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 = 4.0320827 4.0320827 4.0320827 Created orthogonal box = (0.0000000 -41.119337 0.0000000) to (20.559668 41.119337 4.0320827) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7445389 4.7445389 4.0320827 Created 207 atoms using lattice units in orthogonal box = (0.0000000 -41.119337 0.0000000) to (20.559668 41.119337 4.0320827) create_atoms CPU = 0.002 seconds 207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7445389 4.7445389 4.0320827 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.119337 0.0000000) to (20.559668 41.119337 4.0320827) create_atoms CPU = 0.001 seconds 209 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 6 22 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 7.5580544182181 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 412 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_324507536345_003#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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.452 | 4.452 | 4.452 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1351.515 0 -1351.515 6956.7838 78 0 -1379.2509 0 -1379.2509 -3332.7952 Loop time of 1.43806 on 1 procs for 78 steps with 412 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 = -1351.51497177349 -1379.24985960861 -1379.2509213084 Force two-norm initial, final = 47.524799 0.083821168 Force max component initial, final = 16.610256 0.028952173 Final line search alpha, max atom move = 1.0000000 0.028952173 Iterations, force evaluations = 78 147 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4093 | 1.4093 | 1.4093 | 0.0 | 98.00 Neigh | 0.006496 | 0.006496 | 0.006496 | 0.0 | 0.45 Comm | 0.012022 | 0.012022 | 0.012022 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01023 | | | 0.71 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3388.00 ave 3388 max 3388 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: 46676.0 ave 46676 max 46676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46676 Ave neighs/atom = 113.29126 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -1379.2509 0 -1379.2509 -3332.7952 6817.4449 85 0 -1379.3308 0 -1379.3308 -34.692226 6788.4593 Loop time of 0.0883586 on 1 procs for 7 steps with 412 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 = -1379.25092130839 -1379.32980404316 -1379.33083972693 Force two-norm initial, final = 28.840713 0.35268042 Force max component initial, final = 26.521774 0.20295337 Final line search alpha, max atom move = 0.00057727404 0.00011715971 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.085302 | 0.085302 | 0.085302 | 0.0 | 96.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000722 | 0.000722 | 0.000722 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002334 | | | 2.64 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3413.00 ave 3413 max 3413 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: 46580.0 ave 46580 max 46580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46580 Ave neighs/atom = 113.05825 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1379.3308 0 -1379.3308 -34.692226 Loop time of 6.415e-06 on 1 procs for 0 steps with 412 atoms 187.1% 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 | | 6.415e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3413.00 ave 3413 max 3413 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: 50952.0 ave 50952 max 50952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50952 Ave neighs/atom = 123.66990 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 = 7.5580544 ghost atom cutoff = 7.5580544 binsize = 3.7790272, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5580544182181 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) = 4.591 | 4.591 | 4.591 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 -1379.3308 -1379.3308 20.583929 81.683256 4.0374756 -34.692226 -34.692226 -47.95651 -30.335616 -25.784551 2.5952108 236.16235 Loop time of 8.279e-06 on 1 procs for 0 steps with 412 atoms 217.4% 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 | | 8.279e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3413.00 ave 3413 max 3413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25476.0 ave 25476 max 25476 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50952.0 ave 50952 max 50952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50952 Ave neighs/atom = 123.66990 Neighbor list builds = 0 Dangerous builds = 0 412 -1379.33083972693 eV 2.59521077900018 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01