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 -59.116230 0.0000000) to (41.801487 59.116230 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -59.116230 0.0000000) to (41.801487 59.116230 5.1068645) create_atoms CPU = 0.003 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2390280 5.7351567 5.1068645 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -59.116230 0.0000000) to (41.801487 59.116230 5.1068645) create_atoms CPU = 0.003 seconds 1080 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 = 13 37 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 24 atoms, new total = 2128 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_115454747503_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 = 13 37 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) = 5.242 | 5.242 | 5.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8952.3845 0 -8952.3845 2757.927 343 0 -9043.2517 0 -9043.2517 -7305.4615 Loop time of 90.6848 on 1 procs for 343 steps with 2128 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 = -8952.38454138131 -9043.24272675741 -9043.25165305712 Force two-norm initial, final = 66.990893 0.30684469 Force max component initial, final = 12.029217 0.060985762 Final line search alpha, max atom move = 1.0000000 0.060985762 Iterations, force evaluations = 343 649 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 90.369 | 90.369 | 90.369 | 0.0 | 99.65 Neigh | 0.15797 | 0.15797 | 0.15797 | 0.0 | 0.17 Comm | 0.083063 | 0.083063 | 0.083063 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07505 | | | 0.08 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8771.00 ave 8771 max 8771 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: 213446.0 ave 213446 max 213446 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 213446 Ave neighs/atom = 100.30357 Neighbor list builds = 10 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 = 13 37 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 : 343 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.621 | 5.621 | 5.621 Mbytes Step Temp E_pair E_mol TotEng Press Volume 343 0 -9043.2517 0 -9043.2517 -7305.4615 25239.619 376 0 -9068.9314 0 -9068.9314 57.172433 25081.657 Loop time of 6.61826 on 1 procs for 33 steps with 2128 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 = -9043.25165305714 -9068.93020430542 -9068.93144559221 Force two-norm initial, final = 1207.8042 8.9221598 Force max component initial, final = 819.77505 6.5554274 Final line search alpha, max atom move = 0.0011750327 0.0077028417 Iterations, force evaluations = 33 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5481 | 6.5481 | 6.5481 | 0.0 | 98.94 Neigh | 0.048344 | 0.048344 | 0.048344 | 0.0 | 0.73 Comm | 0.0036985 | 0.0036985 | 0.0036985 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0181 | | | 0.27 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9001.00 ave 9001 max 9001 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: 218314.0 ave 218314 max 218314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218314 Ave neighs/atom = 102.59117 Neighbor list builds = 3 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 = 13 38 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) = 5.761 | 5.761 | 5.761 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9068.9314 0 -9068.9314 57.172433 Loop time of 2.19e-06 on 1 procs for 0 steps with 2128 atoms 182.6% 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 | | 2.19e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9032.00 ave 9032 max 9032 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: 218740.0 ave 218740 max 218740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218740 Ave neighs/atom = 102.79135 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 = 13 38 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) = 5.761 | 5.761 | 5.761 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 -9068.9314 -9068.9314 41.299448 121.98408 4.9786181 57.172433 57.172433 413.72108 74.70025 -316.90403 2.3605505 5119.4164 Loop time of 2.636e-06 on 1 procs for 0 steps with 2128 atoms 227.6% 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 | | 2.636e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9032.00 ave 9032 max 9032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109370.0 ave 109370 max 109370 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218740.0 ave 218740 max 218740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218740 Ave neighs/atom = 102.79135 Neighbor list builds = 0 Dangerous builds = 0 2128 -9068.93144559222 eV 2.36055054823493 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:38