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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -54.137842 0.0000000) to (44.203363 54.137842 8.9609594) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4497297 5.1912999 5.9739729 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -54.137842 0.0000000) to (44.203363 54.137842 8.9609594) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4497297 5.1912999 5.9739729 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -54.137842 0.0000000) to (44.203363 54.137842 8.9609594) create_atoms CPU = 0.002 seconds 1757 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 28 3 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_942420706858_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.401 | 7.401 | 7.401 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11645.795 0 -11645.795 125540.04 917 0 -14206.446 0 -14206.446 -52342.569 Loop time of 50.3602 on 1 procs for 917 steps with 3506 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 = -11645.7951011479 -14206.4336741381 -14206.4462821672 Force two-norm initial, final = 2636.8553 0.31501129 Force max component initial, final = 386.23920 0.041375798 Final line search alpha, max atom move = 0.63905780 0.026441526 Iterations, force evaluations = 917 1783 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 49.092 | 49.092 | 49.092 | 0.0 | 97.48 Neigh | 0.81099 | 0.81099 | 0.81099 | 0.0 | 1.61 Comm | 0.20064 | 0.20064 | 0.20064 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2568 | | | 0.51 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11602.0 ave 11602 max 11602 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: 592320.0 ave 592320 max 592320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 592320 Ave neighs/atom = 168.94467 Neighbor list builds = 22 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 917 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.402 | 7.402 | 7.402 Mbytes Step Temp E_pair E_mol TotEng Press Volume 917 0 -14206.446 0 -14206.446 -52342.569 42888.49 971 0 -14287.788 0 -14287.788 219.33428 41582.833 Loop time of 1.59859 on 1 procs for 54 steps with 3506 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 = -14206.446282167 -14287.7857979453 -14287.7877377643 Force two-norm initial, final = 3229.1898 11.945504 Force max component initial, final = 2882.0605 6.2520335 Final line search alpha, max atom move = 0.00011256889 0.00070378445 Iterations, force evaluations = 54 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3759 | 1.3759 | 1.3759 | 0.0 | 86.07 Neigh | 0.18572 | 0.18572 | 0.18572 | 0.0 | 11.62 Comm | 0.0057928 | 0.0057928 | 0.0057928 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03114 | | | 1.95 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11398.0 ave 11398 max 11398 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: 597932.0 ave 597932 max 597932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 597932 Ave neighs/atom = 170.54535 Neighbor list builds = 5 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.536 | 7.536 | 7.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14287.788 0 -14287.788 219.33428 Loop time of 1.819e-06 on 1 procs for 0 steps with 3506 atoms 164.9% 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 | | 1.819e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381.0 ave 11381 max 11381 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: 596896.0 ave 596896 max 596896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 596896 Ave neighs/atom = 170.24986 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.536 | 7.536 | 7.536 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 -14287.788 -14287.788 43.700033 102.99319 9.2389751 219.33428 219.33428 238.1464 225.4687 194.38774 2.2130465 5737.4308 Loop time of 2.078e-06 on 1 procs for 0 steps with 3506 atoms 192.5% 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 | | 2.078e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11381.0 ave 11381 max 11381 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 298448.0 ave 298448 max 298448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 596896.0 ave 596896 max 596896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 596896 Ave neighs/atom = 170.24986 Neighbor list builds = 0 Dangerous builds = 0 3506 -14287.7877377643 eV 2.21304653422099 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:52