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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -63.169636 0.0000000) to (31.582859 63.169636 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3730113 4.3730113 3.9173716 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -63.169636 0.0000000) to (31.582859 63.169636 3.9173716) create_atoms CPU = 0.002 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3730113 4.3730113 3.9173716 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -63.169636 0.0000000) to (31.582859 63.169636 3.9173716) 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 = 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 6 atoms, new total = 1038 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_020840179467_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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5888.7891 0 -5888.7891 20560.575 34 0 -5967.2381 0 -5967.2381 4822.7921 Loop time of 2.60344 on 1 procs for 34 steps with 1038 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 = -5888.7890967508 -5967.23281205721 -5967.23811689208 Force two-norm initial, final = 90.855275 0.28244925 Force max component initial, final = 24.429019 0.050747379 Final line search alpha, max atom move = 1.0000000 0.050747379 Iterations, force evaluations = 34 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5874 | 2.5874 | 2.5874 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0082604 | 0.0082604 | 0.0082604 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007801 | | | 0.30 Nlocal: 1038.00 ave 1038 max 1038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6247.00 ave 6247 max 6247 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: 80760.0 ave 80760 max 80760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80760 Ave neighs/atom = 77.803468 Neighbor list builds = 0 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 : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -5967.2381 0 -5967.2381 4822.7921 15630.922 36 0 -5967.2844 0 -5967.2844 860.41668 15666.073 Loop time of 0.187192 on 1 procs for 2 steps with 1038 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 = -5967.23811689208 -5967.27857807657 -5967.28443387129 Force two-norm initial, final = 55.993041 9.4379669 Force max component initial, final = 49.030918 9.4336118 Final line search alpha, max atom move = 5.8951471e-05 0.00055612529 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18498 | 0.18498 | 0.18498 | 0.0 | 98.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051279 | 0.00051279 | 0.00051279 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001704 | | | 0.91 Nlocal: 1038.00 ave 1038 max 1038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6222.00 ave 6222 max 6222 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: 80432.0 ave 80432 max 80432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80432 Ave neighs/atom = 77.487476 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) = 4.748 | 4.748 | 4.748 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5967.2844 0 -5967.2844 860.41668 Loop time of 6.505e-06 on 1 procs for 0 steps with 1038 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 1038.00 ave 1038 max 1038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6222.00 ave 6222 max 6222 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: 80424.0 ave 80424 max 80424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80424 Ave neighs/atom = 77.479769 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) = 4.748 | 4.748 | 4.748 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 -5967.2844 -5967.2844 31.636271 126.33927 3.9195525 860.41668 860.41668 5.4664637 3541.1005 -965.31694 2.5189257 295.47443 Loop time of 7.517e-06 on 1 procs for 0 steps with 1038 atoms 226.2% 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 | | 7.517e-06 | | |100.00 Nlocal: 1038.00 ave 1038 max 1038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6222.00 ave 6222 max 6222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40212.0 ave 40212 max 40212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80424.0 ave 80424 max 80424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80424 Ave neighs/atom = 77.479769 Neighbor list builds = 0 Dangerous builds = 0 1038 -5967.2844338713 eV 2.51892568588048 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03