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 = 3.1692585 3.1692585 3.1692585 Created orthogonal box = (0.0000000 -60.631485 0.0000000) to (35.005604 60.631485 5.4893167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1647613 4.6384743 5.4893167 Created 732 atoms using lattice units in orthogonal box = (0.0000000 -60.631485 0.0000000) to (35.005604 60.631485 5.4893167) create_atoms CPU = 0.002 seconds 732 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1647613 4.6384743 5.4893167 Created 734 atoms using lattice units in orthogonal box = (0.0000000 -60.631485 0.0000000) to (35.005604 60.631485 5.4893167) 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 37 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 6.6 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_014123846623_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.690 | 4.690 | 4.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15695.752 0 -15695.752 25045.419 25 0 -15867.668 0 -15867.668 9086.1169 Loop time of 18.2235 on 1 procs for 25 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 = -15695.7516301145 -15867.6557468065 -15867.6684741992 Force two-norm initial, final = 183.24318 0.39211003 Force max component initial, final = 60.932968 0.050889913 Final line search alpha, max atom move = 1.0000000 0.050889913 Iterations, force evaluations = 25 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.206 | 18.206 | 18.206 | 0.0 | 99.91 Neigh | 0.0081094 | 0.0081094 | 0.0081094 | 0.0 | 0.04 Comm | 0.0043523 | 0.0043523 | 0.0043523 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004558 | | | 0.03 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6014.00 ave 6014 max 6014 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: 94260.0 ave 94260 max 94260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94260 Ave neighs/atom = 64.297408 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.690 | 4.690 | 4.690 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -15867.668 0 -15867.668 9086.1169 23301.51 29 0 -15867.981 0 -15867.981 -2.6745683 23382.603 Loop time of 3.11893 on 1 procs for 4 steps with 1466 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 = -15867.6684741992 -15867.9796354264 -15867.9807364405 Force two-norm initial, final = 240.95856 0.79097396 Force max component initial, final = 190.29586 0.56236714 Final line search alpha, max atom move = 6.5223308e-05 3.6679445e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1164 | 3.1164 | 3.1164 | 0.0 | 99.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042211 | 0.00042211 | 0.00042211 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002059 | | | 0.07 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6015.00 ave 6015 max 6015 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: 94256.0 ave 94256 max 94256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94256 Ave neighs/atom = 64.294679 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.828 | 4.828 | 4.828 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15867.981 0 -15867.981 -2.6745683 Loop time of 3.254e-06 on 1 procs for 0 steps with 1466 atoms 184.4% 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 | | 3.254e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6013.00 ave 6013 max 6013 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: 94220.0 ave 94220 max 94220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94220 Ave neighs/atom = 64.270123 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.828 | 4.828 | 4.828 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 -15867.981 -15867.981 34.998933 121.6108 5.4937121 -2.6745683 -2.6745683 23.392152 7.1484066 -38.564263 2.5249155 562.155 Loop time of 1.949e-06 on 1 procs for 0 steps with 1466 atoms 205.2% 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 | | 1.949e-06 | | |100.00 Nlocal: 1466.00 ave 1466 max 1466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6013.00 ave 6013 max 6013 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47110.0 ave 47110 max 47110 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94220.0 ave 94220 max 94220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94220 Ave neighs/atom = 64.270123 Neighbor list builds = 0 Dangerous builds = 0 1466 -8018.12878969635 eV 2.52491548942069 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23