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 = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -51.638944 0.0000000) to (36.514248 51.638944 4.0571386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9587250 4.7813837 4.0571386 Created 647 atoms using lattice units in orthogonal box = (0.0000000 -51.638944 0.0000000) to (36.514248 51.638944 4.0571386) create_atoms CPU = 0.002 seconds 647 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9587250 4.7813837 4.0571386 Created 649 atoms using lattice units in orthogonal box = (0.0000000 -51.638944 0.0000000) to (36.514248 51.638944 4.0571386) create_atoms CPU = 0.002 seconds 649 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 21 1 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1291 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.728 | 6.728 | 6.728 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4897.5321 0 -4897.5321 43434.927 574 0 -5339.1901 0 -5339.1901 -6357.3559 Loop time of 21.7254 on 1 procs for 574 steps with 1291 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 = -4897.53213148105 -5339.18567755112 -5339.19014678986 Force two-norm initial, final = 615.50598 0.38574078 Force max component initial, final = 201.09028 0.14863907 Final line search alpha, max atom move = 0.87531061 0.13010536 Iterations, force evaluations = 574 1083 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.861 | 20.861 | 20.861 | 0.0 | 96.02 Neigh | 0.64658 | 0.64658 | 0.64658 | 0.0 | 2.98 Comm | 0.14133 | 0.14133 | 0.14133 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07691 | | | 0.35 Nlocal: 1291.00 ave 1291 max 1291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14603.0 ave 14603 max 14603 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: 506182.0 ave 506182 max 506182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506182 Ave neighs/atom = 392.08521 Neighbor list builds = 26 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 8 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 574 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.732 | 6.732 | 6.732 Mbytes Step Temp E_pair E_mol TotEng Press Volume 574 0 -5339.1901 0 -5339.1901 -6357.3559 15299.934 602 0 -5355.326 0 -5355.326 76.078357 15215.444 Loop time of 0.665704 on 1 procs for 28 steps with 1291 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 = -5339.19014678978 -5355.32582041024 -5355.32600935631 Force two-norm initial, final = 909.56462 2.2562977 Force max component initial, final = 676.22307 1.2163575 Final line search alpha, max atom move = 0.00035449454 0.00043119211 Iterations, force evaluations = 28 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62171 | 0.62171 | 0.62171 | 0.0 | 93.39 Neigh | 0.026888 | 0.026888 | 0.026888 | 0.0 | 4.04 Comm | 0.003455 | 0.003455 | 0.003455 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01365 | | | 2.05 Nlocal: 1291.00 ave 1291 max 1291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14603.0 ave 14603 max 14603 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: 505478.0 ave 505478 max 505478 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505478 Ave neighs/atom = 391.53989 Neighbor list builds = 1 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.850 | 6.850 | 6.850 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5355.326 0 -5355.326 76.078357 Loop time of 2.049e-06 on 1 procs for 0 steps with 1291 atoms 146.4% 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 | | 2.049e-06 | | |100.00 Nlocal: 1291.00 ave 1291 max 1291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12179.0 ave 12179 max 12179 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: 507142.0 ave 507142 max 507142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507142 Ave neighs/atom = 392.82881 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.850 | 6.850 | 6.850 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 -5355.326 -5355.326 35.863272 101.85736 4.1652618 76.078357 76.078357 71.771277 126.31998 30.143812 2.1201865 6766.2234 Loop time of 2.295e-06 on 1 procs for 0 steps with 1291 atoms 217.9% 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 | | 2.295e-06 | | |100.00 Nlocal: 1291.00 ave 1291 max 1291 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12179.0 ave 12179 max 12179 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 253571.0 ave 253571 max 253571 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 507142.0 ave 507142 max 507142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507142 Ave neighs/atom = 392.82881 Neighbor list builds = 0 Dangerous builds = 0 1291 -5355.32600935631 eV 2.1201865258726 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22