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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -51.487887 0.0000000) to (36.407434 51.487887 5.7208764) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7421175 6.9921822 5.7208764 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.487887 0.0000000) to (36.407434 51.487887 5.7208764) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7421175 6.9921822 5.7208764 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.487887 0.0000000) to (36.407434 51.487887 5.7208764) create_atoms CPU = 0.004 seconds 650 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 22 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 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_658278549784_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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.491 | 5.491 | 5.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4313.235 0 -4313.235 17830.304 52 0 -4419.2833 0 -4419.2833 4275.8786 Loop time of 3.13643 on 1 procs for 52 steps with 1298 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 = -4313.23495327752 -4419.27935261384 -4419.28332473776 Force two-norm initial, final = 153.44257 0.14655970 Force max component initial, final = 45.974898 0.028599936 Final line search alpha, max atom move = 1.0000000 0.028599936 Iterations, force evaluations = 52 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1018 | 3.1018 | 3.1018 | 0.0 | 98.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01909 | 0.01909 | 0.01909 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01558 | | | 0.50 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8661.00 ave 8661 max 8661 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: 290300.0 ave 290300 max 290300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290300 Ave neighs/atom = 223.65177 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.501 | 5.501 | 5.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -4419.2833 0 -4419.2833 4275.8786 21448.045 58 0 -4419.516 0 -4419.516 -2.9472483 21561.037 Loop time of 0.2875 on 1 procs for 6 steps with 1298 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 = -4419.28332473775 -4419.51508622931 -4419.51600203844 Force two-norm initial, final = 106.74802 0.40139712 Force max component initial, final = 88.652145 0.23652871 Final line search alpha, max atom move = 0.00013319976 3.1505568e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28006 | 0.28006 | 0.28006 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017697 | 0.0017697 | 0.0017697 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005674 | | | 1.97 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9250.00 ave 9250 max 9250 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: 283880.0 ave 283880 max 283880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 283880 Ave neighs/atom = 218.70570 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.639 | 5.639 | 5.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4419.516 0 -4419.516 -2.9472483 Loop time of 6.465e-06 on 1 procs for 0 steps with 1298 atoms 170.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9232.00 ave 9232 max 9232 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: 281444.0 ave 281444 max 281444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281444 Ave neighs/atom = 216.82897 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.639 | 5.639 | 5.639 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 -4419.516 -4419.516 36.437812 103.50449 5.7168678 -2.9472483 -2.9472483 17.302471 -8.5803471 -17.563869 2.6620656 580.04722 Loop time of 6.996e-06 on 1 procs for 0 steps with 1298 atoms 257.3% 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 | | 6.996e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9232.00 ave 9232 max 9232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 140722.0 ave 140722 max 140722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 281444.0 ave 281444 max 281444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 281444 Ave neighs/atom = 216.82897 Neighbor list builds = 0 Dangerous builds = 0 1298 -4419.51600203844 eV 2.66206560450383 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04