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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3533032 4.3533032 3.5213917 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) create_atoms CPU = 0.002 seconds 426 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3533032 4.3533032 3.5213917 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -51.275759 0.0000000) to (25.636119 51.275759 3.5213917) create_atoms CPU = 0.001 seconds 426 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 840 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3709.4116 0 -3709.4116 2318.1679 20 0 -3720.8343 0 -3720.8343 -6431.5627 Loop time of 4.03238 on 1 procs for 20 steps with 840 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3709.41162487197 -3720.83097747173 -3720.83431099287 Force two-norm initial, final = 26.852056 0.20047476 Force max component initial, final = 8.6753754 0.049439680 Final line search alpha, max atom move = 1.0000000 0.049439680 Iterations, force evaluations = 20 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0218 | 4.0218 | 4.0218 | 0.0 | 99.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057223 | 0.0057223 | 0.0057223 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004873 | | | 0.12 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6270.00 ave 6270 max 6270 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: 72380.0 ave 72380 max 72380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72380 Ave neighs/atom = 86.166667 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -3720.8343 0 -3720.8343 -6431.5627 9257.8196 23 0 -3720.8874 0 -3720.8874 -1205.6797 9231.4587 Loop time of 0.680898 on 1 procs for 3 steps with 840 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3720.83431099287 -3720.88518931326 -3720.88739406434 Force two-norm initial, final = 48.072407 0.21605780 Force max component initial, final = 39.098052 0.049594335 Final line search alpha, max atom move = 0.00021253295 1.0540430e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67684 | 0.67684 | 0.67684 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091184 | 0.00091184 | 0.00091184 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003146 | | | 0.46 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300.00 ave 6300 max 6300 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: 73208.0 ave 73208 max 73208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73208 Ave neighs/atom = 87.152381 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.710 | 4.710 | 4.710 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3720.8874 0 -3720.8874 -1205.6797 Loop time of 8.429e-06 on 1 procs for 0 steps with 840 atoms 166.1% 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 | | 8.429e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300.00 ave 6300 max 6300 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: 73240.0 ave 73240 max 73240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73240 Ave neighs/atom = 87.190476 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.710 | 4.710 | 4.710 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 -3720.8874 -3720.8874 25.623538 102.55152 3.5130889 -1205.6797 -1205.6797 -2.5421756 -3615.2401 0.74317643 2.2795762 336.39896 Loop time of 8.209e-06 on 1 procs for 0 steps with 840 atoms 243.6% 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 | | 8.209e-06 | | |100.00 Nlocal: 840.000 ave 840 max 840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6300.00 ave 6300 max 6300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36620.0 ave 36620 max 36620 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73240.0 ave 73240 max 73240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73240 Ave neighs/atom = 87.190476 Neighbor list builds = 0 Dangerous builds = 0 840 -3720.88739406434 eV 2.27957616542732 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05