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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -57.144416 0.0000000) to (28.572208 57.144416 3.6582963) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1523654 5.1523654 3.6582963 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -57.144416 0.0000000) to (28.572208 57.144416 3.6582963) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1523654 5.1523654 3.6582963 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -57.144416 0.0000000) to (28.572208 57.144416 3.6582963) create_atoms CPU = 0.001 seconds 490 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_942420706858_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3376.6412 0 -3376.6412 116477.44 265 0 -3928.7676 0 -3928.7676 -12497.881 Loop time of 4.71702 on 1 procs for 265 steps with 978 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3376.64115411645 -3928.76449464158 -3928.76762720545 Force two-norm initial, final = 606.64348 0.15354640 Force max component initial, final = 121.23241 0.013806556 Final line search alpha, max atom move = 1.0000000 0.013806556 Iterations, force evaluations = 265 512 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6128 | 4.6128 | 4.6128 | 0.0 | 97.79 Neigh | 0.045437 | 0.045437 | 0.045437 | 0.0 | 0.96 Comm | 0.035141 | 0.035141 | 0.035141 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02362 | | | 0.50 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8582.00 ave 8582 max 8582 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: 171732.0 ave 171732 max 171732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171732 Ave neighs/atom = 175.59509 Neighbor list builds = 5 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 265 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 265 0 -3928.7676 0 -3928.7676 -12497.881 11946.109 324 0 -3947.6823 0 -3947.6823 -224.28607 11825.916 Loop time of 0.618992 on 1 procs for 59 steps with 978 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3928.76762720545 -3947.68170772897 -3947.6823465162 Force two-norm initial, final = 541.33553 3.8529373 Force max component initial, final = 382.01919 2.4112899 Final line search alpha, max atom move = 0.00037027538 0.00089284128 Iterations, force evaluations = 59 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55905 | 0.55905 | 0.55905 | 0.0 | 90.32 Neigh | 0.037083 | 0.037083 | 0.037083 | 0.0 | 5.99 Comm | 0.0046266 | 0.0046266 | 0.0046266 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01823 | | | 2.95 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8591.00 ave 8591 max 8591 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: 165868.0 ave 165868 max 165868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165868 Ave neighs/atom = 169.59918 Neighbor list builds = 4 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3947.6823 0 -3947.6823 -224.28607 Loop time of 1.569e-06 on 1 procs for 0 steps with 978 atoms 127.5% 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 | | 1.569e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8597.00 ave 8597 max 8597 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: 166104.0 ave 166104 max 166104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166104 Ave neighs/atom = 169.84049 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.173 | 5.173 | 5.173 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 -3947.6823 -3947.6823 28.105002 109.46676 3.8438717 -224.28607 -224.28607 -321.34002 -116.86339 -234.65479 2.2296212 195.3848 Loop time of 1.679e-06 on 1 procs for 0 steps with 978 atoms 178.7% 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 | | 1.679e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8597.00 ave 8597 max 8597 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 83052.0 ave 83052 max 83052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 166104.0 ave 166104 max 166104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166104 Ave neighs/atom = 169.84049 Neighbor list builds = 0 Dangerous builds = 0 978 -3947.68234651619 eV 2.22962117383662 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05