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 -47.820624 0.0000000) to (29.281825 47.820624 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3239682 5.4337523 5.8858683 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -47.820624 0.0000000) to (29.281825 47.820624 8.8288024) create_atoms CPU = 0.001 seconds 1072 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3239682 5.4337523 5.8858683 Created 1072 atoms using lattice units in orthogonal box = (0.0000000 -47.820624 0.0000000) to (29.281825 47.820624 8.8288024) create_atoms CPU = 0.001 seconds 1072 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 = 10 32 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 80 atoms, new total = 2064 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 = 10 32 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) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8678.2169 0 -8678.2169 -10569.294 59 0 -8749.0737 0 -8749.0737 -34642.218 Loop time of 6.2006 on 1 procs for 59 steps with 2064 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 = -8678.21686816703 -8749.0674797852 -8749.07367361746 Force two-norm initial, final = 8.6833755 0.18129295 Force max component initial, final = 1.2317342 0.019852131 Final line search alpha, max atom move = 1.0000000 0.019852131 Iterations, force evaluations = 59 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1596 | 6.1596 | 6.1596 | 0.0 | 99.34 Neigh | 0.024288 | 0.024288 | 0.024288 | 0.0 | 0.39 Comm | 0.0063041 | 0.0063041 | 0.0063041 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01038 | | | 0.17 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5713.00 ave 5713 max 5713 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: 160542.0 ave 160542 max 160542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160542 Ave neighs/atom = 77.781977 Neighbor list builds = 2 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 = 10 32 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -8749.0737 0 -8749.0737 -34642.218 24725.505 72 0 -8754.0887 0 -8754.0887 -5704.1639 24261.438 Loop time of 0.93136 on 1 procs for 13 steps with 2064 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 = -8749.07367361748 -8754.08094591962 -8754.0886872561 Force two-norm initial, final = 713.59171 8.4506359 Force max component initial, final = 555.18842 7.5323557 Final line search alpha, max atom move = 5.7668608e-05 0.00043438047 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92599 | 0.92599 | 0.92599 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069988 | 0.00069988 | 0.00069988 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004671 | | | 0.50 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5715.00 ave 5715 max 5715 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: 160512.0 ave 160512 max 160512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160512 Ave neighs/atom = 77.767442 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 = 10 32 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) = 5.253 | 5.253 | 5.253 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8754.0887 0 -8754.0887 -5704.1639 Loop time of 1.875e-06 on 1 procs for 0 steps with 2064 atoms 213.3% 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 | | 1.875e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5779.00 ave 5779 max 5779 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: 160668.0 ave 160668 max 160668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160668 Ave neighs/atom = 77.843023 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 = 10 32 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) = 5.253 | 5.253 | 5.253 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 -8754.0887 -8754.0887 28.919948 95.641249 8.7714987 -5704.1639 -5704.1639 -491.27424 -16371.295 -249.92232 2.455146 487.62033 Loop time of 2.069e-06 on 1 procs for 0 steps with 2064 atoms 193.3% 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 | | 2.069e-06 | | |100.00 Nlocal: 2064.00 ave 2064 max 2064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5779.00 ave 5779 max 5779 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80334.0 ave 80334 max 80334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160668.0 ave 160668 max 160668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160668 Ave neighs/atom = 77.843023 Neighbor list builds = 0 Dangerous builds = 0 2064 -8754.0886872561 eV 2.45514604553273 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07