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 = 4.1768978 4.1768978 4.1768978 Created orthogonal box = (0.0000000 -79.912937 0.0000000) to (46.135344 79.912937 7.2345992) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8068541 6.1132385 7.2345992 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -79.912937 0.0000000) to (46.135344 79.912937 7.2345992) create_atoms CPU = 0.009 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8068541 6.1132385 7.2345992 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -79.912937 0.0000000) to (46.135344 79.912937 7.2345992) create_atoms CPU = 0.008 seconds 1466 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 14 49 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 2900 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_072689718616_001#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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.387 | 5.387 | 5.387 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -21271.987 0 -21271.987 -3412.8387 631 0 -21465.706 0 -21465.706 -26483.786 Loop time of 243.31 on 1 procs for 631 steps with 2900 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 = -21271.9866307563 -21465.6892189879 -21465.7061386875 Force two-norm initial, final = 43.721508 0.45767213 Force max component initial, final = 8.2285306 0.064220244 Final line search alpha, max atom move = 1.0000000 0.064220244 Iterations, force evaluations = 631 1122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 241.92 | 241.92 | 241.92 | 0.0 | 99.43 Neigh | 0.80575 | 0.80575 | 0.80575 | 0.0 | 0.33 Comm | 0.23922 | 0.23922 | 0.23922 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3439 | | | 0.14 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8619.00 ave 8619 max 8619 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: 178300.0 ave 178300 max 178300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178300 Ave neighs/atom = 61.482759 Neighbor list builds = 24 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 631 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.383 | 5.383 | 5.383 Mbytes Step Temp E_pair E_mol TotEng Press Volume 631 0 -21465.706 0 -21465.706 -26483.786 53345.198 644 0 -21472.555 0 -21472.555 -8832.6514 52835.816 Loop time of 3.04922 on 1 procs for 13 steps with 2900 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -21465.7061386876 -21472.5536447877 -21472.5552811387 Force two-norm initial, final = 1166.9273 4.0919076 Force max component initial, final = 1151.7932 3.0836025 Final line search alpha, max atom move = 7.6671797e-05 0.00023642535 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0324 | 3.0324 | 3.0324 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028117 | 0.0028117 | 0.0028117 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01399 | | | 0.46 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8611.00 ave 8611 max 8611 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: 178408.0 ave 178408 max 178408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178408 Ave neighs/atom = 61.520000 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.521 | 5.521 | 5.521 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -21472.555 0 -21472.555 -8832.6514 Loop time of 6.374e-06 on 1 procs for 0 steps with 2900 atoms 172.6% 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 | | 6.374e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8622.00 ave 8622 max 8622 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: 179152.0 ave 179152 max 179152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179152 Ave neighs/atom = 61.776552 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.521 | 5.521 | 5.521 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 -21472.555 -21472.555 45.576644 159.82587 7.253356 -8832.6514 -8832.6514 -92.373821 -26341.776 -63.803982 2.588965 8795.9903 Loop time of 6.876e-06 on 1 procs for 0 steps with 2900 atoms 290.9% 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 | | 6.876e-06 | | |100.00 Nlocal: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8622.00 ave 8622 max 8622 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89576.0 ave 89576 max 89576 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179152.0 ave 179152 max 179152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179152 Ave neighs/atom = 61.776552 Neighbor list builds = 0 Dangerous builds = 0 2900 -21472.5552811387 eV 2.58896504801189 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:04:07