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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -54.138856 0.0000000) to (44.204191 54.138856 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498317 5.1913971 5.9740848 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -54.138856 0.0000000) to (44.204191 54.138856 8.9611272) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498317 5.1913971 5.9740848 Created 1759 atoms using lattice units in orthogonal box = (0.0000000 -54.138856 0.0000000) to (44.204191 54.138856 8.9611272) create_atoms CPU = 0.002 seconds 1759 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 3503 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.970 | 6.970 | 6.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12604.707 0 -12604.707 86346.278 860 0 -14148.411 0 -14148.411 -48788.618 Loop time of 41.3239 on 1 procs for 860 steps with 3503 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 = -12604.7071269012 -14148.3965404974 -14148.4106745503 Force two-norm initial, final = 1940.7144 0.35420897 Force max component initial, final = 311.43201 0.067003133 Final line search alpha, max atom move = 0.80774068 0.054121156 Iterations, force evaluations = 860 1692 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 40.347 | 40.347 | 40.347 | 0.0 | 97.64 Neigh | 0.55267 | 0.55267 | 0.55267 | 0.0 | 1.34 Comm | 0.17422 | 0.17422 | 0.17422 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2502 | | | 0.61 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10914.0 ave 10914 max 10914 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: 532012.0 ave 532012 max 532012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 532012 Ave neighs/atom = 151.87325 Neighbor list builds = 16 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 860 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.971 | 6.971 | 6.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 860 0 -14148.411 0 -14148.411 -48788.618 42890.899 898 0 -14201.396 0 -14201.396 -16.23852 41570.09 Loop time of 1.02724 on 1 procs for 38 steps with 3503 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 = -14148.4106745503 -14201.3930095986 -14201.3959468972 Force two-norm initial, final = 2721.6098 9.2398994 Force max component initial, final = 2025.2968 5.2323004 Final line search alpha, max atom move = 0.00014569305 0.00076230979 Iterations, force evaluations = 38 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90015 | 0.90015 | 0.90015 | 0.0 | 87.63 Neigh | 0.10034 | 0.10034 | 0.10034 | 0.0 | 9.77 Comm | 0.0040441 | 0.0040441 | 0.0040441 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02271 | | | 2.21 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10870.0 ave 10870 max 10870 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: 551542.0 ave 551542 max 551542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 551542 Ave neighs/atom = 157.44847 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.108 | 7.108 | 7.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14201.396 0 -14201.396 -16.23852 Loop time of 2.039e-06 on 1 procs for 0 steps with 3503 atoms 147.1% 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 | | 2.039e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10854.0 ave 10854 max 10854 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: 552178.0 ave 552178 max 552178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552178 Ave neighs/atom = 157.63003 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.108 | 7.108 | 7.108 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 -14201.396 -14201.396 43.082713 105.07284 9.1830609 -16.23852 -16.23852 62.421255 95.518645 -206.65546 2.2191106 6306.3338 Loop time of 2.489e-06 on 1 procs for 0 steps with 3503 atoms 281.2% 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 | | 2.489e-06 | | |100.00 Nlocal: 3503.00 ave 3503 max 3503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10854.0 ave 10854 max 10854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 276089.0 ave 276089 max 276089 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 552178.0 ave 552178 max 552178 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552178 Ave neighs/atom = 157.63003 Neighbor list builds = 0 Dangerous builds = 0 3503 -14201.3959468972 eV 2.21911058640002 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:42