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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -62.165833 0.0000000) to (31.082917 62.165833 3.6133157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0404730 5.0404730 3.6133157 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.165833 0.0000000) to (31.082917 62.165833 3.6133157) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0404730 5.0404730 3.6133157 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.165833 0.0000000) to (31.082917 62.165833 3.6133157) create_atoms CPU = 0.001 seconds 594 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_353393547686_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.030 | 5.030 | 5.030 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3979.5492 0 -3979.5492 49551.224 83 0 -4187.6015 0 -4187.6015 7373.7957 Loop time of 5.5378 on 1 procs for 83 steps with 1186 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 = -3979.54923752451 -4187.59766041067 -4187.60153392791 Force two-norm initial, final = 292.10574 0.20058612 Force max component initial, final = 57.097406 0.060002705 Final line search alpha, max atom move = 1.0000000 0.060002705 Iterations, force evaluations = 83 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.5044 | 5.5044 | 5.5044 | 0.0 | 99.40 Neigh | 0.008467 | 0.008467 | 0.008467 | 0.0 | 0.15 Comm | 0.013425 | 0.013425 | 0.013425 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01151 | | | 0.21 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7338.00 ave 7338 max 7338 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: 102208.0 ave 102208 max 102208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102208 Ave neighs/atom = 86.178752 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.043 | 5.043 | 5.043 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4187.6015 0 -4187.6015 7373.7957 13963.987 90 0 -4187.9581 0 -4187.9581 -477.34418 14040.45 Loop time of 0.414427 on 1 procs for 7 steps with 1186 atoms 81.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4187.60153392791 -4187.95598943434 -4187.95814382663 Force two-norm initial, final = 131.89663 7.9085973 Force max component initial, final = 119.63629 6.7685799 Final line search alpha, max atom move = 0.00024337575 0.0016473082 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41047 | 0.41047 | 0.41047 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066676 | 0.00066676 | 0.00066676 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003286 | | | 0.79 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8094.00 ave 8094 max 8094 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: 102164.0 ave 102164 max 102164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102164 Ave neighs/atom = 86.141653 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.181 | 5.181 | 5.181 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4187.9581 0 -4187.9581 -477.34418 Loop time of 2.561e-06 on 1 procs for 0 steps with 1186 atoms 156.2% 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 | | 2.561e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8094.00 ave 8094 max 8094 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: 102072.0 ave 102072 max 102072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102072 Ave neighs/atom = 86.064081 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.181 | 5.181 | 5.181 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 -4187.9581 -4187.9581 31.062085 125.12571 3.6124668 -477.34418 -477.34418 -337.66038 -322.18093 -772.19122 2.3021046 324.46233 Loop time of 2.753e-06 on 1 procs for 0 steps with 1186 atoms 217.9% 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 | | 2.753e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8094.00 ave 8094 max 8094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51036.0 ave 51036 max 51036 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102072.0 ave 102072 max 102072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102072 Ave neighs/atom = 86.064081 Neighbor list builds = 0 Dangerous builds = 0 1186 -4187.95814382663 eV 2.30210456829972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06