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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -45.684024 0.0000000) to (32.303483 45.684024 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5152289 6.1283447 5.0449565 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.684024 0.0000000) to (32.303483 45.684024 5.0449565) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5152289 6.1283447 5.0449565 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.684024 0.0000000) to (32.303483 45.684024 5.0449565) create_atoms CPU = 0.001 seconds 660 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 33 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5188.1978 0 -5188.1978 45381.794 139 0 -5504.6059 0 -5504.6059 47171.525 Loop time of 10.6047 on 1 procs for 139 steps with 1304 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5188.19777778513 -5504.6021723035 -5504.60586386048 Force two-norm initial, final = 464.62643 0.54990062 Force max component initial, final = 113.61643 0.10520621 Final line search alpha, max atom move = 1.0000000 0.10520621 Iterations, force evaluations = 139 263 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.557 | 10.557 | 10.557 | 0.0 | 99.55 Neigh | 0.0069534 | 0.0069534 | 0.0069534 | 0.0 | 0.07 Comm | 0.019242 | 0.019242 | 0.019242 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02132 | | | 0.20 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5060.00 ave 5060 max 5060 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: 75792.0 ave 75792 max 75792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75792 Ave neighs/atom = 58.122699 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 139 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press Volume 139 0 -5504.6059 0 -5504.6059 47171.525 14890.221 155 0 -5509.2993 0 -5509.2993 -18.496053 15115.075 Loop time of 0.741439 on 1 procs for 16 steps with 1304 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5504.60586386049 -5509.29627130239 -5509.299315291 Force two-norm initial, final = 792.03797 3.2731477 Force max component initial, final = 620.64548 0.96191541 Final line search alpha, max atom move = 0.00013694969 0.00013173402 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72778 | 0.72778 | 0.72778 | 0.0 | 98.16 Neigh | 0.0070816 | 0.0070816 | 0.0070816 | 0.0 | 0.96 Comm | 0.0010388 | 0.0010388 | 0.0010388 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005536 | | | 0.75 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5181.00 ave 5181 max 5181 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: 75120.0 ave 75120 max 75120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75120 Ave neighs/atom = 57.607362 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.786 | 4.786 | 4.786 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5509.2993 0 -5509.2993 -18.496053 Loop time of 2.443e-06 on 1 procs for 0 steps with 1304 atoms 204.7% 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 | | 2.443e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5181.00 ave 5181 max 5181 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: 74648.0 ave 74648 max 74648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74648 Ave neighs/atom = 57.245399 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.786 | 4.786 | 4.786 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 -5509.2993 -5509.2993 32.349842 92.784192 5.0357499 -18.496053 -18.496053 -40.816543 -103.54201 88.870391 2.3671237 1348.0554 Loop time of 2.75e-06 on 1 procs for 0 steps with 1304 atoms 290.9% 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 | | 2.75e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5181.00 ave 5181 max 5181 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37324.0 ave 37324 max 37324 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74648.0 ave 74648 max 74648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74648 Ave neighs/atom = 57.245399 Neighbor list builds = 0 Dangerous builds = 0 1304 -5509.29931529099 eV 2.36712366671555 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11