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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -47.158526 0.0000000) to (22.230742 47.158526 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6801562 5.7913979 5.1000820 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -47.158526 0.0000000) to (22.230742 47.158526 5.1000820) create_atoms CPU = 0.001 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6801562 5.7913979 5.1000820 Created 463 atoms using lattice units in orthogonal box = (0.0000000 -47.158526 0.0000000) to (22.230742 47.158526 5.1000820) create_atoms CPU = 0.001 seconds 463 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 912 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.688 | 6.688 | 6.688 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3734.375 0 -3734.375 25523.767 21 0 -3808.5445 0 -3808.5445 7734.4204 Loop time of 1.06983 on 1 procs for 21 steps with 912 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3734.37504966873 -3808.54115669477 -3808.5444620433 Force two-norm initial, final = 97.920015 0.23819325 Force max component initial, final = 17.232407 0.019789207 Final line search alpha, max atom move = 1.0000000 0.019789207 Iterations, force evaluations = 21 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.06 | 1.06 | 1.06 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.006557 | 0.006557 | 0.006557 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003302 | | | 0.31 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12676.0 ave 12676 max 12676 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: 569590.0 ave 569590 max 569590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 569590 Ave neighs/atom = 624.55044 Neighbor list builds = 0 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.688 | 6.688 | 6.688 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -3808.5445 0 -3808.5445 7734.4204 10693.536 27 0 -3808.7755 0 -3808.7755 -329.87765 10743.497 Loop time of 0.224943 on 1 procs for 6 steps with 912 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 = -3808.54446204328 -3808.77328842354 -3808.77546504905 Force two-norm initial, final = 108.18289 4.5148878 Force max component initial, final = 101.00646 3.9280807 Final line search alpha, max atom move = 0.00012625028 0.00049592128 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22069 | 0.22069 | 0.22069 | 0.0 | 98.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008241 | 0.0008241 | 0.0008241 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003431 | | | 1.53 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12676.0 ave 12676 max 12676 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: 566620.0 ave 566620 max 566620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 566620 Ave neighs/atom = 621.29386 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.827 | 6.827 | 6.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3808.7755 0 -3808.7755 -329.87765 Loop time of 1.926e-06 on 1 procs for 0 steps with 912 atoms 155.8% 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 | | 1.926e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12724.0 ave 12724 max 12724 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: 565362.0 ave 565362 max 565362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 565362 Ave neighs/atom = 619.91447 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 4 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 6.827 | 6.827 | 6.827 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 -3808.7755 -3808.7755 22.209643 94.769002 5.1043187 -329.87765 -329.87765 -585.23825 -310.65201 -93.742687 2.3094352 501.26647 Loop time of 2.386e-06 on 1 procs for 0 steps with 912 atoms 293.4% 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 | | 2.386e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12724.0 ave 12724 max 12724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 282681.0 ave 282681 max 282681 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 565362.0 ave 565362 max 565362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 565362 Ave neighs/atom = 619.91447 Neighbor list builds = 0 Dangerous builds = 0 912 -3808.77546504905 eV 2.30943516636616 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01