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 = 2.8599988 2.8599988 2.8599988 Created orthogonal box = (0.0000000 -36.625856 0.0000000) to (18.312928 36.625856 2.8599988) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0199110 4.0199110 2.8599988 Created 164 atoms using lattice units in orthogonal box = (0.0000000 -36.625856 0.0000000) to (18.312928 36.625856 2.8599988) create_atoms CPU = 0.001 seconds 164 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0199110 4.0199110 2.8599988 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -36.625856 0.0000000) to (18.312928 36.625856 2.8599988) create_atoms CPU = 0.001 seconds 165 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 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 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 329 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_763197941039_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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1041.9281 0 -1041.9281 229286.02 425 0 -1413.5576 0 -1413.5576 59662.66 Loop time of 4.86332 on 1 procs for 425 steps with 329 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1041.9281069553 -1413.55624455816 -1413.55761112162 Force two-norm initial, final = 1041.0189 0.18686754 Force max component initial, final = 361.12818 0.061557070 Final line search alpha, max atom move = 1.0000000 0.061557070 Iterations, force evaluations = 425 841 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7157 | 4.7157 | 4.7157 | 0.0 | 96.96 Neigh | 0.024081 | 0.024081 | 0.024081 | 0.0 | 0.50 Comm | 0.071949 | 0.071949 | 0.071949 | 0.0 | 1.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0516 | | | 1.06 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3870.00 ave 3870 max 3870 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: 43892.0 ave 43892 max 43892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43892 Ave neighs/atom = 133.41033 Neighbor list builds = 4 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 425 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes Step Temp E_pair E_mol TotEng Press Volume 425 0 -1413.5576 0 -1413.5576 59662.66 3836.5549 527 0 -1441.3711 0 -1441.3711 -965.84838 3871.4062 Loop time of 0.632486 on 1 procs for 102 steps with 329 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 = -1413.55761112162 -1441.37008331867 -1441.37113807418 Force two-norm initial, final = 522.68371 4.6309208 Force max component initial, final = 362.15589 2.4466193 Final line search alpha, max atom move = 0.0010162245 0.0024863144 Iterations, force evaluations = 102 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57618 | 0.57618 | 0.57618 | 0.0 | 91.10 Neigh | 0.01825 | 0.01825 | 0.01825 | 0.0 | 2.89 Comm | 0.0092019 | 0.0092019 | 0.0092019 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02886 | | | 4.56 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4022.00 ave 4022 max 4022 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: 44378.0 ave 44378 max 44378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44378 Ave neighs/atom = 134.88754 Neighbor list builds = 3 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1441.3711 0 -1441.3711 -965.84838 Loop time of 6.004e-06 on 1 procs for 0 steps with 329 atoms 183.2% 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 | | 6.004e-06 | | |100.00 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4065.00 ave 4065 max 4065 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: 44570.0 ave 44570 max 44570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44570 Ave neighs/atom = 135.47112 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 = 7.18 ghost atom cutoff = 7.18 binsize = 3.59, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.18 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) = 4.585 | 4.585 | 4.585 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 -1441.3711 -1441.3711 19.22775 77.039378 2.61353 -965.84838 -965.84838 -1063.1112 -1026.2565 -808.17745 2.3802962 1355.6472 Loop time of 6.666e-06 on 1 procs for 0 steps with 329 atoms 240.0% 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 | | 6.666e-06 | | |100.00 Nlocal: 329.000 ave 329 max 329 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4065.00 ave 4065 max 4065 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22285.0 ave 22285 max 22285 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44570.0 ave 44570 max 44570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44570 Ave neighs/atom = 135.47112 Neighbor list builds = 0 Dangerous builds = 0 329 -1441.37113807418 eV 2.38029618728374 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05