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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -58.166815 0.0000000) to (29.083407 58.166815 3.6073527) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0269333 4.0269333 3.6073527 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.166815 0.0000000) to (29.083407 58.166815 3.6073527) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0269333 4.0269333 3.6073527 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.166815 0.0000000) to (29.083407 58.166815 3.6073527) create_atoms CPU = 0.001 seconds 522 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 20 1 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_151002396060_004#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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 11.00 | 11.00 | 11.00 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3352.4055 0 -3352.4055 35762.31 69 0 -3646.2376 0 -3646.2376 -1062.1654 Loop time of 3.95254 on 1 procs for 69 steps with 1036 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3352.40548858951 -3646.23519446644 -3646.23756961228 Force two-norm initial, final = 493.23772 0.16797519 Force max component initial, final = 162.95466 0.012992784 Final line search alpha, max atom move = 1.0000000 0.012992784 Iterations, force evaluations = 69 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8835 | 3.8835 | 3.8835 | 0.0 | 98.25 Neigh | 0.032999 | 0.032999 | 0.032999 | 0.0 | 0.83 Comm | 0.024519 | 0.024519 | 0.024519 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01149 | | | 0.29 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16167.0 ave 16167 max 16167 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: 651168.0 ave 651168 max 651168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651168 Ave neighs/atom = 628.54054 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.00 | 11.00 | 11.00 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3646.2376 0 -3646.2376 -1062.1654 12205.039 75 0 -3646.3119 0 -3646.3119 29.802257 12195.24 Loop time of 0.281849 on 1 procs for 6 steps with 1036 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 = -3646.23756961228 -3646.31191464598 -3646.31192630936 Force two-norm initial, final = 27.884302 0.55718696 Force max component initial, final = 22.896891 0.38422245 Final line search alpha, max atom move = 0.0021794159 0.00083738052 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27568 | 0.27568 | 0.27568 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012538 | 0.0012538 | 0.0012538 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004913 | | | 1.74 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16167.0 ave 16167 max 16167 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: 650408.0 ave 650408 max 650408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 650408 Ave neighs/atom = 627.80695 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 10.51 | 10.51 | 10.51 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3646.3119 0 -3646.3119 29.802257 Loop time of 2.238e-06 on 1 procs for 0 steps with 1036 atoms 178.7% 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 | | 2.238e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16181.0 ave 16181 max 16181 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: 651072.0 ave 651072 max 651072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651072 Ave neighs/atom = 628.44788 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 10.51 | 10.51 | 10.51 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 -3646.3119 -3646.3119 29.043902 115.90125 3.6228242 29.802257 29.802257 10.087558 28.624649 50.694565 2.297361 218.02522 Loop time of 3.307e-06 on 1 procs for 0 steps with 1036 atoms 211.7% 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 | | 3.307e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16181.0 ave 16181 max 16181 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 325536.0 ave 325536 max 325536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 651072.0 ave 651072 max 651072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 651072 Ave neighs/atom = 628.44788 Neighbor list builds = 0 Dangerous builds = 0 1036 -3646.31192630936 eV 2.29736098807799 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04