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 -41.746968 0.0000000) to (14.758670 41.746968 4.4499064) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3667890 4.7436161 4.4499064 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (14.758670 41.746968 4.4499064) create_atoms CPU = 0.002 seconds 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3667890 4.7436161 4.4499064 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -41.746968 0.0000000) to (14.758670 41.746968 4.4499064) create_atoms CPU = 0.001 seconds 178 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 348 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_486450342170_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2340.6422 0 -2340.6422 7196.0315 21 0 -2355.8606 0 -2355.8606 -17999.606 Loop time of 0.953362 on 1 procs for 21 steps with 348 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 = -2340.64222822195 -2355.85890381493 -2355.86060176073 Force two-norm initial, final = 36.160002 0.21513353 Force max component initial, final = 10.058678 0.042790340 Final line search alpha, max atom move = 1.0000000 0.042790340 Iterations, force evaluations = 21 36 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94798 | 0.94798 | 0.94798 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028804 | 0.0028804 | 0.0028804 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002501 | | | 0.26 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3198.00 ave 3198 max 3198 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: 22496.0 ave 22496 max 22496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22496 Ave neighs/atom = 64.643678 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.445 | 4.445 | 4.445 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -2355.8606 0 -2355.8606 -17999.606 5483.4391 25 0 -2356.0289 0 -2356.0289 -3225.4886 5451.9906 Loop time of 0.151594 on 1 procs for 4 steps with 348 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 = -2355.86060176074 -2356.02869971785 -2356.02886116645 Force two-norm initial, final = 82.905615 1.0370127 Force max component initial, final = 61.613531 0.99313924 Final line search alpha, max atom move = 0.00048910585 0.00048575021 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14981 | 0.14981 | 0.14981 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040779 | 0.00040779 | 0.00040779 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001378 | | | 0.91 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3198.00 ave 3198 max 3198 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: 22808.0 ave 22808 max 22808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22808 Ave neighs/atom = 65.540230 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2356.0289 0 -2356.0289 -3225.4886 Loop time of 6.395e-06 on 1 procs for 0 steps with 348 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3198.00 ave 3198 max 3198 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: 22872.0 ave 22872 max 22872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22872 Ave neighs/atom = 65.724138 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.583 | 4.583 | 4.583 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 -2356.0289 -2356.0289 14.720451 83.493937 4.4358724 -3225.4886 -3225.4886 291.09805 -9998.2561 30.692217 2.4678674 336.87578 Loop time of 6.725e-06 on 1 procs for 0 steps with 348 atoms 252.8% 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 | | 6.725e-06 | | |100.00 Nlocal: 348.000 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3198.00 ave 3198 max 3198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11436.0 ave 11436 max 11436 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 22872.0 ave 22872 max 22872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 22872 Ave neighs/atom = 65.724138 Neighbor list builds = 0 Dangerous builds = 0 348 -2356.02886116645 eV 2.46786743898814 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01