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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -56.989753 0.0000000) to (20.147808 56.989753 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4055095 4.8647103 4.4499064 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -56.989753 0.0000000) to (20.147808 56.989753 4.4499064) create_atoms CPU = 0.003 seconds 330 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4055095 4.8647103 4.4499064 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -56.989753 0.0000000) to (20.147808 56.989753 4.4499064) create_atoms CPU = 0.003 seconds 330 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 34 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 652 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4371.7198 0 -4371.7198 25077.768 22 0 -4422.6312 0 -4422.6312 -8723.1766 Loop time of 1.91316 on 1 procs for 22 steps with 652 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 = -4371.71980848228 -4422.62689580884 -4422.63116715502 Force two-norm initial, final = 146.37922 0.35306409 Force max component initial, final = 42.323531 0.081366501 Final line search alpha, max atom move = 1.0000000 0.081366501 Iterations, force evaluations = 22 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9046 | 1.9046 | 1.9046 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0045379 | 0.0045379 | 0.0045379 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004017 | | | 0.21 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 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: 42144.0 ave 42144 max 42144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42144 Ave neighs/atom = 64.638037 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -4422.6312 0 -4422.6312 -8723.1766 10218.931 25 0 -4422.7219 0 -4422.7219 -833.51429 10188.062 Loop time of 0.278044 on 1 procs for 3 steps with 652 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 = -4422.63116715502 -4422.72158376362 -4422.72191341487 Force two-norm initial, final = 83.360170 0.35970272 Force max component initial, final = 64.024125 0.081606368 Final line search alpha, max atom move = 0.00042835349 3.4956373e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27541 | 0.27541 | 0.27541 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061875 | 0.00061875 | 0.00061875 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002017 | | | 0.73 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 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: 42800.0 ave 42800 max 42800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42800 Ave neighs/atom = 65.644172 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4422.7219 0 -4422.7219 -833.51429 Loop time of 6.144e-06 on 1 procs for 0 steps with 652 atoms 162.8% 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 | | 6.144e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 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: 42864.0 ave 42864 max 42864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42864 Ave neighs/atom = 65.742331 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.665 | 4.665 | 4.665 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 -4422.7219 -4422.7219 20.124042 113.97951 4.4417039 -833.51429 -833.51429 -8.7285136 -2491.989 0.17461982 2.4538939 370.69598 Loop time of 6.596e-06 on 1 procs for 0 steps with 652 atoms 272.9% 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 | | 6.596e-06 | | |100.00 Nlocal: 652.000 ave 652 max 652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4811.00 ave 4811 max 4811 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21432.0 ave 21432 max 21432 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42864.0 ave 42864 max 42864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42864 Ave neighs/atom = 65.742331 Neighbor list builds = 0 Dangerous builds = 0 652 -4422.72191341487 eV 2.45389392409025 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02