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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -53.758383 0.0000000) to (38.010400 53.758383 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0016421 5.1868689 5.0346005 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.758383 0.0000000) to (38.010400 53.758383 5.0346005) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0016421 5.1868689 5.0346005 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.758383 0.0000000) to (38.010400 53.758383 5.0346005) create_atoms CPU = 0.002 seconds 916 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 1800 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.975 | 5.975 | 5.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7822.8656 0 -7822.8656 -7578.4374 110 0 -7901.3096 0 -7901.3096 -13526.319 Loop time of 3.21358 on 1 procs for 110 steps with 1800 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 = -7822.86559965839 -7901.30215715276 -7901.30962704968 Force two-norm initial, final = 38.926393 0.40816599 Force max component initial, final = 8.2007991 0.094601109 Final line search alpha, max atom move = 1.0000000 0.094601109 Iterations, force evaluations = 110 207 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.143 | 3.143 | 3.143 | 0.0 | 97.81 Neigh | 0.03491 | 0.03491 | 0.03491 | 0.0 | 1.09 Comm | 0.018934 | 0.018934 | 0.018934 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01669 | | | 0.52 Nlocal: 1800.00 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9784.00 ave 9784 max 9784 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: 314384.0 ave 314384 max 314384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314384 Ave neighs/atom = 174.65778 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.975 | 5.975 | 5.975 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -7901.3096 0 -7901.3096 -13526.319 20575.18 117 0 -7902.1797 0 -7902.1797 524.43552 20421.777 Loop time of 0.155896 on 1 procs for 7 steps with 1800 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 = -7901.30962704967 -7902.17887165865 -7902.17970095044 Force two-norm initial, final = 288.60704 0.60301057 Force max component initial, final = 244.01590 0.15412219 Final line search alpha, max atom move = 0.00010267377 1.5824305e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15177 | 0.15177 | 0.15177 | 0.0 | 97.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072202 | 0.00072202 | 0.00072202 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003404 | | | 2.18 Nlocal: 1800.00 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9784.00 ave 9784 max 9784 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: 314520.0 ave 314520 max 314520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314520 Ave neighs/atom = 174.73333 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.113 | 6.113 | 6.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7902.1797 0 -7902.1797 524.43552 Loop time of 1.746e-06 on 1 procs for 0 steps with 1800 atoms 171.8% 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 | | 1.746e-06 | | |100.00 Nlocal: 1800.00 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9792.00 ave 9792 max 9792 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: 314848.0 ave 314848 max 314848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314848 Ave neighs/atom = 174.91556 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.113 | 6.113 | 6.113 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 -7902.1797 -7902.1797 37.947855 107.51677 5.0053 524.43552 524.43552 -9.6918462 1595.0196 -12.02118 2.3767744 632.96827 Loop time of 2.057e-06 on 1 procs for 0 steps with 1800 atoms 243.1% 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 | | 2.057e-06 | | |100.00 Nlocal: 1800.00 ave 1800 max 1800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9792.00 ave 9792 max 9792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157424.0 ave 157424 max 157424 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 314848.0 ave 314848 max 314848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314848 Ave neighs/atom = 174.91556 Neighbor list builds = 0 Dangerous builds = 0 1800 -7902.17970095044 eV 2.37677443848017 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03