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 = 3.6390875 3.6390875 3.6390875 Created orthogonal box = (0.0000000 -50.029182 0.0000000) to (13.616219 50.029182 8.9139075) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8355223 5.5587980 5.9426050 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -50.029182 0.0000000) to (13.616219 50.029182 8.9139075) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8355223 5.5587980 5.9426050 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -50.029182 0.0000000) to (13.616219 50.029182 8.9139075) create_atoms CPU = 0.001 seconds 508 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 3 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1008 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_945691923444_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3229.0415 0 -3229.0415 34623.05 38 0 -3296.1867 0 -3296.1867 5389.0627 Loop time of 0.678052 on 1 procs for 38 steps with 1008 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 = -3229.04154750148 -3296.18471651254 -3296.18669182623 Force two-norm initial, final = 183.36027 0.10633399 Force max component initial, final = 44.039347 0.0068892899 Final line search alpha, max atom move = 1.0000000 0.0068892899 Iterations, force evaluations = 38 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67089 | 0.67089 | 0.67089 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.003618 | 0.003618 | 0.003618 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003546 | | | 0.52 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6021.00 ave 6021 max 6021 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: 177488.0 ave 177488 max 177488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177488 Ave neighs/atom = 176.07937 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -3296.1867 0 -3296.1867 5389.0627 12144.455 44 0 -3296.3498 0 -3296.3498 1.7292814 12189.815 Loop time of 0.0883684 on 1 procs for 6 steps with 1008 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 = -3296.18669182624 -3296.34974062681 -3296.34981174148 Force two-norm initial, final = 81.417051 0.20899406 Force max component initial, final = 73.527822 0.096627944 Final line search alpha, max atom move = 0.00064289179 6.2121312e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085682 | 0.085682 | 0.085682 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043326 | 0.00043326 | 0.00043326 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002253 | | | 2.55 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5972.00 ave 5972 max 5972 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: 176848.0 ave 176848 max 176848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176848 Ave neighs/atom = 175.44444 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3296.3498 0 -3296.3498 1.7292814 Loop time of 9.02e-06 on 1 procs for 0 steps with 1008 atoms 133.0% 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 | | 9.02e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5972.00 ave 5972 max 5972 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: 176768.0 ave 176768 max 176768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176768 Ave neighs/atom = 175.36508 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.190 | 5.190 | 5.190 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 -3296.3498 -3296.3498 13.613069 100.53931 8.9064605 1.7292814 1.7292814 -8.2571772 0.75527348 12.689748 2.2776712 401.93387 Loop time of 2.341e-06 on 1 procs for 0 steps with 1008 atoms 213.6% 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 | | 2.341e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5972.00 ave 5972 max 5972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88384.0 ave 88384 max 88384 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176768.0 ave 176768 max 176768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176768 Ave neighs/atom = 175.36508 Neighbor list builds = 0 Dangerous builds = 0 1008 -3296.34981174148 eV 2.27767117531347 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01