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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2535503 4.0518441 4.6627256 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) create_atoms CPU = 0.001 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2535503 4.0518441 4.6627256 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -42.254946 0.0000000) to (34.501019 42.254946 6.9940884) create_atoms CPU = 0.001 seconds 878 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1744 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.571 | 5.571 | 5.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5337.0323 0 -5337.0323 206034.75 117 0 -7151.2279 0 -7151.2279 1486.5496 Loop time of 2.7222 on 1 procs for 117 steps with 1744 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5337.03234428587 -7151.22126204465 -7151.22790238208 Force two-norm initial, final = 3362.7716 0.28470673 Force max component initial, final = 733.64857 0.055508936 Final line search alpha, max atom move = 1.0000000 0.055508936 Iterations, force evaluations = 117 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6395 | 2.6395 | 2.6395 | 0.0 | 96.96 Neigh | 0.048471 | 0.048471 | 0.048471 | 0.0 | 1.78 Comm | 0.016379 | 0.016379 | 0.016379 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01789 | | | 0.66 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7735.00 ave 7735 max 7735 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: 289232.0 ave 289232 max 289232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289232 Ave neighs/atom = 165.84404 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 117 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.574 | 5.574 | 5.574 Mbytes Step Temp E_pair E_mol TotEng Press Volume 117 0 -7151.2279 0 -7151.2279 1486.5496 20392.505 121 0 -7151.4213 0 -7151.4213 -74.959052 20411.603 Loop time of 0.0802452 on 1 procs for 4 steps with 1744 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 = -7151.22790238207 -7151.41410378134 -7151.42125045089 Force two-norm initial, final = 95.328146 2.7129665 Force max component initial, final = 90.368290 2.3773435 Final line search alpha, max atom move = 6.9696680e-05 0.00016569295 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.076965 | 0.076965 | 0.076965 | 0.0 | 95.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042237 | 0.00042237 | 0.00042237 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002858 | | | 3.56 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8018.00 ave 8018 max 8018 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: 289340.0 ave 289340 max 289340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289340 Ave neighs/atom = 165.90596 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.712 | 5.712 | 5.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7151.4213 0 -7151.4213 -74.959052 Loop time of 2.33e-06 on 1 procs for 0 steps with 1744 atoms 171.7% 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 | | 2.33e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8055.00 ave 8055 max 8055 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: 289236.0 ave 289236 max 289236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289236 Ave neighs/atom = 165.84633 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.712 | 5.712 | 5.712 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 -7151.4213 -7151.4213 34.463909 84.822933 6.9823127 -74.959052 -74.959052 -186.4051 -84.966708 46.494657 2.2471145 1120.5548 Loop time of 2.592e-06 on 1 procs for 0 steps with 1744 atoms 231.5% 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 | | 2.592e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8055.00 ave 8055 max 8055 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144618.0 ave 144618 max 144618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289236.0 ave 289236 max 289236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289236 Ave neighs/atom = 165.84633 Neighbor list builds = 0 Dangerous builds = 0 1744 -7151.42125045089 eV 2.24711454931602 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03