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 = 3.5192945 3.5192945 3.5192945 Created orthogonal box = (0.0000000 -50.269098 0.0000000) to (35.543132 50.269098 4.9770340) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5753932 4.4351981 4.9770340 Created 823 atoms using lattice units in orthogonal box = (0.0000000 -50.269098 0.0000000) to (35.543132 50.269098 4.9770340) create_atoms CPU = 0.002 seconds 823 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5753932 4.4351981 4.9770340 Created 823 atoms using lattice units in orthogonal box = (0.0000000 -50.269098 0.0000000) to (35.543132 50.269098 4.9770340) create_atoms CPU = 0.001 seconds 823 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 27 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 22 atoms, new total = 1624 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 27 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) = 5.550 | 5.550 | 5.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7156.7574 0 -7156.7574 14846.318 36 0 -7202.5027 0 -7202.5027 628.01146 Loop time of 0.955778 on 1 procs for 36 steps with 1624 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7156.75736480701 -7202.49553159596 -7202.50271680112 Force two-norm initial, final = 59.824115 0.30435127 Force max component initial, final = 8.9631159 0.022191461 Final line search alpha, max atom move = 1.0000000 0.022191461 Iterations, force evaluations = 36 69 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94457 | 0.94457 | 0.94457 | 0.0 | 98.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057787 | 0.0057787 | 0.0057787 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005427 | | | 0.57 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 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: 283550.0 ave 283550 max 283550 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283550 Ave neighs/atom = 174.59975 Neighbor list builds = 0 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 27 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 : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.550 | 5.550 | 5.550 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -7202.5027 0 -7202.5027 628.01146 17785.144 37 0 -7202.5058 0 -7202.5058 1116.537 17780.184 Loop time of 0.0412703 on 1 procs for 1 steps with 1624 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 = -7202.50271680111 -7202.50271680111 -7202.50575219107 Force two-norm initial, final = 13.553979 2.8766347 Force max component initial, final = 12.820084 2.7011731 Final line search alpha, max atom move = 7.8002611e-05 0.00021069856 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040361 | 0.040361 | 0.040361 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019695 | 0.00019695 | 0.00019695 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007119 | | | 1.72 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9048.00 ave 9048 max 9048 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: 283196.0 ave 283196 max 283196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283196 Ave neighs/atom = 174.38177 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 27 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) = 5.688 | 5.688 | 5.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7202.5058 0 -7202.5058 1116.537 Loop time of 1.908e-06 on 1 procs for 0 steps with 1624 atoms 157.2% 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 | | 1.908e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 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: 283236.0 ave 283236 max 283236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283236 Ave neighs/atom = 174.40640 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 27 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) = 5.688 | 5.688 | 5.688 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 -7202.5058 -7202.5058 35.528063 100.5382 4.9777563 1116.537 1116.537 84.738689 3021.4336 243.43866 2.3144158 560.16667 Loop time of 1.908e-06 on 1 procs for 0 steps with 1624 atoms 157.2% 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 | | 1.908e-06 | | |100.00 Nlocal: 1624.00 ave 1624 max 1624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 141618.0 ave 141618 max 141618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 283236.0 ave 283236 max 283236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283236 Ave neighs/atom = 174.40640 Neighbor list builds = 0 Dangerous builds = 0 1624 -7202.50575219107 eV 2.31441576802092 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01