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 = 3.5162328 3.5162328 3.5162328 Created orthogonal box = (0.0000000 -41.005968 0.0000000) to (14.497799 41.005968 4.9727041) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9696820 6.0302895 4.9727041 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.005968 0.0000000) to (14.497799 41.005968 4.9727041) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9696820 6.0302895 4.9727041 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.005968 0.0000000) to (14.497799 41.005968 4.9727041) create_atoms CPU = 0.001 seconds 274 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 4 19 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 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_047308317761_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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 4 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2416.1394 0 -2416.1394 140949.67 50 0 -2654.1482 0 -2654.1482 9671.2876 Loop time of 0.957517 on 1 procs for 50 steps with 546 atoms 80.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2416.13938548975 -2654.14572789631 -2654.14823944513 Force two-norm initial, final = 481.81750 0.17791015 Force max component initial, final = 151.81934 0.040120012 Final line search alpha, max atom move = 1.0000000 0.040120012 Iterations, force evaluations = 50 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94728 | 0.94728 | 0.94728 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0066028 | 0.0066028 | 0.0066028 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003636 | | | 0.38 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6132.00 ave 6132 max 6132 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: 137324.0 ave 137324 max 137324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 137324 Ave neighs/atom = 251.50916 Neighbor list builds = 0 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 4 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.948 | 4.948 | 4.948 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -2654.1482 0 -2654.1482 9671.2876 5912.5083 54 0 -2654.2478 0 -2654.2478 -2.3805062 5943.596 Loop time of 0.0614134 on 1 procs for 4 steps with 546 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 = -2654.14823944512 -2654.24727608292 -2654.24775902103 Force two-norm initial, final = 62.728048 0.33228633 Force max component initial, final = 44.143268 0.20132857 Final line search alpha, max atom move = 0.00047301145 9.5230719e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059717 | 0.059717 | 0.059717 | 0.0 | 97.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034063 | 0.00034063 | 0.00034063 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001356 | | | 2.21 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6138.00 ave 6138 max 6138 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: 141772.0 ave 141772 max 141772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141772 Ave neighs/atom = 259.65568 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 4 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.086 | 5.086 | 5.086 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2654.2478 0 -2654.2478 -2.3805062 Loop time of 2.019e-06 on 1 procs for 0 steps with 546 atoms 148.6% 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 | | 2.019e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6134.00 ave 6134 max 6134 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: 141072.0 ave 141072 max 141072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141072 Ave neighs/atom = 258.37363 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 = 8.9 ghost atom cutoff = 8.9 binsize = 4.45, bins = 4 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.9 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) = 5.086 | 5.086 | 5.086 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 -2654.2478 -2654.2478 14.537609 82.103758 4.9795861 -2.3805062 -2.3805062 -0.90310159 48.107524 -54.345941 2.3308659 369.63895 Loop time of 2.156e-06 on 1 procs for 0 steps with 546 atoms 231.9% 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 | | 2.156e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6134.00 ave 6134 max 6134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70536.0 ave 70536 max 70536 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141072.0 ave 141072 max 141072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141072 Ave neighs/atom = 258.37363 Neighbor list builds = 0 Dangerous builds = 0 546 -2654.24775902103 eV 2.33086589473158 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01