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 = 2.8601955 2.8601955 2.8601955 Created orthogonal box = (0.0000000 -52.739398 0.0000000) to (26.369699 52.739398 2.8601955) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0330128 4.0330128 2.8601955 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -52.739398 0.0000000) to (26.369699 52.739398 2.8601955) create_atoms CPU = 0.002 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0330128 4.0330128 2.8601955 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -52.739398 0.0000000) to (26.369699 52.739398 2.8601955) create_atoms CPU = 0.001 seconds 341 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 681 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_137964310702_004#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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.264 | 5.264 | 5.264 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2802.7498 0 -2802.7498 33685.446 37 0 -2906.2589 0 -2906.2589 5166.0519 Loop time of 7.6901 on 1 procs for 37 steps with 681 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 = -2802.74978523581 -2906.25666175327 -2906.25891798568 Force two-norm initial, final = 188.85116 0.37837126 Force max component initial, final = 67.464857 0.17180679 Final line search alpha, max atom move = 0.77301396 0.13280905 Iterations, force evaluations = 37 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.6779 | 7.6779 | 7.6779 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005962 | 0.005962 | 0.005962 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006271 | | | 0.08 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4054.00 ave 4054 max 4054 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: 39434.0 ave 39434 max 39434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39434 Ave neighs/atom = 57.906021 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.265 | 5.265 | 5.265 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -2906.2589 0 -2906.2589 5166.0519 7955.4738 42 0 -2906.3562 0 -2906.3562 -552.94724 7980.619 Loop time of 0.804046 on 1 procs for 5 steps with 681 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 = -2906.25891798568 -2906.3539569929 -2906.35621172327 Force two-norm initial, final = 54.924081 5.6239975 Force max component initial, final = 51.975106 5.1465051 Final line search alpha, max atom move = 0.00018456659 0.00094987290 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80133 | 0.80133 | 0.80133 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056674 | 0.00056674 | 0.00056674 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002154 | | | 0.27 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4155.00 ave 4155 max 4155 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: 39410.0 ave 39410 max 39410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39410 Ave neighs/atom = 57.870778 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.403 | 5.403 | 5.403 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2906.3562 0 -2906.3562 -552.94724 Loop time of 6.755e-06 on 1 procs for 0 steps with 681 atoms 0.0% 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 | | 6.755e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4197.00 ave 4197 max 4197 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: 39400.0 ave 39400 max 39400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39400 Ave neighs/atom = 57.856094 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.403 | 5.403 | 5.403 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 -2906.3562 -2906.3562 26.391511 105.88627 2.8558322 -552.94724 -552.94724 -272.4437 -354.76991 -1031.6281 2.2944348 115.65295 Loop time of 6.565e-06 on 1 procs for 0 steps with 681 atoms 258.9% 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 | | 6.565e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4197.00 ave 4197 max 4197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19700.0 ave 19700 max 19700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39400.0 ave 39400 max 39400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39400 Ave neighs/atom = 57.856094 Neighbor list builds = 0 Dangerous builds = 0 681 -2906.35621172327 eV 2.29443482721415 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09