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 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) create_atoms CPU = 0.002 seconds 1690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9693600 5.4832072 5.8858683 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -42.650772 0.0000000) to (52.231900 42.650772 8.8288024) create_atoms CPU = 0.002 seconds 1690 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 = 18 28 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 74 atoms, new total = 3306 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 = 18 28 3 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) = 5.683 | 5.683 | 5.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13939.033 0 -13939.033 -8925.3784 203 0 -14001.312 0 -14001.312 -23082.037 Loop time of 44.6089 on 1 procs for 203 steps with 3306 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 = -13939.0333467815 -14001.298515331 -14001.3122451005 Force two-norm initial, final = 9.4250612 0.33241045 Force max component initial, final = 1.0561238 0.055389829 Final line search alpha, max atom move = 0.82784661 0.045854283 Iterations, force evaluations = 203 389 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 44.451 | 44.451 | 44.451 | 0.0 | 99.65 Neigh | 0.061808 | 0.061808 | 0.061808 | 0.0 | 0.14 Comm | 0.036604 | 0.036604 | 0.036604 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05941 | | | 0.13 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7861.00 ave 7861 max 7861 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: 254048.0 ave 254048 max 254048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 254048 Ave neighs/atom = 76.844525 Neighbor list builds = 3 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 = 18 28 3 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 : 203 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.681 | 5.681 | 5.681 Mbytes Step Temp E_pair E_mol TotEng Press Volume 203 0 -14001.312 0 -14001.312 -23082.037 39336.391 223 0 -14011.009 0 -14011.009 -1665.7102 38790.805 Loop time of 2.77754 on 1 procs for 20 steps with 3306 atoms 88.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14001.3122451005 -14011.0091653354 -14011.0093758702 Force two-norm initial, final = 1069.5414 1.9523627 Force max component initial, final = 1054.4805 1.3384576 Final line search alpha, max atom move = 0.00029170924 0.00039044046 Iterations, force evaluations = 20 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.718 | 2.718 | 2.718 | 0.0 | 97.85 Neigh | 0.04732 | 0.04732 | 0.04732 | 0.0 | 1.70 Comm | 0.0016357 | 0.0016357 | 0.0016357 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01063 | | | 0.38 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7786.00 ave 7786 max 7786 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: 255340.0 ave 255340 max 255340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255340 Ave neighs/atom = 77.235330 Neighbor list builds = 1 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 = 17 28 3 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) = 5.818 | 5.818 | 5.818 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14011.009 0 -14011.009 -1665.7102 Loop time of 2.267e-06 on 1 procs for 0 steps with 3306 atoms 176.4% 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 | | 2.267e-06 | | |100.00 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7787.00 ave 7787 max 7787 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: 255266.0 ave 255266 max 255266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255266 Ave neighs/atom = 77.212946 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 = 17 28 3 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) = 5.818 | 5.818 | 5.818 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 -14011.009 -14011.009 51.243251 85.301544 8.874323 -1665.7102 -1665.7102 41.841601 -5094.5396 55.567342 2.3821804 6697.315 Loop time of 2.195e-06 on 1 procs for 0 steps with 3306 atoms 227.8% 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 | | 2.195e-06 | | |100.00 Nlocal: 3306.00 ave 3306 max 3306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7787.00 ave 7787 max 7787 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127633.0 ave 127633 max 127633 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255266.0 ave 255266 max 255266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255266 Ave neighs/atom = 77.212946 Neighbor list builds = 0 Dangerous builds = 0 3306 -14011.0093758702 eV 2.38218036724519 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:48