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 -50.721213 0.0000000) to (11.954255 50.721213 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4337523 6.1475889 5.0973115 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.721213 0.0000000) to (11.954255 50.721213 5.0973115) create_atoms CPU = 0.001 seconds 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4337523 6.1475889 5.0973115 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -50.721213 0.0000000) to (11.954255 50.721213 5.0973115) create_atoms CPU = 0.001 seconds 266 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 = 4 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 12 atoms, new total = 520 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 = 4 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) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2190.9634 0 -2190.9634 -6030.9829 41 0 -2201.9128 0 -2201.9128 -21115.746 Loop time of 1.18598 on 1 procs for 41 steps with 520 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 = -2190.96342114566 -2201.91059570935 -2201.91279418457 Force two-norm initial, final = 6.4133819 0.14618202 Force max component initial, final = 1.9945835 0.023570562 Final line search alpha, max atom move = 1.0000000 0.023570562 Iterations, force evaluations = 41 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1787 | 1.1787 | 1.1787 | 0.0 | 99.38 Neigh | 0.0031898 | 0.0031898 | 0.0031898 | 0.0 | 0.27 Comm | 0.0019456 | 0.0019456 | 0.0019456 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002184 | | | 0.18 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3278.00 ave 3278 max 3278 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: 40404.0 ave 40404 max 40404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40404 Ave neighs/atom = 77.700000 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 = 4 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -2201.9128 0 -2201.9128 -21115.746 6181.3497 57 0 -2202.7472 0 -2202.7472 -1421.8247 6103.6619 Loop time of 0.329822 on 1 procs for 16 steps with 520 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 = -2201.91279418456 -2202.74639120836 -2202.74723915526 Force two-norm initial, final = 127.56126 0.32011447 Force max component initial, final = 116.33390 0.11585550 Final line search alpha, max atom move = 0.00056496754 6.5454597e-05 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3272 | 0.3272 | 0.3272 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044303 | 0.00044303 | 0.00044303 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002177 | | | 0.66 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3250.00 ave 3250 max 3250 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: 40352.0 ave 40352 max 40352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40352 Ave neighs/atom = 77.600000 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 = 4 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2202.7472 0 -2202.7472 -1421.8247 Loop time of 1.861e-06 on 1 procs for 0 steps with 520 atoms 161.2% 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 | | 1.861e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3282.00 ave 3282 max 3282 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: 40352.0 ave 40352 max 40352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40352 Ave neighs/atom = 77.600000 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 = 4 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) = 4.642 | 4.642 | 4.642 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 -2202.7472 -2202.7472 11.769187 101.44243 5.1123948 -1421.8247 -1421.8247 -14.829922 -4220.1427 -30.501399 2.360748 399.37788 Loop time of 1.784e-06 on 1 procs for 0 steps with 520 atoms 224.2% 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 | | 1.784e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3282.00 ave 3282 max 3282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20176.0 ave 20176 max 20176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40352.0 ave 40352 max 40352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40352 Ave neighs/atom = 77.600000 Neighbor list builds = 0 Dangerous builds = 0 520 -2202.74723915526 eV 2.36074800829071 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01