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 = 2.8599988 2.8599988 2.8599988 Created orthogonal box = (0.0000000 -28.884572 0.0000000) to (20.424477 28.884572 4.0446491) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6043195 4.5309133 4.0446491 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -28.884572 0.0000000) to (20.424477 28.884572 4.0446491) create_atoms CPU = 0.001 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6043195 4.5309133 4.0446491 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -28.884572 0.0000000) to (20.424477 28.884572 4.0446491) create_atoms CPU = 0.000 seconds 206 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 17 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 410 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1505.7578 0 -1505.7578 161078.85 126 0 -1786.0719 0 -1786.0719 72979.632 Loop time of 0.671102 on 1 procs for 126 steps with 410 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 = -1505.75777351051 -1786.07032945653 -1786.0718559202 Force two-norm initial, final = 430.96033 0.20345451 Force max component initial, final = 149.85713 0.033422254 Final line search alpha, max atom move = 1.0000000 0.033422254 Iterations, force evaluations = 126 229 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65375 | 0.65375 | 0.65375 | 0.0 | 97.41 Neigh | 0.0069378 | 0.0069378 | 0.0069378 | 0.0 | 1.03 Comm | 0.0060701 | 0.0060701 | 0.0060701 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004342 | | | 0.65 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3611.00 ave 3611 max 3611 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: 55328.0 ave 55328 max 55328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55328 Ave neighs/atom = 134.94634 Neighbor list builds = 2 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 126 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 126 0 -1786.0719 0 -1786.0719 72979.632 4772.3 159 0 -1790.7333 0 -1790.7333 -217.30953 4910.8249 Loop time of 0.116665 on 1 procs for 33 steps with 410 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 = -1786.0718559202 -1790.73271176431 -1790.73329265095 Force two-norm initial, final = 405.65707 2.4158513 Force max component initial, final = 307.46954 1.5011602 Final line search alpha, max atom move = 0.00033414543 0.00050160583 Iterations, force evaluations = 33 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1107 | 0.1107 | 0.1107 | 0.0 | 94.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010776 | 0.0010776 | 0.0010776 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004887 | | | 4.19 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3965.00 ave 3965 max 3965 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: 55284.0 ave 55284 max 55284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55284 Ave neighs/atom = 134.83902 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.589 | 4.589 | 4.589 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1790.7333 0 -1790.7333 -217.30953 Loop time of 1.522e-06 on 1 procs for 0 steps with 410 atoms 131.4% 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 | | 1.522e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3094.00 ave 3094 max 3094 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: 52236.0 ave 52236 max 52236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52236 Ave neighs/atom = 127.40488 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.589 | 4.589 | 4.589 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 -1790.7333 -1790.7333 20.278057 58.660902 4.1283772 -217.30953 -217.30953 -58.053228 -93.977277 -499.89808 2.3270216 2578.0847 Loop time of 1.718e-06 on 1 procs for 0 steps with 410 atoms 116.4% 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 | | 1.718e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3094.00 ave 3094 max 3094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26118.0 ave 26118 max 26118 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52236.0 ave 52236 max 52236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52236 Ave neighs/atom = 127.40488 Neighbor list builds = 0 Dangerous builds = 0 410 -1790.73329265095 eV 2.32702158648237 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01