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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.239259 0.0000000) to (27.746346 39.239259 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1382123 5.3287883 4.3599177 Created 324 atoms using lattice units in orthogonal box = (0.0000000 -39.239259 0.0000000) to (27.746346 39.239259 4.3599177) create_atoms CPU = 0.001 seconds 324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1382123 5.3287883 4.3599177 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -39.239259 0.0000000) to (27.746346 39.239259 4.3599177) create_atoms CPU = 0.001 seconds 326 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 1 atoms, new total = 649 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.271 | 5.271 | 5.271 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2331.7357 0 -2331.7357 443075.83 152 0 -4201.6796 0 -4201.6796 11200.335 Loop time of 59.8377 on 1 procs for 152 steps with 649 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 = -2331.73572131872 -4201.67588614834 -4201.6795563364 Force two-norm initial, final = 6047.6390 0.29510746 Force max component initial, final = 3057.2774 0.094229570 Final line search alpha, max atom move = 1.0000000 0.094229570 Iterations, force evaluations = 152 280 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 59.701 | 59.701 | 59.701 | 0.0 | 99.77 Neigh | 0.11124 | 0.11124 | 0.11124 | 0.0 | 0.19 Comm | 0.013833 | 0.013833 | 0.013833 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01192 | | | 0.02 Nlocal: 649.000 ave 649 max 649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4431.00 ave 4431 max 4431 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: 49186.0 ave 49186 max 49186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49186 Ave neighs/atom = 75.787365 Neighbor list builds = 4 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 152 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.653 | 5.653 | 5.653 Mbytes Step Temp E_pair E_mol TotEng Press Volume 152 0 -4201.6796 0 -4201.6796 11200.335 9493.6866 158 0 -4202.0429 0 -4202.0429 179.67167 9541.8649 Loop time of 1.52487 on 1 procs for 6 steps with 649 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 = -4201.67955633639 -4202.04184597121 -4202.0429397436 Force two-norm initial, final = 139.32128 2.0644719 Force max component initial, final = 123.88797 1.2698897 Final line search alpha, max atom move = 0.00018802694 0.00023877348 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5231 | 1.5231 | 1.5231 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028876 | 0.00028876 | 0.00028876 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001484 | | | 0.10 Nlocal: 649.000 ave 649 max 649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4417.00 ave 4417 max 4417 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: 50146.0 ave 50146 max 50146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50146 Ave neighs/atom = 77.266564 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.791 | 5.791 | 5.791 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4202.0429 0 -4202.0429 179.67167 Loop time of 2.094e-06 on 1 procs for 0 steps with 649 atoms 191.0% 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 | | 2.094e-06 | | |100.00 Nlocal: 649.000 ave 649 max 649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4399.00 ave 4399 max 4399 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: 49486.0 ave 49486 max 49486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49486 Ave neighs/atom = 76.249615 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.791 | 5.791 | 5.791 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 -4202.0429 -4202.0429 27.888801 78.622257 4.3516896 179.67167 179.67167 214.32219 180.05166 144.64116 2.4699768 2470.2086 Loop time of 2.182e-06 on 1 procs for 0 steps with 649 atoms 137.5% 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 | | 2.182e-06 | | |100.00 Nlocal: 649.000 ave 649 max 649 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4399.00 ave 4399 max 4399 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24743.0 ave 24743 max 24743 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 49486.0 ave 49486 max 49486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49486 Ave neighs/atom = 76.249615 Neighbor list builds = 0 Dangerous builds = 0 649 -4202.0429397436 eV 2.4699768477182 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:02