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 = 4.2107185 4.2107185 4.2107185 Created orthogonal box = (0.0000000 -52.083712 0.0000000) to (17.361237 52.083712 4.2107185) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1062463 5.1062463 4.2107185 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -52.083712 0.0000000) to (17.361237 52.083712 4.2107185) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1062463 5.1062463 4.2107185 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -52.083712 0.0000000) to (17.361237 52.083712 4.2107185) create_atoms CPU = 0.001 seconds 206 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 ghost atom cutoff = 9 binsize = 4.5, bins = 4 24 1 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 410 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_137572817842_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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 4 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1783.0279 0 -1783.0279 -250294.73 31 0 -45867.438 0 -45867.438 -188285.77 Loop time of 1.67204 on 1 procs for 31 steps with 410 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -1783.02792927362 -45867.438462323 -45867.438462323 Force two-norm initial, final = 1081.3441 23256.516 Force max component initial, final = 312.90173 8857.9444 Final line search alpha, max atom move = 3.3818237e-17 2.9956006e-13 Iterations, force evaluations = 31 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6187 | 1.6187 | 1.6187 | 0.0 | 96.81 Neigh | 0.020508 | 0.020508 | 0.020508 | 0.0 | 1.23 Comm | 0.021182 | 0.021182 | 0.021182 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01161 | | | 0.69 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4939.00 ave 4939 max 4939 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: 71996.0 ave 71996 max 71996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71996 Ave neighs/atom = 175.60000 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 4 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.491 | 4.491 | 4.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -45867.438 0 -45867.438 -188285.77 7614.9808 35 0 -46018.45 0 -46018.45 -174576.02 7588.5461 Loop time of 0.720358 on 1 procs for 4 steps with 410 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -45867.4384623243 -46018.4498201933 -46018.4498201933 Force two-norm initial, final = 23308.270 15944.896 Force max component initial, final = 8857.9444 5154.0118 Final line search alpha, max atom move = 3.1905386e-17 1.6444073e-13 Iterations, force evaluations = 4 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68927 | 0.68927 | 0.68927 | 0.0 | 95.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0080741 | 0.0080741 | 0.0080741 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02301 | | | 3.19 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4939.00 ave 4939 max 4939 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: 72000.0 ave 72000 max 72000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72000 Ave neighs/atom = 175.60976 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 ghost atom cutoff = 9 binsize = 4.5, bins = 4 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -46018.45 0 -46018.45 -174576.02 Loop time of 6.264e-06 on 1 procs for 0 steps with 410 atoms 175.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4939.00 ave 4939 max 4939 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: 72020.0 ave 72020 max 72020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72020 Ave neighs/atom = 175.65854 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 ghost atom cutoff = 9 binsize = 4.5, bins = 4 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.629 | 4.629 | 4.629 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 -46018.45 -46018.45 17.342177 104.04001 4.2058577 -174576.02 -174576.02 -161910.23 -192356.3 -169461.55 0.0025927511 352.64945 Loop time of 6.886e-06 on 1 procs for 0 steps with 410 atoms 246.9% 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 | | 6.886e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4939.00 ave 4939 max 4939 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36010.0 ave 36010 max 36010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72020.0 ave 72020 max 72020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72020 Ave neighs/atom = 175.65854 Neighbor list builds = 0 Dangerous builds = 0 410 -45979.0696563933 eV 0.00259275114858496 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02