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 = 3.6150002 3.6150002 3.6150002 Created orthogonal box = (0.0000000 -46.294590 0.0000000) to (23.147295 46.294590 3.6150002) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0811136 5.0811136 3.6150002 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -46.294590 0.0000000) to (23.147295 46.294590 3.6150002) create_atoms CPU = 0.002 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0811136 5.0811136 3.6150002 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -46.294590 0.0000000) to (23.147295 46.294590 3.6150002) create_atoms CPU = 0.001 seconds 330 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 25 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_020851069572_000#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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.937 | 4.937 | 4.937 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2244.707 0 -2244.707 25083.615 64 0 -2323.1136 0 -2323.1136 8235.3191 Loop time of 1.42215 on 1 procs for 64 steps with 658 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 = -2244.70704817888 -2323.1114341156 -2323.11359065664 Force two-norm initial, final = 60.579917 0.15005263 Force max component initial, final = 9.1794101 0.039139180 Final line search alpha, max atom move = 1.0000000 0.039139180 Iterations, force evaluations = 64 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3794 | 1.3794 | 1.3794 | 0.0 | 96.99 Neigh | 0.012926 | 0.012926 | 0.012926 | 0.0 | 0.91 Comm | 0.017609 | 0.017609 | 0.017609 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01225 | | | 0.86 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5787.00 ave 5787 max 5787 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: 110296.0 ave 110296 max 110296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110296 Ave neighs/atom = 167.62310 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.932 | 4.932 | 4.932 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -2323.1136 0 -2323.1136 8235.3191 7747.6289 71 0 -2323.3279 0 -2323.3279 -194.2044 7794.5015 Loop time of 0.118007 on 1 procs for 7 steps with 658 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 = -2323.11359065664 -2323.32763236857 -2323.32787109604 Force two-norm initial, final = 78.447816 1.9906443 Force max component initial, final = 65.015998 1.7339904 Final line search alpha, max atom move = 0.00050316121 0.00087247670 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11283 | 0.11283 | 0.11283 | 0.0 | 95.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001201 | 0.001201 | 0.001201 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003975 | | | 3.37 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5702.00 ave 5702 max 5702 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: 111272.0 ave 111272 max 111272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111272 Ave neighs/atom = 169.10638 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.070 | 5.070 | 5.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2323.3279 0 -2323.3279 -194.2044 Loop time of 6.134e-06 on 1 procs for 0 steps with 658 atoms 179.3% 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 | | 6.134e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5717.00 ave 5717 max 5717 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: 108064.0 ave 108064 max 108064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108064 Ave neighs/atom = 164.23100 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.070 | 5.070 | 5.070 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 -2323.3279 -2323.3279 23.098032 93.076266 3.6255543 -194.2044 -194.2044 -194.70656 -358.3005 -29.606139 2.3008779 154.81293 Loop time of 6.595e-06 on 1 procs for 0 steps with 658 atoms 257.8% 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 | | 6.595e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5717.00 ave 5717 max 5717 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54032.0 ave 54032 max 54032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108064.0 ave 108064 max 108064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108064 Ave neighs/atom = 164.23100 Neighbor list builds = 0 Dangerous builds = 0 658 -2323.32787109604 eV 2.3008779172575 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01