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 = 3.5898365 3.5898365 3.5898365 Created orthogonal box = (0.0000000 -40.135592 0.0000000) to (8.0271184 40.135592 3.5898365) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8162710 4.8162710 3.5898365 Created 100 atoms using lattice units in orthogonal box = (0.0000000 -40.135592 0.0000000) to (8.0271184 40.135592 3.5898365) create_atoms CPU = 0.001 seconds 100 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8162710 4.8162710 3.5898365 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -40.135592 0.0000000) to (8.0271184 40.135592 3.5898365) create_atoms CPU = 0.000 seconds 102 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 3 22 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 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 200 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_115316750986_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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 3 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -674.87936 0 -674.87936 40264.603 18 0 -699.6796 0 -699.6796 11788.433 Loop time of 0.124489 on 1 procs for 18 steps with 200 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 = -674.879360556021 -699.679127202164 -699.679598111083 Force two-norm initial, final = 83.409894 0.064720036 Force max component initial, final = 29.486855 0.0076219299 Final line search alpha, max atom move = 1.0000000 0.0076219299 Iterations, force evaluations = 18 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12255 | 0.12255 | 0.12255 | 0.0 | 98.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011695 | 0.0011695 | 0.0011695 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007693 | | | 0.62 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3601.00 ave 3601 max 3601 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: 35008.0 ave 35008 max 35008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35008 Ave neighs/atom = 175.04000 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 3 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -699.6796 0 -699.6796 11788.433 2313.0978 30 0 -699.83087 0 -699.83087 202.28317 2332.85 Loop time of 0.0972328 on 1 procs for 12 steps with 200 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -699.679598111083 -699.830767501188 -699.830872254254 Force two-norm initial, final = 34.140769 0.60667267 Force max component initial, final = 30.671550 0.41868005 Final line search alpha, max atom move = 0.0028723337 0.0012025888 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.092853 | 0.092853 | 0.092853 | 0.0 | 95.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080925 | 0.00080925 | 0.00080925 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003571 | | | 3.67 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3601.00 ave 3601 max 3601 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: 33936.0 ave 33936 max 33936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33936 Ave neighs/atom = 169.68000 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 3 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.577 | 4.577 | 4.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -699.83087 0 -699.83087 202.28317 Loop time of 3.599e-06 on 1 procs for 0 steps with 200 atoms 138.9% 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 | | 3.599e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3601.00 ave 3601 max 3601 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: 32800.0 ave 32800 max 32800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32800 Ave neighs/atom = 164.00000 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 = 7.6187641 ghost atom cutoff = 7.6187641 binsize = 3.809382, bins = 3 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.618764085891188 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) = 4.577 | 4.577 | 4.577 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 -699.83087 -699.83087 8.0211182 81.126626 3.5849944 202.28317 202.28317 192.00847 290.60934 124.23171 2.3111359 122.89095 Loop time of 3.665e-06 on 1 procs for 0 steps with 200 atoms 136.4% 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 | | 3.665e-06 | | |100.00 Nlocal: 200.000 ave 200 max 200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3601.00 ave 3601 max 3601 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 16400.0 ave 16400 max 16400 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32800.0 ave 32800 max 32800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32800 Ave neighs/atom = 164.00000 Neighbor list builds = 0 Dangerous builds = 0 200 -699.830872254254 eV 2.31113585968656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00