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 = 3.1674131 3.1674131 3.1674131 Created orthogonal box = (0.0000000 -60.596181 0.0000000) to (34.985221 60.596181 5.4861205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1617540 4.6357734 5.4861205 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -60.596181 0.0000000) to (34.985221 60.596181 5.4861205) create_atoms CPU = 0.002 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1617540 4.6357734 5.4861205 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -60.596181 0.0000000) to (34.985221 60.596181 5.4861205) create_atoms CPU = 0.001 seconds 734 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 31 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 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1466 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_269937397263_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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9838.0486 0 -9838.0486 16525.834 59 0 -9953.7685 0 -9953.7685 5873.5938 Loop time of 14.808 on 1 procs for 59 steps with 1466 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 = -9838.04862073541 -9953.76001577955 -9953.76852812858 Force two-norm initial, final = 73.222796 0.31333769 Force max component initial, final = 14.045731 0.054490707 Final line search alpha, max atom move = 0.40010361 0.021801929 Iterations, force evaluations = 59 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.781 | 14.781 | 14.781 | 0.0 | 99.82 Neigh | 0.011868 | 0.011868 | 0.011868 | 0.0 | 0.08 Comm | 0.0079619 | 0.0079619 | 0.0079619 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007546 | | | 0.05 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7922.00 ave 7922 max 7922 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: 198232.0 ave 198232 max 198232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198232 Ave neighs/atom = 135.21965 Neighbor list builds = 1 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.501 | 5.501 | 5.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -9953.7685 0 -9953.7685 5873.5938 23260.83 63 0 -9954.0512 0 -9954.0512 -490.65501 23321.171 Loop time of 0.811617 on 1 procs for 4 steps with 1466 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 = -9953.7685281286 -9954.04681479484 -9954.05123628401 Force two-norm initial, final = 180.53527 14.121348 Force max component initial, final = 164.49752 12.172892 Final line search alpha, max atom move = 5.4868003e-05 0.00066790227 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.80963 | 0.80963 | 0.80963 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035723 | 0.00035723 | 0.00035723 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001633 | | | 0.20 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8182.00 ave 8182 max 8182 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: 198308.0 ave 198308 max 198308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198308 Ave neighs/atom = 135.27149 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.639 | 5.639 | 5.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9954.0512 0 -9954.0512 -490.65501 Loop time of 1.584e-06 on 1 procs for 0 steps with 1466 atoms 189.4% 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 | | 1.584e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8174.00 ave 8174 max 8174 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: 198156.0 ave 198156 max 198156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198156 Ave neighs/atom = 135.16780 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 = 7.9 ghost atom cutoff = 7.9 binsize = 3.95, bins = 9 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.9 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) = 5.639 | 5.639 | 5.639 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 -9954.0512 -9954.0512 35.004294 121.59726 5.4790495 -490.65501 -490.65501 -457.79567 -178.96326 -835.20608 2.4973885 536.13603 Loop time of 2.016e-06 on 1 procs for 0 steps with 1466 atoms 644.8% 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 | | 2.016e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8174.00 ave 8174 max 8174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 99078.0 ave 99078 max 99078 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 198156.0 ave 198156 max 198156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 198156 Ave neighs/atom = 135.16780 Neighbor list builds = 0 Dangerous builds = 0 1466 -9954.05123628401 eV 2.49738845104558 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16