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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.001 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.001 seconds 629 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 = 10 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1251 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_924736622203_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 = 10 23 2 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) = 5.038 | 5.038 | 5.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4782.3698 0 -4782.3698 86690.875 357 0 -5292.6104 0 -5292.6104 17856.88 Loop time of 60.7789 on 1 procs for 357 steps with 1251 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 = -4782.36983088276 -5292.60563802078 -5292.61038189534 Force two-norm initial, final = 585.62531 0.24302399 Force max component initial, final = 134.29456 0.067336579 Final line search alpha, max atom move = 1.0000000 0.067336579 Iterations, force evaluations = 357 662 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 60.575 | 60.575 | 60.575 | 0.0 | 99.66 Neigh | 0.10547 | 0.10547 | 0.10547 | 0.0 | 0.17 Comm | 0.048061 | 0.048061 | 0.048061 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05056 | | | 0.08 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5106.00 ave 5106 max 5106 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: 123862.0 ave 123862 max 123862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123862 Ave neighs/atom = 99.010392 Neighbor list builds = 11 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 = 10 23 2 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 : 357 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press Volume 357 0 -5292.6104 0 -5292.6104 17856.88 14691.719 369 0 -5294.2564 0 -5294.2564 76.285069 14842.071 Loop time of 1.48883 on 1 procs for 12 steps with 1251 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 = -5292.61038189533 -5294.25637146424 -5294.25642385488 Force two-norm initial, final = 321.94779 1.5298520 Force max component initial, final = 267.96136 0.78177539 Final line search alpha, max atom move = 0.0013704346 0.0010713720 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.484 | 1.484 | 1.484 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065822 | 0.00065822 | 0.00065822 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004176 | | | 0.28 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5107.00 ave 5107 max 5107 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: 123776.0 ave 123776 max 123776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123776 Ave neighs/atom = 98.941647 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 = 10 23 2 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) = 5.171 | 5.171 | 5.171 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5294.2564 0 -5294.2564 76.285069 Loop time of 2.285e-06 on 1 procs for 0 steps with 1251 atoms 218.8% 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 | | 2.285e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5057.00 ave 5057 max 5057 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: 122942.0 ave 122942 max 122942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122942 Ave neighs/atom = 98.274980 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 = 10 23 2 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) = 5.171 | 5.171 | 5.171 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 -5294.2564 -5294.2564 32.031292 73.310459 6.3205388 76.285069 76.285069 84.758971 79.205311 64.890923 2.2853261 2610.1044 Loop time of 2.484e-06 on 1 procs for 0 steps with 1251 atoms 241.5% 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 | | 2.484e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5057.00 ave 5057 max 5057 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61471.0 ave 61471 max 61471 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122942.0 ave 122942 max 122942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122942 Ave neighs/atom = 98.274980 Neighbor list builds = 0 Dangerous builds = 0 1251 -5294.25642385488 eV 2.28532611347274 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:02