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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -35.243066 0.0000000) to (17.619771 35.243066 3.5239542) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9335359 4.9335359 3.5239542 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.243066 0.0000000) to (17.619771 35.243066 3.5239542) create_atoms CPU = 0.002 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9335359 4.9335359 3.5239542 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -35.243066 0.0000000) to (17.619771 35.243066 3.5239542) create_atoms CPU = 0.001 seconds 201 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 19 1 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 396 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1733.4551 0 -1733.4551 9264.5212 53 0 -1747.8123 0 -1747.8123 -7570.1616 Loop time of 0.766772 on 1 procs for 53 steps with 396 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 = -1733.45509994043 -1747.81063104325 -1747.81229812612 Force two-norm initial, final = 15.948875 0.11672933 Force max component initial, final = 4.6251692 0.013823648 Final line search alpha, max atom move = 1.0000000 0.013823648 Iterations, force evaluations = 53 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74138 | 0.74138 | 0.74138 | 0.0 | 96.69 Neigh | 0.0093453 | 0.0093453 | 0.0093453 | 0.0 | 1.22 Comm | 0.0092844 | 0.0092844 | 0.0092844 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006762 | | | 0.88 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4557.00 ave 4557 max 4557 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: 69130.0 ave 69130 max 69130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69130 Ave neighs/atom = 174.57071 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1747.8123 0 -1747.8123 -7570.1616 4376.5731 56 0 -1747.8392 0 -1747.8392 -2162.7457 4363.298 Loop time of 0.0524912 on 1 procs for 3 steps with 396 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1747.81229812612 -1747.83841501718 -1747.83921472312 Force two-norm initial, final = 24.262199 0.12625425 Force max component initial, final = 18.398462 0.017668771 Final line search alpha, max atom move = 0.00052356621 9.2507715e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05022 | 0.05022 | 0.05022 | 0.0 | 95.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055316 | 0.00055316 | 0.00055316 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001718 | | | 3.27 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4565.00 ave 4565 max 4565 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: 69124.0 ave 69124 max 69124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69124 Ave neighs/atom = 174.55556 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.618 | 4.618 | 4.618 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1747.8392 0 -1747.8392 -2162.7457 Loop time of 6.525e-06 on 1 procs for 0 steps with 396 atoms 168.6% 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 | | 6.525e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4565.00 ave 4565 max 4565 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: 69146.0 ave 69146 max 69146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69146 Ave neighs/atom = 174.61111 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.618 | 4.618 | 4.618 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 -1747.8392 -1747.8392 17.60543 70.486132 3.516127 -2162.7457 -2162.7457 -3.4324336 -6486.1215 1.3167577 2.2188632 148.30838 Loop time of 6.675e-06 on 1 procs for 0 steps with 396 atoms 239.7% 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 | | 6.675e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4565.00 ave 4565 max 4565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34573.0 ave 34573 max 34573 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69146.0 ave 69146 max 69146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69146 Ave neighs/atom = 174.61111 Neighbor list builds = 0 Dangerous builds = 0 396 -1747.83921472312 eV 2.21886321583517 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01