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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -62.982450 0.0000000) to (31.491225 62.982450 4.0320382) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6787455 5.6787455 4.0320382 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -62.982450 0.0000000) to (31.491225 62.982450 4.0320382) create_atoms CPU = 0.003 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6787455 5.6787455 4.0320382 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -62.982450 0.0000000) to (31.491225 62.982450 4.0320382) 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 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 8.68 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3195.8705 0 -3195.8705 13991.219 86 0 -3280.205 0 -3280.205 4311.203 Loop time of 3.34084 on 1 procs for 86 steps with 978 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3195.87051685725 -3280.20176546272 -3280.2049800762 Force two-norm initial, final = 49.532919 0.15194203 Force max component initial, final = 7.9343360 0.029303635 Final line search alpha, max atom move = 1.0000000 0.029303635 Iterations, force evaluations = 86 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2655 | 3.2655 | 3.2655 | 0.0 | 97.75 Neigh | 0.021032 | 0.021032 | 0.021032 | 0.0 | 0.63 Comm | 0.032052 | 0.032052 | 0.032052 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02223 | | | 0.67 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7972.00 ave 7972 max 7972 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: 169976.0 ave 169976 max 169976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169976 Ave neighs/atom = 173.79959 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.026 | 5.026 | 5.026 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -3280.205 0 -3280.205 4311.203 15994.245 93 0 -3280.4337 0 -3280.4337 3.7484742 16073.184 Loop time of 0.229216 on 1 procs for 7 steps with 978 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 = -3280.2049800762 -3280.43365397522 -3280.43368082414 Force two-norm initial, final = 86.734076 0.27929192 Force max component initial, final = 75.267932 0.12038793 Final line search alpha, max atom move = 0.0012545076 0.00015102758 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22096 | 0.22096 | 0.22096 | 0.0 | 96.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017998 | 0.0017998 | 0.0017998 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006461 | | | 2.82 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7642.00 ave 7642 max 7642 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: 170256.0 ave 170256 max 170256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170256 Ave neighs/atom = 174.08589 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.164 | 5.164 | 5.164 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3280.4337 0 -3280.4337 3.7484742 Loop time of 6.255e-06 on 1 procs for 0 steps with 978 atoms 207.8% 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 | | 6.255e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7647.00 ave 7647 max 7647 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: 169924.0 ave 169924 max 169924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169924 Ave neighs/atom = 173.74642 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.164 | 5.164 | 5.164 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 -3280.4337 -3280.4337 31.418476 126.69592 4.0378872 3.7484742 3.7484742 11.972558 8.8889444 -9.6160794 2.5845 198.16355 Loop time of 6.475e-06 on 1 procs for 0 steps with 978 atoms 231.7% 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 | | 6.475e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7647.00 ave 7647 max 7647 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 84962.0 ave 84962 max 84962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 169924.0 ave 169924 max 169924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169924 Ave neighs/atom = 173.74642 Neighbor list builds = 0 Dangerous builds = 0 978 -3280.43368082414 eV 2.58449997393671 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04