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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0939085 6.2241747 5.1120000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) create_atoms CPU = 0.007 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0939085 6.2241747 5.1120000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.581224 0.0000000) to (38.594754 54.581224 5.1120000) create_atoms CPU = 0.006 seconds 916 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_887933271505_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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5972.5797 0 -5972.5797 63975.155 77 0 -6490.6123 0 -6490.6123 2427.9855 Loop time of 3.14933 on 1 procs for 77 steps with 1828 atoms 60.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5972.57969533276 -6490.60643213309 -6490.61229313171 Force two-norm initial, final = 450.68506 0.23404486 Force max component initial, final = 88.475605 0.023033579 Final line search alpha, max atom move = 1.0000000 0.023033579 Iterations, force evaluations = 77 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0568 | 3.0568 | 3.0568 | 0.0 | 97.06 Neigh | 0.035143 | 0.035143 | 0.035143 | 0.0 | 1.12 Comm | 0.027442 | 0.027442 | 0.027442 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02994 | | | 0.95 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5984.00 ave 5984 max 5984 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: 101232.0 ave 101232 max 101232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101232 Ave neighs/atom = 55.378556 Neighbor list builds = 2 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.136 | 5.136 | 5.136 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -6490.6123 0 -6490.6123 2427.9855 21537.356 81 0 -6490.7488 0 -6490.7488 -316.95594 21579.605 Loop time of 0.119628 on 1 procs for 4 steps with 1828 atoms 63.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6490.61229313171 -6490.74519625546 -6490.74875311711 Force two-norm initial, final = 81.387741 7.7522341 Force max component initial, final = 80.363617 5.3440093 Final line search alpha, max atom move = 8.7868666e-05 0.00046957097 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1148 | 0.1148 | 0.1148 | 0.0 | 95.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095559 | 0.00095559 | 0.00095559 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003875 | | | 3.24 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5996.00 ave 5996 max 5996 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: 101600.0 ave 101600 max 101600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101600 Ave neighs/atom = 55.579869 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.274 | 5.274 | 5.274 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6490.7488 0 -6490.7488 -316.95594 Loop time of 6.735e-06 on 1 procs for 0 steps with 1828 atoms 133.6% 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 | | 6.735e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5990.00 ave 5990 max 5990 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: 101592.0 ave 101592 max 101592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101592 Ave neighs/atom = 55.575492 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 15 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 5.274 | 5.274 | 5.274 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 -6490.7488 -6490.7488 38.557297 109.09121 5.130352 -316.95594 -316.95594 -396.38059 -376.76908 -177.71815 2.4045242 909.45391 Loop time of 6.756e-06 on 1 procs for 0 steps with 1828 atoms 222.0% 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 | | 6.756e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5990.00 ave 5990 max 5990 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50796.0 ave 50796 max 50796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101592.0 ave 101592 max 101592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101592 Ave neighs/atom = 55.575492 Neighbor list builds = 0 Dangerous builds = 0 1828 -6490.74875311711 eV 2.40452421511397 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03