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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -40.052304 0.0000000) to (9.4396769 40.052304 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2442649 4.4499063 4.4499063 Created 109 atoms using lattice units in orthogonal box = (0.0000000 -40.052304 0.0000000) to (9.4396769 40.052304 4.4499063) create_atoms CPU = 0.002 seconds 109 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2442649 4.4499063 4.4499063 Created 109 atoms using lattice units in orthogonal box = (0.0000000 -40.052304 0.0000000) to (9.4396769 40.052304 4.4499063) create_atoms CPU = 0.001 seconds 109 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 4 28 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 214 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_805823015127_000#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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 4 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.397 | 4.397 | 4.397 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1439.4412 0 -1439.4412 -302.22394 35 0 -1448.6232 0 -1448.6232 -10543.148 Loop time of 0.790893 on 1 procs for 35 steps with 214 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 = -1439.4412199779 -1448.62218231415 -1448.62321866994 Force two-norm initial, final = 13.805673 0.096224460 Force max component initial, final = 6.4991057 0.021283900 Final line search alpha, max atom move = 1.0000000 0.021283900 Iterations, force evaluations = 35 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78336 | 0.78336 | 0.78336 | 0.0 | 99.05 Neigh | 0.0021395 | 0.0021395 | 0.0021395 | 0.0 | 0.27 Comm | 0.0027325 | 0.0027325 | 0.0027325 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002658 | | | 0.34 Nlocal: 214.000 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1686.00 ave 1686 max 1686 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: 12260.0 ave 12260 max 12260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12260 Ave neighs/atom = 57.289720 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 4 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.397 | 4.397 | 4.397 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1448.6232 0 -1448.6232 -10543.148 3364.8483 38 0 -1448.6857 0 -1448.6857 964.45853 3349.9434 Loop time of 0.0670413 on 1 procs for 3 steps with 214 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 = -1448.62321866994 -1448.68484154397 -1448.6857176927 Force two-norm initial, final = 39.710789 0.18659699 Force max component initial, final = 28.628657 0.11166949 Final line search alpha, max atom move = 0.00028282153 3.1582535e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066011 | 0.066011 | 0.066011 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022673 | 0.00022673 | 0.00022673 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008032 | | | 1.20 Nlocal: 214.000 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1694.00 ave 1694 max 1694 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: 12242.0 ave 12242 max 12242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12242 Ave neighs/atom = 57.205607 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 4 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.535 | 4.535 | 4.535 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1448.6857 0 -1448.6857 964.45853 Loop time of 6.265e-06 on 1 procs for 0 steps with 214 atoms 175.6% 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 | | 6.265e-06 | | |100.00 Nlocal: 214.000 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1697.00 ave 1697 max 1697 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: 12242.0 ave 12242 max 12242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12242 Ave neighs/atom = 57.205607 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 4 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.535 | 4.535 | 4.535 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 -1448.6857 -1448.6857 9.4193071 80.104607 4.4397756 964.45853 964.45853 51.423103 2895.239 -53.286545 2.4199987 211.60628 Loop time of 8.82e-06 on 1 procs for 0 steps with 214 atoms 249.4% 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 | | 8.82e-06 | | |100.00 Nlocal: 214.000 ave 214 max 214 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1697.00 ave 1697 max 1697 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6121.00 ave 6121 max 6121 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12242.0 ave 12242 max 12242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12242 Ave neighs/atom = 57.205607 Neighbor list builds = 0 Dangerous builds = 0 214 -1448.6857176927 eV 2.41999874199354 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01