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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -62.612339 0.0000000) to (25.561380 62.612339 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1347313 5.4264027 5.9031479 Created 1195 atoms using lattice units in orthogonal box = (0.0000000 -62.612339 0.0000000) to (25.561380 62.612339 8.8547219) create_atoms CPU = 0.006 seconds 1195 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1347313 5.4264027 5.9031479 Created 1203 atoms using lattice units in orthogonal box = (0.0000000 -62.612339 0.0000000) to (25.561380 62.612339 8.8547219) create_atoms CPU = 0.005 seconds 1203 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 33 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2398 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.062 | 6.062 | 6.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7920.4431 0 -7920.4431 55349.966 74 0 -8470.6332 0 -8470.6332 1647.4634 Loop time of 4.43501 on 1 procs for 74 steps with 2398 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 = -7920.44312139034 -8470.62602481155 -8470.63322334633 Force two-norm initial, final = 1744.6188 0.25245542 Force max component initial, final = 635.35487 0.022419543 Final line search alpha, max atom move = 1.0000000 0.022419543 Iterations, force evaluations = 74 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2033 | 4.2033 | 4.2033 | 0.0 | 94.78 Neigh | 0.16893 | 0.16893 | 0.16893 | 0.0 | 3.81 Comm | 0.028689 | 0.028689 | 0.028689 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03404 | | | 0.77 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9018.00 ave 9018 max 9018 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: 341652.0 ave 341652 max 341652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 341652 Ave neighs/atom = 142.47373 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.062 | 6.062 | 6.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -8470.6332 0 -8470.6332 1647.4634 28343.218 78 0 -8470.7863 0 -8470.7863 -116.66132 28378.749 Loop time of 0.205639 on 1 procs for 4 steps with 2398 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 = -8470.63322334633 -8470.78535969064 -8470.78632503582 Force two-norm initial, final = 92.421666 5.2703580 Force max component initial, final = 91.945697 4.6048410 Final line search alpha, max atom move = 0.00011033546 0.00050807724 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19982 | 0.19982 | 0.19982 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011291 | 0.0011291 | 0.0011291 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004693 | | | 2.28 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9026.00 ave 9026 max 9026 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: 342456.0 ave 342456 max 342456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342456 Ave neighs/atom = 142.80901 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.200 | 6.200 | 6.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8470.7863 0 -8470.7863 -116.66132 Loop time of 6.074e-06 on 1 procs for 0 steps with 2398 atoms 197.6% 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 | | 6.074e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9034.00 ave 9034 max 9034 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: 342152.0 ave 342152 max 342152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342152 Ave neighs/atom = 142.68224 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 7 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.200 | 6.200 | 6.200 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 -8470.7863 -8470.7863 25.534195 125.62351 8.8470837 -116.66132 -116.66132 -136.14576 45.912641 -259.75084 2.3657199 986.32638 Loop time of 6.635e-06 on 1 procs for 0 steps with 2398 atoms 301.4% 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 | | 6.635e-06 | | |100.00 Nlocal: 2398.00 ave 2398 max 2398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9034.00 ave 9034 max 9034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 171076.0 ave 171076 max 171076 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 342152.0 ave 342152 max 342152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 342152 Ave neighs/atom = 142.68224 Neighbor list builds = 0 Dangerous builds = 0 2398 -8470.79831503583 eV 2.36571994101452 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05