4% 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 | | 2.658e-06 | | |100.00 Nlocal: 3500.00 ave 3500 max 3500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9583.00 ave 9583 max 9583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229417.0 ave 229417 max 229417 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 458834.0 ave 458834 max 458834 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458834 Ave neighs/atom = 131.09543 Neighbor list builds = 0 Dangerous builds = 0 3500 -11734.5370745808 eV 2.59255620157022 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03