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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) create_atoms CPU = 0.003 seconds 681 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0822973 5.0822973 3.6043435 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -66.464415 0.0000000) to (33.230405 66.464415 3.6043435) create_atoms CPU = 0.002 seconds 681 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 44 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1359 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5714.4928 0 -5714.4928 10563.023 43 0 -5763.4189 0 -5763.4189 199.04852 Loop time of 7.83476 on 1 procs for 43 steps with 1359 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 = -5714.49283707045 -5763.41348511156 -5763.41892823203 Force two-norm initial, final = 36.802735 0.23787220 Force max component initial, final = 9.7061800 0.095299510 Final line search alpha, max atom move = 1.0000000 0.095299510 Iterations, force evaluations = 43 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.7944 | 7.7944 | 7.7944 | 0.0 | 99.48 Neigh | 0.016877 | 0.016877 | 0.016877 | 0.0 | 0.22 Comm | 0.011428 | 0.011428 | 0.011428 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01209 | | | 0.15 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6789.00 ave 6789 max 6789 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: 105708.0 ave 105708 max 105708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105708 Ave neighs/atom = 77.783664 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -5763.4189 0 -5763.4189 199.04852 15921.39 51 0 -5763.6782 0 -5763.6782 -2306.1597 15945.667 Loop time of 1.15162 on 1 procs for 8 steps with 1359 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 = -5763.41892823203 -5763.67778343641 -5763.67823158245 Force two-norm initial, final = 54.707171 0.36372710 Force max component initial, final = 44.113446 0.12107623 Final line search alpha, max atom move = 0.00054787874 6.6335094e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1446 | 1.1446 | 1.1446 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015081 | 0.0015081 | 0.0015081 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005504 | | | 0.48 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6781.00 ave 6781 max 6781 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: 105870.0 ave 105870 max 105870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105870 Ave neighs/atom = 77.902870 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.191 | 5.191 | 5.191 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5763.6782 0 -5763.6782 -2306.1597 Loop time of 7.006e-06 on 1 procs for 0 steps with 1359 atoms 199.8% 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 | | 7.006e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6785.00 ave 6785 max 6785 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: 105840.0 ave 105840 max 105840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105840 Ave neighs/atom = 77.880795 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.191 | 5.191 | 5.191 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 -5763.6782 -5763.6782 33.040035 132.92883 3.6306385 -2306.1597 -2306.1597 2.2777429 -6917.3624 -3.3944065 2.287914 155.07174 Loop time of 6.425e-06 on 1 procs for 0 steps with 1359 atoms 264.6% 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 | | 6.425e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6785.00 ave 6785 max 6785 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52920.0 ave 52920 max 52920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 105840.0 ave 105840 max 105840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105840 Ave neighs/atom = 77.880795 Neighbor list builds = 0 Dangerous builds = 0 1359 -5763.67823158245 eV 2.28791402812939 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09