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 = 3.5618363 3.5618363 3.5618363 Created orthogonal box = (0.0000000 -55.637662 0.0000000) to (27.818831 55.637662 3.5618363) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0165105 5.0165105 3.5618363 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -55.637662 0.0000000) to (27.818831 55.637662 3.5618363) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0165105 5.0165105 3.5618363 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.637662 0.0000000) to (27.818831 55.637662 3.5618363) create_atoms CPU = 0.002 seconds 490 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 27 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 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_322509103239_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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3642.2893 0 -3642.2893 46097.353 93 0 -3840.6403 0 -3840.6403 6372.7033 Loop time of 3.82611 on 1 procs for 93 steps with 978 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 = -3642.28926332402 -3840.63732635428 -3840.6403390082 Force two-norm initial, final = 239.54862 0.23036647 Force max component initial, final = 45.563821 0.034815346 Final line search alpha, max atom move = 1.0000000 0.034815346 Iterations, force evaluations = 93 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7038 | 3.7038 | 3.7038 | 0.0 | 96.80 Neigh | 0.058861 | 0.058861 | 0.058861 | 0.0 | 1.54 Comm | 0.039835 | 0.039835 | 0.039835 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02363 | | | 0.62 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9924.00 ave 9924 max 9924 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: 218876.0 ave 218876 max 218876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218876 Ave neighs/atom = 223.79959 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -3840.6403 0 -3840.6403 6372.7033 11025.841 99 0 -3840.8445 0 -3840.8445 -5.6488206 11064.944 Loop time of 0.205485 on 1 procs for 6 steps with 978 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 = -3840.6403390082 -3840.84450994396 -3840.84454294642 Force two-norm initial, final = 98.326645 0.36782267 Force max component initial, final = 76.809539 0.17050027 Final line search alpha, max atom move = 0.0010173908 0.00017346540 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19755 | 0.19755 | 0.19755 | 0.0 | 96.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019329 | 0.0019329 | 0.0019329 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006001 | | | 2.92 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9930.00 ave 9930 max 9930 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: 218988.0 ave 218988 max 218988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218988 Ave neighs/atom = 223.91411 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.574 | 5.574 | 5.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3840.8445 0 -3840.8445 -5.6488206 Loop time of 6.485e-06 on 1 procs for 0 steps with 978 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 | | 6.485e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9948.00 ave 9948 max 9948 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: 218868.0 ave 218868 max 218868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218868 Ave neighs/atom = 223.79141 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 = 8.5097 ghost atom cutoff = 8.5097 binsize = 4.25485, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.509699999999999 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) = 5.574 | 5.574 | 5.574 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 -3840.8445 -3840.8445 27.751005 111.4515 3.5775406 -5.6488206 -5.6488206 -24.627825 -4.7305794 12.411943 2.2435954 145.74684 Loop time of 7.978e-06 on 1 procs for 0 steps with 978 atoms 238.2% 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 | | 7.978e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9948.00 ave 9948 max 9948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109434.0 ave 109434 max 109434 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 218868.0 ave 218868 max 218868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218868 Ave neighs/atom = 223.79141 Neighbor list builds = 0 Dangerous builds = 0 978 -3840.84454294642 eV 2.243595354661 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04