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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -37.447028 0.0000000) to (17.652698 37.447028 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7163575 4.5987578 4.0498067 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -37.447028 0.0000000) to (17.652698 37.447028 4.0498067) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7163575 4.5987578 4.0498067 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -37.447028 0.0000000) to (17.652698 37.447028 4.0498067) create_atoms CPU = 0.000 seconds 230 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 = 6 24 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 6 atoms, new total = 452 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_179420363944_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 = 6 24 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) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1860.0859 0 -1860.0859 29778.73 45 0 -1928.0095 0 -1928.0095 -5578.3701 Loop time of 2.73408 on 1 procs for 45 steps with 452 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 = -1860.08588759803 -1928.00774211987 -1928.00946914475 Force two-norm initial, final = 162.18095 0.14385918 Force max component initial, final = 56.389238 0.025824080 Final line search alpha, max atom move = 1.0000000 0.025824080 Iterations, force evaluations = 45 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7261 | 2.7261 | 2.7261 | 0.0 | 99.71 Neigh | 0.0028851 | 0.0028851 | 0.0028851 | 0.0 | 0.11 Comm | 0.0024622 | 0.0024622 | 0.0024622 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002643 | | | 0.10 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3228.00 ave 3228 max 3228 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: 48776.0 ave 48776 max 48776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48776 Ave neighs/atom = 107.91150 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 6 24 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.463 | 4.463 | 4.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -1928.0095 0 -1928.0095 -5578.3701 5354.1773 49 0 -1928.0477 0 -1928.0477 0.2626047 5336.5485 Loop time of 0.290097 on 1 procs for 4 steps with 452 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 = -1928.00946914475 -1928.04749340323 -1928.04767065301 Force two-norm initial, final = 33.343283 0.16852671 Force max component initial, final = 24.909387 0.030575012 Final line search alpha, max atom move = 0.00076478401 2.3383280e-05 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28891 | 0.28891 | 0.28891 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021788 | 0.00021788 | 0.00021788 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009701 | | | 0.33 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3228.00 ave 3228 max 3228 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: 49080.0 ave 49080 max 49080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49080 Ave neighs/atom = 108.58407 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 = 6 23 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1928.0477 0 -1928.0477 0.2626047 Loop time of 1.918e-06 on 1 procs for 0 steps with 452 atoms 156.4% 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 | | 1.918e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3244.00 ave 3244 max 3244 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: 49172.0 ave 49172 max 49172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49172 Ave neighs/atom = 108.78761 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 = 6 23 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) = 4.601 | 4.601 | 4.601 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 -1928.0477 -1928.0477 17.658216 74.723914 4.0443992 0.2626047 0.2626047 -2.9272548 -1.2182811 4.93335 2.2860532 320.68549 Loop time of 1.591e-06 on 1 procs for 0 steps with 452 atoms 188.6% 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 | | 1.591e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3244.00 ave 3244 max 3244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24586.0 ave 24586 max 24586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49172.0 ave 49172 max 49172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49172 Ave neighs/atom = 108.78761 Neighbor list builds = 0 Dangerous builds = 0 452 -1928.04767065301 eV 2.28605319044252 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03