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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -74.583720 0.0000000) to (37.289838 74.583720 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7031516 5.7031516 4.0446508 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -74.583720 0.0000000) to (37.289838 74.583720 4.0446508) create_atoms CPU = 0.003 seconds 681 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7031516 5.7031516 4.0446508 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -74.583720 0.0000000) to (37.289838 74.583720 4.0446508) create_atoms CPU = 0.002 seconds 681 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1356 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_616482358807_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4521.5428 0 -4521.5428 5213.8341 90 0 -4550.1396 0 -4550.1396 -938.70596 Loop time of 16.6209 on 1 procs for 90 steps with 1356 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 = -4521.54276301569 -4550.13548540746 -4550.13961069013 Force two-norm initial, final = 20.395227 0.16002811 Force max component initial, final = 5.2131516 0.037977410 Final line search alpha, max atom move = 1.0000000 0.037977410 Iterations, force evaluations = 90 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.525 | 16.525 | 16.525 | 0.0 | 99.42 Neigh | 0.045849 | 0.045849 | 0.045849 | 0.0 | 0.28 Comm | 0.024624 | 0.024624 | 0.024624 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02575 | | | 0.15 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6612.00 ave 6612 max 6612 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: 103738.0 ave 103738 max 103738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103738 Ave neighs/atom = 76.502950 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.048 | 5.048 | 5.048 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -4550.1396 0 -4550.1396 -938.70596 22498.085 92 0 -4550.1497 0 -4550.1497 -51.244735 22472.758 Loop time of 0.567537 on 1 procs for 2 steps with 1356 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 = -4550.13961069013 -4550.14852398321 -4550.1496687258 Force two-norm initial, final = 20.421087 0.16118467 Force max component initial, final = 17.905516 0.036035456 Final line search alpha, max atom move = 0.00029816878 1.0744648e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56436 | 0.56436 | 0.56436 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00073677 | 0.00073677 | 0.00073677 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002444 | | | 0.43 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6572.00 ave 6572 max 6572 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: 104100.0 ave 104100 max 104100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104100 Ave neighs/atom = 76.769912 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.186 | 5.186 | 5.186 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4550.1497 0 -4550.1497 -51.244735 Loop time of 6.335e-06 on 1 procs for 0 steps with 1356 atoms 173.6% 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 | | 6.335e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6572.00 ave 6572 max 6572 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: 104106.0 ave 104106 max 104106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104106 Ave neighs/atom = 76.774336 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 46 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.186 | 5.186 | 5.186 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 -4550.1497 -4550.1497 37.289507 149.16744 4.0401334 -51.244735 -51.244735 -1.2679066 -152.59312 0.12682336 2.5565635 173.86011 Loop time of 6.986e-06 on 1 procs for 0 steps with 1356 atoms 272.0% 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 | | 6.986e-06 | | |100.00 Nlocal: 1356.00 ave 1356 max 1356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6572.00 ave 6572 max 6572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52053.0 ave 52053 max 52053 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104106.0 ave 104106 max 104106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104106 Ave neighs/atom = 76.774336 Neighbor list builds = 0 Dangerous builds = 0 1356 -4550.1496687258 eV 2.55656347320457 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18