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 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3693566 5.1147382 5.8858683 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) create_atoms CPU = 0.002 seconds 1760 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3693566 5.1147382 5.8858683 Created 1760 atoms using lattice units in orthogonal box = (0.0000000 -53.343017 0.0000000) to (43.551448 53.343017 8.8288024) create_atoms CPU = 0.002 seconds 1760 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3464 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.695 | 5.695 | 5.695 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14589.37 0 -14589.37 -2798.4137 65 0 -14659.551 0 -14659.551 -13621.474 Loop time of 12.4456 on 1 procs for 65 steps with 3464 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 = -14589.3703370966 -14659.5384934142 -14659.5513078193 Force two-norm initial, final = 40.140087 0.47910931 Force max component initial, final = 6.8267539 0.071767599 Final line search alpha, max atom move = 1.0000000 0.071767599 Iterations, force evaluations = 65 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.395 | 12.395 | 12.395 | 0.0 | 99.59 Neigh | 0.020319 | 0.020319 | 0.020319 | 0.0 | 0.16 Comm | 0.011648 | 0.011648 | 0.011648 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01895 | | | 0.15 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8365.00 ave 8365 max 8365 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: 267104.0 ave 267104 max 267104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267104 Ave neighs/atom = 77.108545 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.701 | 5.701 | 5.701 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -14659.551 0 -14659.551 -13621.474 41021.541 72 0 -14660.759 0 -14660.759 -2952.0921 40744.403 Loop time of 0.94729 on 1 procs for 7 steps with 3464 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 = -14659.5513078194 -14660.7571342884 -14660.7593959368 Force two-norm initial, final = 426.85065 1.0458994 Force max component initial, final = 365.77080 0.59756568 Final line search alpha, max atom move = 0.00011251483 6.7235000e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.94247 | 0.94247 | 0.94247 | 0.0 | 99.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061458 | 0.00061458 | 0.00061458 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004204 | | | 0.44 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8321.00 ave 8321 max 8321 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: 266896.0 ave 266896 max 266896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266896 Ave neighs/atom = 77.048499 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.839 | 5.839 | 5.839 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14660.759 0 -14660.759 -2952.0921 Loop time of 2.318e-06 on 1 procs for 0 steps with 3464 atoms 215.7% 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 | | 2.318e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8334.00 ave 8334 max 8334 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: 267184.0 ave 267184 max 267184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267184 Ave neighs/atom = 77.131640 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 ghost atom cutoff = 6 binsize = 3, bins = 15 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.839 | 5.839 | 5.839 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 -14660.759 -14660.759 43.27709 106.68603 8.8247485 -2952.0921 -2952.0921 20.60559 -8900.369 23.487056 2.1923721 1991.641 Loop time of 2.212e-06 on 1 procs for 0 steps with 3464 atoms 271.2% 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 | | 2.212e-06 | | |100.00 Nlocal: 3464.00 ave 3464 max 3464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8334.00 ave 8334 max 8334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133592.0 ave 133592 max 133592 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 267184.0 ave 267184 max 267184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 267184 Ave neighs/atom = 77.131640 Neighbor list builds = 0 Dangerous builds = 0 3464 -14660.7593959368 eV 2.19237214498782 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14