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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -47.391804 0.0000000) to (33.508511 47.391804 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2341416 6.0612802 5.1100000 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -47.391804 0.0000000) to (33.508511 47.391804 5.1100000) create_atoms CPU = 0.005 seconds 695 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2341416 6.0612802 5.1100000 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -47.391804 0.0000000) to (33.508511 47.391804 5.1100000) create_atoms CPU = 0.005 seconds 695 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 = 11 30 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 15 atoms, new total = 1375 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_353393547686_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 = 11 30 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) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4772.8724 0 -4772.8724 22040.768 55 0 -4851.6309 0 -4851.6309 4519.5642 Loop time of 9.04386 on 1 procs for 55 steps with 1375 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 = -4772.87236529874 -4851.62694920317 -4851.63087697283 Force two-norm initial, final = 90.158590 0.17159986 Force max component initial, final = 13.894991 0.037922373 Final line search alpha, max atom move = 1.0000000 0.037922373 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.988 | 8.988 | 8.988 | 0.0 | 99.38 Neigh | 0.021567 | 0.021567 | 0.021567 | 0.0 | 0.24 Comm | 0.017509 | 0.017509 | 0.017509 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01681 | | | 0.19 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6753.00 ave 6753 max 6753 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: 119208.0 ave 119208 max 119208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119208 Ave neighs/atom = 86.696727 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 30 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.068 | 5.068 | 5.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -4851.6309 0 -4851.6309 4519.5642 16229.654 57 0 -4851.6755 0 -4851.6755 1281.6425 16266.714 Loop time of 0.344603 on 1 procs for 2 steps with 1375 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 = -4851.63087697283 -4851.67289988212 -4851.67546569753 Force two-norm initial, final = 54.747999 1.8500874 Force max component initial, final = 43.903974 1.6565243 Final line search alpha, max atom move = 8.7110055e-05 0.00014429993 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.342 | 0.342 | 0.342 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060407 | 0.00060407 | 0.00060407 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002001 | | | 0.58 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6733.00 ave 6733 max 6733 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: 119518.0 ave 119518 max 119518 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119518 Ave neighs/atom = 86.922182 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 = 11 30 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) = 5.206 | 5.206 | 5.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4851.6755 0 -4851.6755 1281.6425 Loop time of 6.545e-06 on 1 procs for 0 steps with 1375 atoms 183.3% 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 | | 6.545e-06 | | |100.00 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6733.00 ave 6733 max 6733 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: 119490.0 ave 119490 max 119490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119490 Ave neighs/atom = 86.901818 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 = 11 30 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) = 5.206 | 5.206 | 5.206 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 -4851.6755 -4851.6755 33.553922 94.783608 5.1147369 1281.6425 1281.6425 79.260998 3928.9757 -163.30923 2.3778466 1026.0111 Loop time of 6.956e-06 on 1 procs for 0 steps with 1375 atoms 301.9% 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 | | 6.956e-06 | | |100.00 Nlocal: 1375.00 ave 1375 max 1375 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6733.00 ave 6733 max 6733 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59745.0 ave 59745 max 59745 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 119490.0 ave 119490 max 119490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 119490 Ave neighs/atom = 86.901818 Neighbor list builds = 0 Dangerous builds = 0 1375 -4851.67546569753 eV 2.37784662447991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10