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 = 4.1768978 4.1768978 4.1768978 Created orthogonal box = (0.0000000 -67.354630 0.0000000) to (33.675227 67.354630 4.1768978) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6988845 5.6988845 4.1768978 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -67.354630 0.0000000) to (33.675227 67.354630 4.1768978) create_atoms CPU = 0.003 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6988845 5.6988845 4.1768978 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -67.354630 0.0000000) to (33.675227 67.354630 4.1768978) create_atoms CPU = 0.002 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 41 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7569.2364 0 -7569.2364 8915.931 73 0 -7624.615 0 -7624.615 -2546.2958 Loop time of 9.25745 on 1 procs for 73 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 = -7569.2363892373 -7624.60943434778 -7624.61496812318 Force two-norm initial, final = 41.398216 0.25753162 Force max component initial, final = 12.178273 0.077927252 Final line search alpha, max atom move = 1.0000000 0.077927252 Iterations, force evaluations = 73 124 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.2144 | 9.2144 | 9.2144 | 0.0 | 99.53 Neigh | 0.010467 | 0.010467 | 0.010467 | 0.0 | 0.11 Comm | 0.01604 | 0.01604 | 0.01604 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01657 | | | 0.18 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5288.00 ave 5288 max 5288 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: 59296.0 ave 59296 max 59296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59296 Ave neighs/atom = 57.235521 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.596 | 4.596 | 4.596 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -7624.615 0 -7624.615 -2546.2958 18947.933 78 0 -7624.7625 0 -7624.7625 -2276.5578 18945.115 Loop time of 0.528901 on 1 procs for 5 steps with 1036 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7624.61496812318 -7624.75918462015 -7624.76250978158 Force two-norm initial, final = 50.016617 10.449166 Force max component initial, final = 42.731891 9.5047257 Final line search alpha, max atom move = 0.00010883951 0.0010344897 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.52512 | 0.52512 | 0.52512 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007976 | 0.0007976 | 0.0007976 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00298 | | | 0.56 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5276.00 ave 5276 max 5276 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: 61640.0 ave 61640 max 61640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61640 Ave neighs/atom = 59.498069 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.734 | 4.734 | 4.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7624.7625 0 -7624.7625 -2276.5578 Loop time of 6.856e-06 on 1 procs for 0 steps with 1036 atoms 175.0% 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 | | 6.856e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5276.00 ave 5276 max 5276 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: 64560.0 ave 64560 max 64560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64560 Ave neighs/atom = 62.316602 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.734 | 4.734 | 4.734 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 -7624.7625 -7624.7625 33.540081 134.70926 4.1931045 -2276.5578 -2276.5578 364.0769 -8000.6777 806.92753 2.6557715 506.07248 Loop time of 6.966e-06 on 1 procs for 0 steps with 1036 atoms 287.1% 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 | | 6.966e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5276.00 ave 5276 max 5276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 32280.0 ave 32280 max 32280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 64560.0 ave 64560 max 64560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 64560 Ave neighs/atom = 62.316602 Neighbor list builds = 0 Dangerous builds = 0 1036 -7624.76250978158 eV 2.65577150055992 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10