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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110986) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3791002 4.3791002 3.6110986 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110986) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3791002 4.3791002 3.6110986 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -44.666822 0.0000000) to (14.888941 44.666822 3.6110986) 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 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 2 atoms, new total = 408 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_321233176498_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 = 5 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) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.5421 0 -1669.5421 37388.52 53 0 -1723.7206 0 -1723.7206 8418.265 Loop time of 3.5 on 1 procs for 53 steps with 408 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 = -1669.54206869693 -1723.71908077766 -1723.72057042608 Force two-norm initial, final = 130.75758 0.098708969 Force max component initial, final = 43.448250 0.014459078 Final line search alpha, max atom move = 1.0000000 0.014459078 Iterations, force evaluations = 53 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4805 | 3.4805 | 3.4805 | 0.0 | 99.44 Neigh | 0.0049606 | 0.0049606 | 0.0049606 | 0.0 | 0.14 Comm | 0.0076033 | 0.0076033 | 0.0076033 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006931 | | | 0.20 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 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: 31604.0 ave 31604 max 31604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31604 Ave neighs/atom = 77.460784 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 = 5 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.450 | 4.450 | 4.450 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1723.7206 0 -1723.7206 8418.265 4803.062 61 0 -1723.816 0 -1723.816 -54.772032 4826.7531 Loop time of 0.388348 on 1 procs for 8 steps with 408 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 = -1723.72057042608 -1723.81531546827 -1723.81602306392 Force two-norm initial, final = 44.618210 1.1003339 Force max component initial, final = 32.507464 0.71287094 Final line search alpha, max atom move = 0.00029334251 0.00020911535 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38479 | 0.38479 | 0.38479 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079609 | 0.00079609 | 0.00079609 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002766 | | | 0.71 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 31600.0 ave 31600 max 31600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31600 Ave neighs/atom = 77.450980 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 = 5 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1723.816 0 -1723.816 -54.772032 Loop time of 6.566e-06 on 1 procs for 0 steps with 408 atoms 182.8% 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 | | 6.566e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 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: 31632.0 ave 31632 max 31632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31632 Ave neighs/atom = 77.529412 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 = 5 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) = 4.588 | 4.588 | 4.588 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 -1723.816 -1723.816 14.869587 89.254848 3.6368413 -54.772032 -54.772032 -148.4994 -236.41931 220.60262 2.2962884 186.32506 Loop time of 6.926e-06 on 1 procs for 0 steps with 408 atoms 245.5% 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 | | 6.926e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2960.00 ave 2960 max 2960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15816.0 ave 15816 max 15816 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31632.0 ave 31632 max 31632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31632 Ave neighs/atom = 77.529412 Neighbor list builds = 0 Dangerous builds = 0 408 -1723.81602306392 eV 2.29628840129855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04