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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -62.127689 0.0000000) to (31.063844 62.127689 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0373802 5.0373802 3.6110986 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.127689 0.0000000) to (31.063844 62.127689 3.6110986) create_atoms CPU = 0.002 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0373802 5.0373802 3.6110986 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.127689 0.0000000) to (31.063844 62.127689 3.6110986) create_atoms CPU = 0.002 seconds 594 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_912636107108_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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.641 | 4.641 | 4.641 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4665.8079 0 -4665.8079 54934.582 74 0 -5010.9954 0 -5010.9954 4381.1103 Loop time of 5.62006 on 1 procs for 74 steps with 1184 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 = -4665.80793022765 -5010.99110066609 -5010.995428536 Force two-norm initial, final = 559.31604 0.20508328 Force max component initial, final = 159.74426 0.041797188 Final line search alpha, max atom move = 1.0000000 0.041797188 Iterations, force evaluations = 74 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5912 | 5.5912 | 5.5912 | 0.0 | 99.49 Neigh | 0.0071365 | 0.0071365 | 0.0071365 | 0.0 | 0.13 Comm | 0.011613 | 0.011613 | 0.011613 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01013 | | | 0.18 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6608.00 ave 6608 max 6608 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: 91768.0 ave 91768 max 91768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91768 Ave neighs/atom = 77.506757 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.635 | 4.635 | 4.635 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -5010.9954 0 -5010.9954 4381.1103 13938.298 85 0 -5011.3969 0 -5011.3969 -412.61169 13976.819 Loop time of 0.511235 on 1 procs for 11 steps with 1184 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5010.995428536 -5011.39511653088 -5011.39690590733 Force two-norm initial, final = 88.171044 8.0588706 Force max component initial, final = 74.451020 5.7057017 Final line search alpha, max atom move = 0.00011358581 0.00064808672 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50727 | 0.50727 | 0.50727 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063968 | 0.00063968 | 0.00063968 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003324 | | | 0.65 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6036.00 ave 6036 max 6036 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: 91856.0 ave 91856 max 91856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91856 Ave neighs/atom = 77.581081 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.773 | 4.773 | 4.773 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5011.3969 0 -5011.3969 -412.61169 Loop time of 1.678e-06 on 1 procs for 0 steps with 1184 atoms 178.8% 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 | | 1.678e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6052.00 ave 6052 max 6052 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: 91872.0 ave 91872 max 91872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91872 Ave neighs/atom = 77.594595 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 ghost atom cutoff = 6 binsize = 3, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.773 | 4.773 | 4.773 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 -5011.3969 -5011.3969 30.881665 124.04075 3.6487425 -412.61169 -412.61169 -650.21442 -645.45281 57.832149 2.3042143 306.2305 Loop time of 1.839e-06 on 1 procs for 0 steps with 1184 atoms 217.5% 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 | | 1.839e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6052.00 ave 6052 max 6052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45936.0 ave 45936 max 45936 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91872.0 ave 91872 max 91872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91872 Ave neighs/atom = 77.594595 Neighbor list builds = 0 Dangerous builds = 0 1184 -5011.39690590733 eV 2.30421433393723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06