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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -47.359114 0.0000000) to (33.487951 47.359114 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2303164 6.0575611 5.1068646 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -47.359114 0.0000000) to (33.487951 47.359114 5.1068646) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2303164 6.0575611 5.1068646 Created 696 atoms using lattice units in orthogonal box = (0.0000000 -47.359114 0.0000000) to (33.487951 47.359114 5.1068646) create_atoms CPU = 0.002 seconds 696 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 = 12 32 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 8 atoms, new total = 1376 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_179158257180_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 = 12 32 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5748.7924 0 -5748.7924 21441.071 639 0 -5864.2917 0 -5864.2917 3243.4165 Loop time of 63.6906 on 1 procs for 639 steps with 1376 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 = -5748.79242693833 -5864.28660824522 -5864.29167349339 Force two-norm initial, final = 81.710644 0.23341956 Force max component initial, final = 13.356838 0.056357843 Final line search alpha, max atom move = 1.0000000 0.056357843 Iterations, force evaluations = 639 1211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 63.328 | 63.328 | 63.328 | 0.0 | 99.43 Neigh | 0.18491 | 0.18491 | 0.18491 | 0.0 | 0.29 Comm | 0.085387 | 0.085387 | 0.085387 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.09233 | | | 0.14 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5642.00 ave 5642 max 5642 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: 90560.0 ave 90560 max 90560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90560 Ave neighs/atom = 65.813953 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 32 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 : 639 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.669 | 4.669 | 4.669 Mbytes Step Temp E_pair E_mol TotEng Press Volume 639 0 -5864.2917 0 -5864.2917 3243.4165 16198.562 665 0 -5875.2234 0 -5875.2234 42.889846 16208.128 Loop time of 1.30205 on 1 procs for 26 steps with 1376 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 = -5864.2916734934 -5875.22308586568 -5875.22337474098 Force two-norm initial, final = 672.92719 2.5425214 Force max component initial, final = 497.07540 1.8488917 Final line search alpha, max atom move = 0.00073758524 0.0013637153 Iterations, force evaluations = 26 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2834 | 1.2834 | 1.2834 | 0.0 | 98.57 Neigh | 0.0079653 | 0.0079653 | 0.0079653 | 0.0 | 0.61 Comm | 0.0015752 | 0.0015752 | 0.0015752 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00912 | | | 0.70 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5710.00 ave 5710 max 5710 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: 90264.0 ave 90264 max 90264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90264 Ave neighs/atom = 65.598837 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 = 12 33 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) = 4.808 | 4.808 | 4.808 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5875.2234 0 -5875.2234 42.889846 Loop time of 2.157e-06 on 1 procs for 0 steps with 1376 atoms 185.4% 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 | | 2.157e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5772.00 ave 5772 max 5772 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: 90288.0 ave 90288 max 90288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90288 Ave neighs/atom = 65.616279 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 = 12 33 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) = 4.808 | 4.808 | 4.808 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 -5875.2234 -5875.2234 33.707312 96.526065 4.981546 42.889846 42.889846 183.96048 -46.280249 -9.0106888 2.3468684 2247.0918 Loop time of 2.226e-06 on 1 procs for 0 steps with 1376 atoms 224.6% 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 | | 2.226e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5772.00 ave 5772 max 5772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45144.0 ave 45144 max 45144 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90288.0 ave 90288 max 90288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90288 Ave neighs/atom = 65.616279 Neighbor list builds = 0 Dangerous builds = 0 1376 -5875.22337474098 eV 2.34686839448327 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:05