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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -51.432597 0.0000000) to (36.368338 51.432597 5.7147330) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7348775 6.9846737 5.7147330 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.432597 0.0000000) to (36.368338 51.432597 5.7147330) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7348775 6.9846737 5.7147330 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.432597 0.0000000) to (36.368338 51.432597 5.7147330) create_atoms CPU = 0.001 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1292 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.886 | 5.886 | 5.886 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4913.4773 0 -4913.4773 14985.338 80 0 -5037.9521 0 -5037.9521 345.22993 Loop time of 2.39386 on 1 procs for 80 steps with 1292 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 = -4913.47728651789 -5037.94728221949 -5037.95212147487 Force two-norm initial, final = 198.67889 0.18501917 Force max component initial, final = 64.981589 0.029239609 Final line search alpha, max atom move = 1.0000000 0.029239609 Iterations, force evaluations = 80 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3253 | 2.3253 | 2.3253 | 0.0 | 97.14 Neigh | 0.049484 | 0.049484 | 0.049484 | 0.0 | 2.07 Comm | 0.010538 | 0.010538 | 0.010538 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008544 | | | 0.36 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8884.00 ave 8884 max 8884 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: 319024.0 ave 319024 max 319024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319024 Ave neighs/atom = 246.92260 Neighbor list builds = 3 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.886 | 5.886 | 5.886 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -5037.9521 0 -5037.9521 345.22993 21379.023 82 0 -5037.9673 0 -5037.9673 194.31867 21383.088 Loop time of 0.0731568 on 1 procs for 2 steps with 1292 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 = -5037.95212147489 -5037.96473349934 -5037.96732264342 Force two-norm initial, final = 19.640343 5.5190302 Force max component initial, final = 19.128245 5.1534301 Final line search alpha, max atom move = 0.00013699628 0.00070600074 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071888 | 0.071888 | 0.071888 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026941 | 0.00026941 | 0.00026941 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009994 | | | 1.37 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8893.00 ave 8893 max 8893 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: 319040.0 ave 319040 max 319040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319040 Ave neighs/atom = 246.93498 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.036 | 6.036 | 6.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5037.9673 0 -5037.9673 194.31867 Loop time of 1.776e-06 on 1 procs for 0 steps with 1292 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10087.0 ave 10087 max 10087 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: 318968.0 ave 318968 max 318968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318968 Ave neighs/atom = 246.87926 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 6.036 | 6.036 | 6.036 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 -5037.9673 -5037.9673 36.355499 102.98597 5.7111325 194.31867 194.31867 132.97215 386.58585 63.39801 2.6468558 609.28277 Loop time of 2.275e-06 on 1 procs for 0 steps with 1292 atoms 219.8% 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 | | 2.275e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10087.0 ave 10087 max 10087 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159484.0 ave 159484 max 159484 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318968.0 ave 318968 max 318968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318968 Ave neighs/atom = 246.87926 Neighbor list builds = 0 Dangerous builds = 0 1292 -5037.96732264342 eV 2.64685577285812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02