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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -51.779476 0.0000000) to (42.274909 51.779476 8.5700208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2119751 4.9648198 5.7133472 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -51.779476 0.0000000) to (42.274909 51.779476 8.5700208) create_atoms CPU = 0.005 seconds 1756 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2119751 4.9648198 5.7133472 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -51.779476 0.0000000) to (42.274909 51.779476 8.5700208) create_atoms CPU = 0.005 seconds 1756 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3472 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_715003088863_000#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.400 | 7.400 | 7.400 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14165.529 0 -14165.529 3664.7835 45 0 -14238.92 0 -14238.92 -5416.1523 Loop time of 4.29966 on 1 procs for 45 steps with 3472 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14165.5287526998 -14238.9064681317 -14238.9198847436 Force two-norm initial, final = 51.755341 0.35347929 Force max component initial, final = 7.1538780 0.052757244 Final line search alpha, max atom move = 0.77220374 0.040739341 Iterations, force evaluations = 45 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1779 | 4.1779 | 4.1779 | 0.0 | 97.17 Neigh | 0.078533 | 0.078533 | 0.078533 | 0.0 | 1.83 Comm | 0.018956 | 0.018956 | 0.018956 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02427 | | | 0.56 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11396.0 ave 11396 max 11396 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: 605030.0 ave 605030 max 605030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605030 Ave neighs/atom = 174.25979 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.400 | 7.400 | 7.400 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -14238.92 0 -14238.92 -5416.1523 37519.082 48 0 -14239.081 0 -14239.081 -1757.4118 37402.127 Loop time of 0.34017 on 1 procs for 3 steps with 3472 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 = -14238.9198847436 -14239.0803169061 -14239.0807366262 Force two-norm initial, final = 145.68673 0.48281870 Force max component initial, final = 106.53736 0.11704038 Final line search alpha, max atom move = 0.00024521530 2.8700092e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33349 | 0.33349 | 0.33349 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00103 | 0.00103 | 0.00103 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005648 | | | 1.66 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11424.0 ave 11424 max 11424 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: 605148.0 ave 605148 max 605148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605148 Ave neighs/atom = 174.29378 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.538 | 7.538 | 7.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14239.081 0 -14239.081 -1757.4118 Loop time of 2.1393e-05 on 1 procs for 0 steps with 3472 atoms 0.0% 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 | | 2.139e-05 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11434.0 ave 11434 max 11434 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: 605502.0 ave 605502 max 605502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605502 Ave neighs/atom = 174.39574 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.538 | 7.538 | 7.538 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 -14239.081 -14239.081 42.204449 103.55895 8.557569 -1757.4118 -1757.4118 -2.6347866 -5264.5944 -5.0063168 2.2452639 1460.9333 Loop time of 4.184e-06 on 1 procs for 0 steps with 3472 atoms 215.1% 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 | | 4.184e-06 | | |100.00 Nlocal: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11434.0 ave 11434 max 11434 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 302751.0 ave 302751 max 302751 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 605502.0 ave 605502 max 605502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 605502 Ave neighs/atom = 174.39574 Neighbor list builds = 0 Dangerous builds = 0 3472 -14239.0807366262 eV 2.24526392158637 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06