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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -29.673404 0.0000000) to (20.982265 29.673404 4.0380388) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6627256 3.8465524 4.0380388 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -29.673404 0.0000000) to (20.982265 29.673404 4.0380388) create_atoms CPU = 0.003 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6627256 3.8465524 4.0380388 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.673404 0.0000000) to (20.982265 29.673404 4.0380388) create_atoms CPU = 0.002 seconds 218 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 428 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_737567242631_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1491.4441 0 -1491.4441 141780.53 67 0 -1751.7074 0 -1751.7074 -3285.451 Loop time of 1.01115 on 1 procs for 67 steps with 428 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 = -1491.44414366414 -1751.70576267964 -1751.70739960122 Force two-norm initial, final = 788.39885 0.14183599 Force max component initial, final = 269.62213 0.030693386 Final line search alpha, max atom move = 1.0000000 0.030693386 Iterations, force evaluations = 67 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.98034 | 0.98034 | 0.98034 | 0.0 | 96.95 Neigh | 0.0088594 | 0.0088594 | 0.0088594 | 0.0 | 0.88 Comm | 0.011905 | 0.011905 | 0.011905 | 0.0 | 1.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01005 | | | 0.99 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3632.00 ave 3632 max 3632 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: 58220.0 ave 58220 max 58220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58220 Ave neighs/atom = 136.02804 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1751.7074 0 -1751.7074 -3285.451 5028.2889 70 0 -1751.7247 0 -1751.7247 -81.620716 5018.9722 Loop time of 0.0435343 on 1 procs for 3 steps with 428 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 = -1751.70739960122 -1751.72450831919 -1751.72469083881 Force two-norm initial, final = 19.600367 0.47390679 Force max component initial, final = 16.228255 0.31654583 Final line search alpha, max atom move = 0.00093705222 0.00029661997 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.041636 | 0.041636 | 0.041636 | 0.0 | 95.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043251 | 0.00043251 | 0.00043251 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001466 | | | 3.37 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3604.00 ave 3604 max 3604 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: 58164.0 ave 58164 max 58164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58164 Ave neighs/atom = 135.89720 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1751.7247 0 -1751.7247 -81.620716 Loop time of 6.404e-06 on 1 procs for 0 steps with 428 atoms 187.4% 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 | | 6.404e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3604.00 ave 3604 max 3604 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: 58212.0 ave 58212 max 58212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58212 Ave neighs/atom = 136.00935 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.600 | 4.600 | 4.600 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 -1751.7247 -1751.7247 20.964686 59.395531 4.0306273 -81.620716 -81.620716 -100.96437 -74.906197 -68.991575 2.2878147 358.12036 Loop time of 6.775e-06 on 1 procs for 0 steps with 428 atoms 250.9% 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 | | 6.775e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3604.00 ave 3604 max 3604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29106.0 ave 29106 max 29106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58212.0 ave 58212 max 58212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58212 Ave neighs/atom = 136.00935 Neighbor list builds = 0 Dangerous builds = 0 428 -1751.72469083881 eV 2.28781468806773 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01