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 = 2.8553246 2.8553246 2.8553246 Created orthogonal box = (0.0000000 -56.532543 0.0000000) to (34.618971 56.532543 6.9940884) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0035545 4.0380388 4.6627256 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -56.532543 0.0000000) to (34.618971 56.532543 6.9940884) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0035545 4.0380388 4.6627256 Created 1182 atoms using lattice units in orthogonal box = (0.0000000 -56.532543 0.0000000) to (34.618971 56.532543 6.9940884) create_atoms CPU = 0.001 seconds 1182 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2352 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_267721408934_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.492 | 6.492 | 6.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6591.5631 0 -6591.5631 243580.66 86 0 -9656.0011 0 -9656.0011 7596.1349 Loop time of 2.45386 on 1 procs for 86 steps with 2352 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6591.56314817498 -9655.99303059365 -9656.00106406121 Force two-norm initial, final = 5070.1179 0.39455985 Force max component initial, final = 710.33151 0.053051100 Final line search alpha, max atom move = 1.0000000 0.053051100 Iterations, force evaluations = 86 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3603 | 2.3603 | 2.3603 | 0.0 | 96.19 Neigh | 0.06474 | 0.06474 | 0.06474 | 0.0 | 2.64 Comm | 0.013779 | 0.013779 | 0.013779 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01506 | | | 0.61 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9830.00 ave 9830 max 9830 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: 391632.0 ave 391632 max 391632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391632 Ave neighs/atom = 166.51020 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.111 | 6.111 | 6.111 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -9656.0011 0 -9656.0011 7596.1349 27376.24 93 0 -9656.6555 0 -9656.6555 31.301731 27496.467 Loop time of 0.161053 on 1 procs for 7 steps with 2352 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 = -9656.00106406125 -9656.65533850082 -9656.6555311689 Force two-norm initial, final = 264.03683 1.8834787 Force max component initial, final = 242.24549 1.7105782 Final line search alpha, max atom move = 0.00020458089 0.00034995161 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15639 | 0.15639 | 0.15639 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00072596 | 0.00072596 | 0.00072596 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003935 | | | 2.44 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9869.00 ave 9869 max 9869 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: 391644.0 ave 391644 max 391644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391644 Ave neighs/atom = 166.51531 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.249 | 6.249 | 6.249 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9656.6555 0 -9656.6555 31.301731 Loop time of 1.861e-06 on 1 procs for 0 steps with 2352 atoms 161.2% 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 | | 1.861e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9857.00 ave 9857 max 9857 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: 391440.0 ave 391440 max 391440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391440 Ave neighs/atom = 166.42857 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.249 | 6.249 | 6.249 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 -9656.6555 -9656.6555 34.589071 113.72734 6.9899344 31.301731 31.301731 -16.631249 10.9229 99.613542 2.2361249 963.01794 Loop time of 2.168e-06 on 1 procs for 0 steps with 2352 atoms 230.6% 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 | | 2.168e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9857.00 ave 9857 max 9857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 195720.0 ave 195720 max 195720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 391440.0 ave 391440 max 391440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391440 Ave neighs/atom = 166.42857 Neighbor list builds = 0 Dangerous builds = 0 2352 -9656.6555311689 eV 2.23612488587759 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03