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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0462295 6.2186617 5.0973115 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) create_atoms CPU = 0.002 seconds 690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0462295 6.2186617 5.0973115 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.854218 0.0000000) to (23.635261 66.854218 5.0973115) create_atoms CPU = 0.002 seconds 690 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1368 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5773.3179 0 -5773.3179 1098.0604 137 0 -5801.6603 0 -5801.6603 -7664.0919 Loop time of 11.4509 on 1 procs for 137 steps with 1368 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 = -5773.31791925389 -5801.65540139469 -5801.66034612956 Force two-norm initial, final = 26.265791 0.20822726 Force max component initial, final = 7.9700278 0.050870621 Final line search alpha, max atom move = 0.98284749 0.049998062 Iterations, force evaluations = 137 256 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.395 | 11.395 | 11.395 | 0.0 | 99.51 Neigh | 0.022919 | 0.022919 | 0.022919 | 0.0 | 0.20 Comm | 0.016133 | 0.016133 | 0.016133 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01683 | | | 0.15 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5996.00 ave 5996 max 5996 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: 106328.0 ave 106328 max 106328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106328 Ave neighs/atom = 77.725146 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.076 | 5.076 | 5.076 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -5801.6603 0 -5801.6603 -7664.0919 16108.696 139 0 -5801.72 0 -5801.72 -3664.1098 16068.443 Loop time of 0.176885 on 1 procs for 2 steps with 1368 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 = -5801.66034612957 -5801.71480240951 -5801.72004891225 Force two-norm initial, final = 66.819721 3.5062475 Force max component initial, final = 52.825602 3.0734900 Final line search alpha, max atom move = 5.8071872e-05 0.00017848332 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17586 | 0.17586 | 0.17586 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018144 | 0.00018144 | 0.00018144 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008476 | | | 0.48 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5996.00 ave 5996 max 5996 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: 106440.0 ave 106440 max 106440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106440 Ave neighs/atom = 77.807018 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5801.72 0 -5801.72 -3664.1098 Loop time of 2.093e-06 on 1 procs for 0 steps with 1368 atoms 143.3% 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 | | 2.093e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5996.00 ave 5996 max 5996 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: 106448.0 ave 106448 max 106448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106448 Ave neighs/atom = 77.812865 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 8 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.214 | 5.214 | 5.214 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 -5801.72 -5801.72 23.600426 133.70844 5.0920792 -3664.1098 -3664.1098 -166.68374 -11131.787 306.14159 2.3494436 543.60148 Loop time of 1.857e-06 on 1 procs for 0 steps with 1368 atoms 215.4% 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 | | 1.857e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5996.00 ave 5996 max 5996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53224.0 ave 53224 max 53224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106448.0 ave 106448 max 106448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106448 Ave neighs/atom = 77.812865 Neighbor list builds = 0 Dangerous builds = 0 1368 -5801.72004891225 eV 2.34944358935842 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12