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 -36.222573 0.0000000) to (9.0556432 36.222573 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6222573 3.6222573 2.8636458 Created 80 atoms using lattice units in orthogonal box = (0.0000000 -36.222573 0.0000000) to (9.0556432 36.222573 2.8636458) create_atoms CPU = 0.001 seconds 80 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6222573 3.6222573 2.8636458 Created 82 atoms using lattice units in orthogonal box = (0.0000000 -36.222573 0.0000000) to (9.0556432 36.222573 2.8636458) create_atoms CPU = 0.001 seconds 82 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 = 3 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 160 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_115454747503_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 = 3 23 1 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) = 4.401 | 4.401 | 4.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -675.47558 0 -675.47558 20982.471 13 0 -682.61674 0 -682.61674 10241 Loop time of 0.966358 on 1 procs for 13 steps with 160 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 = -675.475576269787 -682.616078075255 -682.616738589897 Force two-norm initial, final = 27.848449 0.073564789 Force max component initial, final = 9.8194637 0.0088394522 Final line search alpha, max atom move = 1.0000000 0.0088394522 Iterations, force evaluations = 13 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96367 | 0.96367 | 0.96367 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015422 | 0.0015422 | 0.0015422 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001142 | | | 0.12 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2451.00 ave 2451 max 2451 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: 17816.0 ave 17816 max 17816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17816 Ave neighs/atom = 111.35000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 23 1 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 : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.401 | 4.401 | 4.401 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -682.61674 0 -682.61674 10241 1878.6587 28 0 -682.82602 0 -682.82602 5.6230177 1889.4114 Loop time of 0.660294 on 1 procs for 15 steps with 160 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -682.616738589897 -682.825861313445 -682.826018929293 Force two-norm initial, final = 31.861473 0.42787177 Force max component initial, final = 31.672859 0.22027860 Final line search alpha, max atom move = 0.0035055902 0.00077220650 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65345 | 0.65345 | 0.65345 | 0.0 | 98.96 Neigh | 0.0027654 | 0.0027654 | 0.0027654 | 0.0 | 0.42 Comm | 0.001062 | 0.001062 | 0.001062 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003013 | | | 0.46 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2397.00 ave 2397 max 2397 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: 17560.0 ave 17560 max 17560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17560 Ave neighs/atom = 109.75000 Neighbor list builds = 1 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 = 3 23 1 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) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -682.82602 0 -682.82602 5.6230177 Loop time of 6.515e-06 on 1 procs for 0 steps with 160 atoms 168.8% 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 | | 6.515e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2397.00 ave 2397 max 2397 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: 17560.0 ave 17560 max 17560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17560 Ave neighs/atom = 109.75000 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 = 3 23 1 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) = 4.538 | 4.538 | 4.538 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 -682.82602 -682.82602 9.0299554 73.463215 2.8482033 5.6230177 5.6230177 -186.26122 55.185638 147.94464 2.3213792 82.978292 Loop time of 6.605e-06 on 1 procs for 0 steps with 160 atoms 242.2% 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 | | 6.605e-06 | | |100.00 Nlocal: 160.000 ave 160 max 160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2397.00 ave 2397 max 2397 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8780.00 ave 8780 max 8780 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17560.0 ave 17560 max 17560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17560 Ave neighs/atom = 109.75000 Neighbor list builds = 0 Dangerous builds = 0 160 -682.826018929293 eV 2.32137916294925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02