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 -51.483927 0.0000000) to (36.402085 51.483927 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7101310 4.5423814 5.0973115 Created 824 atoms using lattice units in orthogonal box = (0.0000000 -51.483927 0.0000000) to (36.402085 51.483927 5.0973115) create_atoms CPU = 0.001 seconds 824 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7101310 4.5423814 5.0973115 Created 824 atoms using lattice units in orthogonal box = (0.0000000 -51.483927 0.0000000) to (36.402085 51.483927 5.0973115) create_atoms CPU = 0.001 seconds 824 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 = 12 34 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 40 atoms, new total = 1608 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 = 12 34 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) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6775.8581 0 -6775.8581 -6452.2338 131 0 -6809.6822 0 -6809.6822 -20638.45 Loop time of 13.5938 on 1 procs for 131 steps with 1608 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 = -6775.85808833131 -6809.6755050988 -6809.68224219183 Force two-norm initial, final = 12.528361 0.24248510 Force max component initial, final = 2.2321437 0.018166565 Final line search alpha, max atom move = 1.0000000 0.018166565 Iterations, force evaluations = 131 236 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.55 | 13.55 | 13.55 | 0.0 | 99.68 Neigh | 0.0086763 | 0.0086763 | 0.0086763 | 0.0 | 0.06 Comm | 0.016406 | 0.016406 | 0.016406 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01835 | | | 0.13 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6193.00 ave 6193 max 6193 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: 125184.0 ave 125184 max 125184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125184 Ave neighs/atom = 77.850746 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 = 12 34 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 : 131 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.118 | 5.118 | 5.118 Mbytes Step Temp E_pair E_mol TotEng Press Volume 131 0 -6809.6822 0 -6809.6822 -20638.45 19105.97 139 0 -6811.2194 0 -6811.2194 -1197.9386 18869.857 Loop time of 0.586405 on 1 procs for 8 steps with 1608 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 = -6809.68224219183 -6811.21926731442 -6811.21936285639 Force two-norm initial, final = 347.05919 0.42795281 Force max component initial, final = 254.40497 0.099139934 Final line search alpha, max atom move = 0.00068510906 6.7921667e-05 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.58295 | 0.58295 | 0.58295 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053582 | 0.00053582 | 0.00053582 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002923 | | | 0.50 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6437.00 ave 6437 max 6437 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: 124864.0 ave 124864 max 124864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 124864 Ave neighs/atom = 77.651741 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 = 12 34 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) = 5.258 | 5.258 | 5.258 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6811.2194 0 -6811.2194 -1197.9386 Loop time of 1.797e-06 on 1 procs for 0 steps with 1608 atoms 166.9% 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 | | 1.797e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6739.00 ave 6739 max 6739 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: 125052.0 ave 125052 max 125052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125052 Ave neighs/atom = 77.768657 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 = 12 34 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) = 5.258 | 5.258 | 5.258 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 -6811.2194 -6811.2194 36.160696 102.96785 5.0679248 -1197.9386 -1197.9386 2.254021 -3587.7006 -8.3691118 2.3682309 896.0965 Loop time of 2.026e-06 on 1 procs for 0 steps with 1608 atoms 148.1% 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 | | 2.026e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6739.00 ave 6739 max 6739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 62526.0 ave 62526 max 62526 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 125052.0 ave 125052 max 125052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125052 Ave neighs/atom = 77.768657 Neighbor list builds = 0 Dangerous builds = 0 1608 -6811.21936285639 eV 2.36823087000408 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14