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 = 4.1768978 4.1768978 4.1768978 Created orthogonal box = (0.0000000 -44.986566 0.0000000) to (22.493283 44.986566 4.1768978) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4294132 5.4294132 4.1768978 Created 231 atoms using lattice units in orthogonal box = (0.0000000 -44.986566 0.0000000) to (22.493283 44.986566 4.1768978) create_atoms CPU = 0.002 seconds 231 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4294132 5.4294132 4.1768978 Created 233 atoms using lattice units in orthogonal box = (0.0000000 -44.986566 0.0000000) to (22.493283 44.986566 4.1768978) create_atoms CPU = 0.001 seconds 233 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 28 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 464 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_072689718616_001#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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.451 | 4.451 | 4.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3301.7809 0 -3301.7809 35337.535 43 0 -3408.5773 0 -3408.5773 8437.2838 Loop time of 2.64678 on 1 procs for 43 steps with 464 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 = -3301.78094241825 -3408.5750133211 -3408.57733584471 Force two-norm initial, final = 145.30381 0.16642378 Force max component initial, final = 33.444808 0.036421827 Final line search alpha, max atom move = 1.0000000 0.036421827 Iterations, force evaluations = 43 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6305 | 2.6305 | 2.6305 | 0.0 | 99.39 Neigh | 0.0052923 | 0.0052923 | 0.0052923 | 0.0 | 0.20 Comm | 0.005357 | 0.005357 | 0.005357 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005602 | | | 0.21 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2957.00 ave 2957 max 2957 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: 29712.0 ave 29712 max 29712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29712 Ave neighs/atom = 64.034483 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.454 | 4.454 | 4.454 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -3408.5773 0 -3408.5773 8437.2838 8453.1688 55 0 -3408.8868 0 -3408.8868 -0.33848135 8490.2965 Loop time of 0.692024 on 1 procs for 12 steps with 464 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 = -3408.57733584471 -3408.88506990945 -3408.88682664682 Force two-norm initial, final = 83.950217 0.64308001 Force max component initial, final = 71.376796 0.11943368 Final line search alpha, max atom move = 7.2210734e-05 8.6243934e-06 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68493 | 0.68493 | 0.68493 | 0.0 | 98.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014283 | 0.0014283 | 0.0014283 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005667 | | | 0.82 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3316.00 ave 3316 max 3316 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: 30072.0 ave 30072 max 30072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30072 Ave neighs/atom = 64.810345 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3408.8868 0 -3408.8868 -0.33848135 Loop time of 8.69e-06 on 1 procs for 0 steps with 464 atoms 161.1% 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 | | 8.69e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3316.00 ave 3316 max 3316 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: 30480.0 ave 30480 max 30480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30480 Ave neighs/atom = 65.689655 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.592 | 4.592 | 4.592 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 -3408.8868 -3408.8868 22.402324 89.696914 4.2252486 -0.33848135 -0.33848135 11.627185 0.20164224 -12.844271 2.623502 366.40899 Loop time of 6.525e-06 on 1 procs for 0 steps with 464 atoms 306.5% 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 | | 6.525e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3316.00 ave 3316 max 3316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15240.0 ave 15240 max 15240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30480.0 ave 30480 max 30480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30480 Ave neighs/atom = 65.689655 Neighbor list builds = 0 Dangerous builds = 0 464 -3408.88682664682 eV 2.6235019933881 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03