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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -33.727381 0.0000000) to (41.303946 33.727381 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7204510 4.3360111 4.6544275 Created 842 atoms using lattice units in orthogonal box = (0.0000000 -33.727381 0.0000000) to (41.303946 33.727381 6.9816412) create_atoms CPU = 0.002 seconds 842 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7204510 4.3360111 4.6544275 Created 842 atoms using lattice units in orthogonal box = (0.0000000 -33.727381 0.0000000) to (41.303946 33.727381 6.9816412) create_atoms CPU = 0.001 seconds 842 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1664 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.089 | 5.089 | 5.089 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6937.2113 0 -6937.2113 27525.872 71 0 -7097.764 0 -7097.764 -6663.3487 Loop time of 11.0895 on 1 procs for 71 steps with 1664 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 = -6937.21125594492 -7097.75836307513 -7097.76398477266 Force two-norm initial, final = 275.15558 0.22623673 Force max component initial, final = 47.228683 0.023527345 Final line search alpha, max atom move = 1.0000000 0.023527345 Iterations, force evaluations = 71 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.051 | 11.051 | 11.051 | 0.0 | 99.65 Neigh | 0.020637 | 0.020637 | 0.020637 | 0.0 | 0.19 Comm | 0.0067543 | 0.0067543 | 0.0067543 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01099 | | | 0.10 Nlocal: 1664.00 ave 1664 max 1664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 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: 109676.0 ave 109676 max 109676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109676 Ave neighs/atom = 65.911058 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -7097.764 0 -7097.764 -6663.3487 19451.885 74 0 -7097.9045 0 -7097.9045 -1133.6368 19386.113 Loop time of 0.468244 on 1 procs for 3 steps with 1664 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 = -7097.76398477261 -7097.90068842534 -7097.90449154596 Force two-norm initial, final = 110.39736 5.0864787 Force max component initial, final = 95.556888 4.9551562 Final line search alpha, max atom move = 6.7910690e-05 0.00033650807 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46671 | 0.46671 | 0.46671 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022228 | 0.00022228 | 0.00022228 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001307 | | | 0.28 Nlocal: 1664.00 ave 1664 max 1664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5394.00 ave 5394 max 5394 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: 109476.0 ave 109476 max 109476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109476 Ave neighs/atom = 65.790865 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.226 | 5.226 | 5.226 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7097.9045 0 -7097.9045 -1133.6368 Loop time of 2.115e-06 on 1 procs for 0 steps with 1664 atoms 189.1% 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 | | 2.115e-06 | | |100.00 Nlocal: 1664.00 ave 1664 max 1664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 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: 109616.0 ave 109616 max 109616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109616 Ave neighs/atom = 65.875000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.226 | 5.226 | 5.226 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 -7097.9045 -7097.9045 41.267003 67.454762 6.9642633 -1133.6368 -1133.6368 409.15547 -3902.5177 92.451886 2.259431 1690.6293 Loop time of 1.907e-06 on 1 procs for 0 steps with 1664 atoms 209.8% 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 | | 1.907e-06 | | |100.00 Nlocal: 1664.00 ave 1664 max 1664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5437.00 ave 5437 max 5437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54808.0 ave 54808 max 54808 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 109616.0 ave 109616 max 109616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109616 Ave neighs/atom = 65.875000 Neighbor list builds = 0 Dangerous builds = 0 1664 -7097.90449154596 eV 2.25943100403599 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12