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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7242695 5.6655575 6.2546061 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -36.826124 0.0000000) to (31.892359 36.826124 6.2546061) create_atoms CPU = 0.001 seconds 629 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 22 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1249 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4875.6112 0 -4875.6112 73048.432 415 0 -5285.0961 0 -5285.0961 15377.372 Loop time of 82.3264 on 1 procs for 415 steps with 1249 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4875.61124070991 -5285.09125831161 -5285.09614629153 Force two-norm initial, final = 487.86055 0.23940600 Force max component initial, final = 123.60153 0.070888718 Final line search alpha, max atom move = 0.82556306 0.058523106 Iterations, force evaluations = 415 783 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 82.097 | 82.097 | 82.097 | 0.0 | 99.72 Neigh | 0.10398 | 0.10398 | 0.10398 | 0.0 | 0.13 Comm | 0.062679 | 0.062679 | 0.062679 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06243 | | | 0.08 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5402.00 ave 5402 max 5402 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: 140210.0 ave 140210 max 140210 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140210 Ave neighs/atom = 112.25781 Neighbor list builds = 10 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 415 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.042 | 5.042 | 5.042 Mbytes Step Temp E_pair E_mol TotEng Press Volume 415 0 -5285.0961 0 -5285.0961 15377.372 14691.719 439 0 -5292.3247 0 -5292.3247 -11.39427 14809.615 Loop time of 3.01074 on 1 procs for 24 steps with 1249 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5285.09614629153 -5292.32359699459 -5292.32466609543 Force two-norm initial, final = 493.62982 3.5484108 Force max component initial, final = 330.64443 1.6852951 Final line search alpha, max atom move = 0.00041357952 0.00069700355 Iterations, force evaluations = 24 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.991 | 2.991 | 2.991 | 0.0 | 99.35 Neigh | 0.010536 | 0.010536 | 0.010536 | 0.0 | 0.35 Comm | 0.0014095 | 0.0014095 | 0.0014095 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00776 | | | 0.26 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5362.00 ave 5362 max 5362 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: 138840.0 ave 138840 max 138840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138840 Ave neighs/atom = 111.16093 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5292.3247 0 -5292.3247 -11.39427 Loop time of 2.097e-06 on 1 procs for 0 steps with 1249 atoms 190.7% 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 | | 2.097e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 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: 138916.0 ave 138916 max 138916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138916 Ave neighs/atom = 111.22178 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.179 | 5.179 | 5.179 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 -5292.3247 -5292.3247 31.179256 74.902226 6.3413731 -11.39427 -11.39427 178.24676 -156.8887 -55.540872 2.2165244 2610.6504 Loop time of 2.626e-06 on 1 procs for 0 steps with 1249 atoms 304.6% 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 | | 2.626e-06 | | |100.00 Nlocal: 1249.00 ave 1249 max 1249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5366.00 ave 5366 max 5366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69458.0 ave 69458 max 69458 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 138916.0 ave 138916 max 138916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 138916 Ave neighs/atom = 111.22178 Neighbor list builds = 0 Dangerous builds = 0 1249 -5292.32466609542 eV 2.21652438023851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:26