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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -57.778019 0.0000000) to (40.855229 57.778019 5.7208764) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4086634 5.0980605 5.7208764 Created 815 atoms using lattice units in orthogonal box = (0.0000000 -57.778019 0.0000000) to (40.855229 57.778019 5.7208764) create_atoms CPU = 0.004 seconds 815 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4086634 5.0980605 5.7208764 Created 823 atoms using lattice units in orthogonal box = (0.0000000 -57.778019 0.0000000) to (40.855229 57.778019 5.7208764) create_atoms CPU = 0.004 seconds 823 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 25 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1632 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_658278549784_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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.960 | 5.960 | 5.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5073.2551 0 -5073.2551 38209.754 69 0 -5552.1532 0 -5552.1532 4083.2541 Loop time of 5.27183 on 1 procs for 69 steps with 1632 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 = -5073.25511089764 -5552.14904365782 -5552.15316028465 Force two-norm initial, final = 585.50033 0.14117096 Force max component initial, final = 100.88717 0.014492181 Final line search alpha, max atom move = 1.0000000 0.014492181 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1671 | 5.1671 | 5.1671 | 0.0 | 98.01 Neigh | 0.047511 | 0.047511 | 0.047511 | 0.0 | 0.90 Comm | 0.032292 | 0.032292 | 0.032292 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02489 | | | 0.47 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10140.0 ave 10140 max 10140 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: 355694.0 ave 355694 max 355694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 355694 Ave neighs/atom = 217.94975 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.955 | 5.955 | 5.955 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -5552.1532 0 -5552.1532 4083.2541 27008.649 75 0 -5552.4391 0 -5552.4391 -159.42807 27150.631 Loop time of 0.322579 on 1 procs for 6 steps with 1632 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 = -5552.15316028461 -5552.43740708079 -5552.4391436378 Force two-norm initial, final = 128.02752 6.2347461 Force max component initial, final = 105.02977 4.7028680 Final line search alpha, max atom move = 0.00011552686 0.00054330759 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31409 | 0.31409 | 0.31409 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021103 | 0.0021103 | 0.0021103 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006382 | | | 1.98 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10180.0 ave 10180 max 10180 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: 360168.0 ave 360168 max 360168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360168 Ave neighs/atom = 220.69118 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.093 | 6.093 | 6.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5552.4391 0 -5552.4391 -159.42807 Loop time of 6.384e-06 on 1 procs for 0 steps with 1632 atoms 219.3% 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 | | 6.384e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10180.0 ave 10180 max 10180 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: 357994.0 ave 357994 max 357994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357994 Ave neighs/atom = 219.35907 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 6.093 | 6.093 | 6.093 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 -5552.4391 -5552.4391 40.888738 116.17929 5.7154115 -159.42807 -159.42807 -238.59654 37.566561 -277.25422 2.7018087 553.6782 Loop time of 6.836e-06 on 1 procs for 0 steps with 1632 atoms 307.2% 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 | | 6.836e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10180.0 ave 10180 max 10180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178997.0 ave 178997 max 178997 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 357994.0 ave 357994 max 357994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357994 Ave neighs/atom = 219.35907 Neighbor list builds = 0 Dangerous builds = 0 1632 -5552.4391436378 eV 2.70180871823436 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06