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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -39.483605 0.0000000) to (8.0595571 39.483605 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.483605 0.0000000) to (8.0595571 39.483605 8.8288024) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8357343 5.2644806 5.8858683 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.483605 0.0000000) to (8.0595571 39.483605 8.8288024) create_atoms CPU = 0.000 seconds 242 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 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1658.1607 0 -1658.1607 204359.05 67 0 -2030.945 0 -2030.945 5395.0516 Loop time of 2.22286 on 1 procs for 67 steps with 480 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1658.1607126456 -2030.94318569921 -2030.94497587321 Force two-norm initial, final = 1262.3877 0.15664855 Force max component initial, final = 354.50526 0.042377982 Final line search alpha, max atom move = 1.0000000 0.042377982 Iterations, force evaluations = 67 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2112 | 2.2112 | 2.2112 | 0.0 | 99.48 Neigh | 0.0034843 | 0.0034843 | 0.0034843 | 0.0 | 0.16 Comm | 0.0038382 | 0.0038382 | 0.0038382 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004346 | | | 0.20 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2778.00 ave 2778 max 2778 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: 37200.0 ave 37200 max 37200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37200 Ave neighs/atom = 77.500000 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 ghost atom cutoff = 6 binsize = 3, bins = 3 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -2030.945 0 -2030.945 5395.0516 5619.0095 82 0 -2031.5475 0 -2031.5475 -1.9736488 5636.7152 Loop time of 0.32088 on 1 procs for 15 steps with 480 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 = -2030.94497587321 -2031.54616887471 -2031.54750266687 Force two-norm initial, final = 69.072275 0.69595894 Force max component initial, final = 43.754450 0.12525754 Final line search alpha, max atom move = 0.00053297962 6.6759718e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31483 | 0.31483 | 0.31483 | 0.0 | 98.11 Neigh | 0.0032332 | 0.0032332 | 0.0032332 | 0.0 | 1.01 Comm | 0.00050767 | 0.00050767 | 0.00050767 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002312 | | | 0.72 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 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: 37012.0 ave 37012 max 37012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37012 Ave neighs/atom = 77.108333 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 3 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2031.5475 0 -2031.5475 -1.9736488 Loop time of 2.365e-06 on 1 procs for 0 steps with 480 atoms 169.1% 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 | | 2.365e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2852.00 ave 2852 max 2852 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: 37000.0 ave 37000 max 37000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37000 Ave neighs/atom = 77.083333 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 ghost atom cutoff = 6 binsize = 3, bins = 3 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.598 | 4.598 | 4.598 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 -2031.5475 -2031.5475 8.1483267 77.832005 8.8879058 -1.9736488 -1.9736488 -31.371365 35.09131 -9.6408918 2.2145231 347.71763 Loop time of 2.587e-06 on 1 procs for 0 steps with 480 atoms 270.6% 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 | | 2.587e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2852.00 ave 2852 max 2852 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18500.0 ave 18500 max 18500 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37000.0 ave 37000 max 37000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37000 Ave neighs/atom = 77.083333 Neighbor list builds = 0 Dangerous builds = 0 480 -2031.54750266687 eV 2.21452313601451 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03