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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -59.522392 0.0000000) to (21.044344 59.522392 5.7275449) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4559409 6.6135992 5.7275449 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -59.522392 0.0000000) to (21.044344 59.522392 5.7275449) create_atoms CPU = 0.005 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4559409 6.6135992 5.7275449 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -59.522392 0.0000000) to (21.044344 59.522392 5.7275449) create_atoms CPU = 0.003 seconds 434 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 ghost atom cutoff = 6 binsize = 3, bins = 8 40 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 866 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_022920256108_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 8 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2815.5152 0 -2815.5152 16240.893 37 0 -2895.6566 0 -2895.6566 5292.3492 Loop time of 2.11395 on 1 procs for 37 steps with 866 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 = -2815.51515787247 -2895.65383766845 -2895.65663699577 Force two-norm initial, final = 105.22024 0.16586844 Force max component initial, final = 31.449216 0.029907598 Final line search alpha, max atom move = 1.0000000 0.029907598 Iterations, force evaluations = 37 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0925 | 2.0925 | 2.0925 | 0.0 | 98.99 Neigh | 0.0078555 | 0.0078555 | 0.0078555 | 0.0 | 0.37 Comm | 0.0060402 | 0.0060402 | 0.0060402 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007523 | | | 0.36 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3595.00 ave 3595 max 3595 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: 46636.0 ave 46636 max 46636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46636 Ave neighs/atom = 53.852194 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 ghost atom cutoff = 6 binsize = 3, bins = 8 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -2895.6566 0 -2895.6566 5292.3492 14348.756 48 0 -2896.096 0 -2896.096 -33.939269 14464.144 Loop time of 0.474898 on 1 procs for 11 steps with 866 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2895.65663699577 -2896.09571092162 -2896.0959697323 Force two-norm initial, final = 99.755527 0.65218152 Force max component initial, final = 92.337945 0.44273408 Final line search alpha, max atom move = 0.0010116245 0.00044788066 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45943 | 0.45943 | 0.45943 | 0.0 | 96.74 Neigh | 0.0086059 | 0.0086059 | 0.0086059 | 0.0 | 1.81 Comm | 0.0013365 | 0.0013365 | 0.0013365 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00553 | | | 1.16 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3600.00 ave 3600 max 3600 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: 46476.0 ave 46476 max 46476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46476 Ave neighs/atom = 53.667436 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.694 | 4.694 | 4.694 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2896.096 0 -2896.096 -33.939269 Loop time of 6.425e-06 on 1 procs for 0 steps with 866 atoms 0.0% 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 | | 6.425e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3606.00 ave 3606 max 3606 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: 46476.0 ave 46476 max 46476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46476 Ave neighs/atom = 53.667436 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 ghost atom cutoff = 6 binsize = 3, bins = 8 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.694 | 4.694 | 4.694 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 -2896.096 -2896.096 21.038291 120.24399 5.7176676 -33.939269 -33.939269 -41.585334 -11.275903 -48.956571 2.5713785 540.39621 Loop time of 6.946e-06 on 1 procs for 0 steps with 866 atoms 273.5% 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 | | 6.946e-06 | | |100.00 Nlocal: 866.000 ave 866 max 866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3606.00 ave 3606 max 3606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23238.0 ave 23238 max 23238 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46476.0 ave 46476 max 46476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46476 Ave neighs/atom = 53.667436 Neighbor list builds = 0 Dangerous builds = 0 866 -2896.0959697323 eV 2.57137848561931 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03