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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -65.781753 0.0000000) to (32.889093 65.781753 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0300966 5.0300966 3.5673230 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -65.781753 0.0000000) to (32.889093 65.781753 3.5673230) create_atoms CPU = 0.003 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0300966 5.0300966 3.5673230 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -65.781753 0.0000000) to (32.889093 65.781753 3.5673230) create_atoms CPU = 0.002 seconds 682 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 47 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1344 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.675 | 4.675 | 4.675 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5650.2038 0 -5650.2038 -6579.6639 62 0 -5676.105 0 -5676.105 11561.611 Loop time of 10.4414 on 1 procs for 62 steps with 1344 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 = -5650.20379896329 -5676.10009006819 -5676.10500370459 Force two-norm initial, final = 10.073974 0.37415497 Force max component initial, final = 2.3783011 0.048078990 Final line search alpha, max atom move = 1.0000000 0.048078990 Iterations, force evaluations = 62 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.402 | 10.402 | 10.402 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019824 | 0.019824 | 0.019824 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0194 | | | 0.19 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7386.00 ave 7386 max 7386 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: 72212.0 ave 72212 max 72212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72212 Ave neighs/atom = 53.729167 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 47 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.677 | 4.677 | 4.677 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -5676.105 0 -5676.105 11561.611 15435.822 82 0 -5679.0815 0 -5679.0815 3801.0208 15571.414 Loop time of 2.39773 on 1 procs for 20 steps with 1344 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5676.10500370458 -5679.07612374084 -5679.08148890503 Force two-norm initial, final = 359.97741 6.9729704 Force max component initial, final = 317.08700 5.7884638 Final line search alpha, max atom move = 3.0290007e-05 0.00017533261 Iterations, force evaluations = 20 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3764 | 2.3764 | 2.3764 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0044711 | 0.0044711 | 0.0044711 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01689 | | | 0.70 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7442.00 ave 7442 max 7442 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: 77740.0 ave 77740 max 77740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77740 Ave neighs/atom = 57.842262 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.818 | 4.818 | 4.818 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5679.0815 0 -5679.0815 3801.0208 Loop time of 6.695e-06 on 1 procs for 0 steps with 1344 atoms 179.2% 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 | | 6.695e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7418.00 ave 7418 max 7418 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: 76408.0 ave 76408 max 76408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76408 Ave neighs/atom = 56.851190 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 12 47 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.818 | 4.818 | 4.818 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 -5679.0815 -5679.0815 33.380519 131.56351 3.54568 3801.0208 3801.0208 -287.57284 11098.661 591.97412 2.3285334 176.91873 Loop time of 6.825e-06 on 1 procs for 0 steps with 1344 atoms 278.4% 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 | | 6.825e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7418.00 ave 7418 max 7418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38204.0 ave 38204 max 38204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 76408.0 ave 76408 max 76408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 76408 Ave neighs/atom = 56.851190 Neighbor list builds = 0 Dangerous builds = 0 1344 -5679.08148890503 eV 2.32853336327316 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13