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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -44.528390 0.0000000) to (11.131217 44.528390 3.5200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4524870 4.4524870 3.5200000 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.528390 0.0000000) to (11.131217 44.528390 3.5200000) create_atoms CPU = 0.002 seconds 162 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4524870 4.4524870 3.5200000 Created 162 atoms using lattice units in orthogonal box = (0.0000000 -44.528390 0.0000000) to (11.131217 44.528390 3.5200000) create_atoms CPU = 0.001 seconds 162 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 316 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_937008984446_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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1386.3307 0 -1386.3307 11186.964 60 0 -1400.5312 0 -1400.5312 -12289.087 Loop time of 3.20997 on 1 procs for 60 steps with 316 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 = -1386.33070145595 -1400.5302040465 -1400.53124990562 Force two-norm initial, final = 36.656682 0.095425151 Force max component initial, final = 13.283276 0.015434861 Final line search alpha, max atom move = 1.0000000 0.015434861 Iterations, force evaluations = 60 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1904 | 3.1904 | 3.1904 | 0.0 | 99.39 Neigh | 0.0044497 | 0.0044497 | 0.0044497 | 0.0 | 0.14 Comm | 0.0083093 | 0.0083093 | 0.0083093 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006836 | | | 0.21 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2971.00 ave 2971 max 2971 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: 24544.0 ave 24544 max 24544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24544 Ave neighs/atom = 77.670886 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 4 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.435 | 4.435 | 4.435 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1400.5312 0 -1400.5312 -12289.087 3489.4126 64 0 -1400.6015 0 -1400.6015 -2065.7264 3469.9994 Loop time of 0.170401 on 1 procs for 4 steps with 316 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 = -1400.53124990562 -1400.60097845108 -1400.60151232213 Force two-norm initial, final = 35.265783 0.16257865 Force max component initial, final = 25.641843 0.051343723 Final line search alpha, max atom move = 0.00086695489 4.4512692e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16874 | 0.16874 | 0.16874 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042018 | 0.00042018 | 0.00042018 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001242 | | | 0.73 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2956.00 ave 2956 max 2956 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: 24548.0 ave 24548 max 24548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24548 Ave neighs/atom = 77.683544 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1400.6015 0 -1400.6015 -2065.7264 Loop time of 6.435e-06 on 1 procs for 0 steps with 316 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2956.00 ave 2956 max 2956 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: 24564.0 ave 24564 max 24564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24564 Ave neighs/atom = 77.734177 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 ghost atom cutoff = 6 binsize = 3, bins = 4 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.573 | 4.573 | 4.573 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 -1400.6015 -1400.6015 11.107808 89.05678 3.5077939 -2065.7264 -2065.7264 -19.751873 -6169.41 -8.017496 2.3032269 163.89046 Loop time of 6.715e-06 on 1 procs for 0 steps with 316 atoms 223.4% 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 | | 6.715e-06 | | |100.00 Nlocal: 316.000 ave 316 max 316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2956.00 ave 2956 max 2956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12282.0 ave 12282 max 12282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24564.0 ave 24564 max 24564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24564 Ave neighs/atom = 77.734177 Neighbor list builds = 0 Dangerous builds = 0 316 -1400.60151232213 eV 2.30322694221552 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03