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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -35.423222 0.0000000) to (25.045820 35.423222 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7948213 4.8300189 4.3599177 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -35.423222 0.0000000) to (25.045820 35.423222 4.3599177) create_atoms CPU = 0.000 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7948213 4.8300189 4.3599177 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -35.423222 0.0000000) to (25.045820 35.423222 4.3599177) create_atoms CPU = 0.000 seconds 266 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 9 atoms, new total = 523 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.233 | 5.233 | 5.233 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3221.8916 0 -3221.8916 69781.391 120 0 -3387.0605 0 -3387.0605 -12481.808 Loop time of 11.7794 on 1 procs for 120 steps with 523 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 = -3221.89164322547 -3387.05751580579 -3387.06050604935 Force two-norm initial, final = 374.91803 0.26413988 Force max component initial, final = 117.75224 0.053977105 Final line search alpha, max atom move = 1.0000000 0.053977105 Iterations, force evaluations = 120 220 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.756 | 11.756 | 11.756 | 0.0 | 99.80 Neigh | 0.014885 | 0.014885 | 0.014885 | 0.0 | 0.13 Comm | 0.0058665 | 0.0058665 | 0.0058665 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002474 | | | 0.02 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3378.00 ave 3378 max 3378 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: 38534.0 ave 38534 max 38534 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38534 Ave neighs/atom = 73.678776 Neighbor list builds = 2 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 120 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.236 | 5.236 | 5.236 Mbytes Step Temp E_pair E_mol TotEng Press Volume 120 0 -3387.0605 0 -3387.0605 -12481.808 7736.2698 128 0 -3387.4798 0 -3387.4798 2588.9518 7681.7403 Loop time of 0.528513 on 1 procs for 8 steps with 523 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 = -3387.06050604936 -3387.47950940025 -3387.47983237079 Force two-norm initial, final = 136.77442 0.57224034 Force max component initial, final = 123.01692 0.11077111 Final line search alpha, max atom move = 0.00026006783 2.8808003e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52779 | 0.52779 | 0.52779 | 0.0 | 99.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001764 | 0.0001764 | 0.0001764 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005465 | | | 0.10 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 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: 38510.0 ave 38510 max 38510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38510 Ave neighs/atom = 73.632887 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.374 | 5.374 | 5.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3387.4798 0 -3387.4798 2588.9518 Loop time of 1.8e-06 on 1 procs for 0 steps with 523 atoms 166.7% 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 | | 1.8e-06 | | |100.00 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 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: 39314.0 ave 39314 max 39314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39314 Ave neighs/atom = 75.170172 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.374 | 5.374 | 5.374 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 -3387.4798 -3387.4798 25.031947 70.846444 4.331586 2588.9518 2588.9518 14.321039 7729.5809 22.95334 2.4667675 1369.1007 Loop time of 1.9e-06 on 1 procs for 0 steps with 523 atoms 157.9% 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 | | 1.9e-06 | | |100.00 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19657.0 ave 19657 max 19657 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39314.0 ave 39314 max 39314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39314 Ave neighs/atom = 75.170172 Neighbor list builds = 0 Dangerous builds = 0 523 -3387.47983237079 eV 2.46676746562245 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12