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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -36.960819 0.0000000) to (18.478597 36.960819 3.6239511) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2642917 4.2642917 3.6239511 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -36.960819 0.0000000) to (18.478597 36.960819 3.6239511) create_atoms CPU = 0.000 seconds 210 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2642917 4.2642917 3.6239511 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -36.960819 0.0000000) to (18.478597 36.960819 3.6239511) create_atoms CPU = 0.000 seconds 210 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 408 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1689.594 0 -1689.594 -6409.7413 46 0 -1700.7156 0 -1700.7156 -23308.405 Loop time of 4.19544 on 1 procs for 46 steps with 408 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 = -1689.59398573366 -1700.71420455477 -1700.71559682346 Force two-norm initial, final = 11.434706 0.10775087 Force max component initial, final = 4.7179482 0.025488453 Final line search alpha, max atom move = 1.0000000 0.025488453 Iterations, force evaluations = 46 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1781 | 4.1781 | 4.1781 | 0.0 | 99.59 Neigh | 0.0065413 | 0.0065413 | 0.0065413 | 0.0 | 0.16 Comm | 0.0059649 | 0.0059649 | 0.0059649 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004809 | | | 0.11 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3443.00 ave 3443 max 3443 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: 53556.0 ave 53556 max 53556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53556 Ave neighs/atom = 131.26471 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 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 46 0 -1700.7156 0 -1700.7156 -23308.405 4950.2018 191 0 -1707.152 0 -1707.152 15087.205 4820.4435 Loop time of 8.94189 on 1 procs for 145 steps with 408 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 = -1700.71559682346 -1707.15027092544 -1707.15196460886 Force two-norm initial, final = 89.193369 3.3569300 Force max component initial, final = 82.984325 1.5683952 Final line search alpha, max atom move = 0.00031687200 0.00049698053 Iterations, force evaluations = 145 160 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.8822 | 8.8822 | 8.8822 | 0.0 | 99.33 Neigh | 0.0066894 | 0.0066894 | 0.0066894 | 0.0 | 0.07 Comm | 0.0094105 | 0.0094105 | 0.0094105 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04361 | | | 0.49 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3535.00 ave 3535 max 3535 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: 53800.0 ave 53800 max 53800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53800 Ave neighs/atom = 131.86275 Neighbor list builds = 1 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1707.152 0 -1707.152 15087.205 Loop time of 3.631e-06 on 1 procs for 0 steps with 408 atoms 165.2% 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 | | 3.631e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617.00 ave 3617 max 3617 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: 50912.0 ave 50912 max 50912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50912 Ave neighs/atom = 124.78431 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.596 | 4.596 | 4.596 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 -1707.152 -1707.152 16.781032 73.921637 3.8859458 15087.205 15087.205 312.12999 44390.51 558.97616 2.2537397 253.85234 Loop time of 4.138e-06 on 1 procs for 0 steps with 408 atoms 169.2% 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 | | 4.138e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3617.00 ave 3617 max 3617 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25456.0 ave 25456 max 25456 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50912.0 ave 50912 max 50912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50912 Ave neighs/atom = 124.78431 Neighbor list builds = 0 Dangerous builds = 0 408 -1707.15196460886 eV 2.25373972215706 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13