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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296738 5.3548974 5.7481359 Created 1666 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) create_atoms CPU = 0.003 seconds 1666 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296738 5.3548974 5.7481359 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -41.649202 0.0000000) to (51.009646 41.649202 8.6222039) create_atoms CPU = 0.003 seconds 1690 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 20 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3356 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_592013496703_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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 7.891 | 7.891 | 7.891 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14148.148 0 -14148.148 48812.923 93 0 -14875.513 0 -14875.513 7176.4958 Loop time of 5.34385 on 1 procs for 93 steps with 3356 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 = -14148.1478039372 -14875.4985902562 -14875.5131250105 Force two-norm initial, final = 512.70195 0.46330997 Force max component initial, final = 64.928279 0.15904543 Final line search alpha, max atom move = 0.63112776 0.10037798 Iterations, force evaluations = 93 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.046 | 5.046 | 5.046 | 0.0 | 94.43 Neigh | 0.24845 | 0.24845 | 0.24845 | 0.0 | 4.65 Comm | 0.021667 | 0.021667 | 0.021667 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02772 | | | 0.52 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12832.0 ave 12832 max 12832 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: 750438.0 ave 750438 max 750438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 750438 Ave neighs/atom = 223.61085 Neighbor list builds = 6 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.891 | 7.891 | 7.891 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -14875.513 0 -14875.513 7176.4958 36635.935 99 0 -14876.261 0 -14876.261 -2.3907205 36785.298 Loop time of 0.300054 on 1 procs for 6 steps with 3356 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 = -14875.5131250106 -14876.2607689253 -14876.2613470888 Force two-norm initial, final = 341.83405 0.69738418 Force max component initial, final = 316.37367 0.19659023 Final line search alpha, max atom move = 0.00010335141 2.0317878e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29401 | 0.29401 | 0.29401 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085925 | 0.00085925 | 0.00085925 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00519 | | | 1.73 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12832.0 ave 12832 max 12832 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: 750334.0 ave 750334 max 750334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 750334 Ave neighs/atom = 223.57986 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 8.028 | 8.028 | 8.028 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14876.261 0 -14876.261 -2.3907205 Loop time of 2.129e-06 on 1 procs for 0 steps with 3356 atoms 187.9% 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 | | 2.129e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12736.0 ave 12736 max 12736 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: 749696.0 ave 749696 max 749696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749696 Ave neighs/atom = 223.38975 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 13 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 8.028 | 8.028 | 8.028 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 -14876.261 -14876.261 51.019196 83.707298 8.6134541 -2.3907205 -2.3907205 2.3325068 -3.1403372 -6.3643309 2.2465942 1620.2025 Loop time of 4.561e-06 on 1 procs for 0 steps with 3356 atoms 241.2% 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 | | 4.561e-06 | | |100.00 Nlocal: 3356.00 ave 3356 max 3356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12736.0 ave 12736 max 12736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 374848.0 ave 374848 max 374848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 749696.0 ave 749696 max 749696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 749696 Ave neighs/atom = 223.38975 Neighbor list builds = 0 Dangerous builds = 0 3356 -14876.2613470888 eV 2.24659417966975 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06