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 -53.339413 0.0000000) to (43.551448 53.339413 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3693566 5.1147382 5.8858683 Created 1752 atoms using lattice units in orthogonal box = (0.0000000 -53.339413 0.0000000) to (43.551448 53.339413 8.8288024) create_atoms CPU = 0.003 seconds 1752 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 -53.339413 0.0000000) to (43.551448 53.339413 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 15 35 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 0 atoms, new total = 3512 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 = 15 35 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) = 5.689 | 5.689 | 5.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14067.094 0 -14067.094 83597.979 103 0 -14864.826 0 -14864.826 8311.7866 Loop time of 22.1768 on 1 procs for 103 steps with 3512 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 = -14067.093958381 -14864.8139607374 -14864.8260324458 Force two-norm initial, final = 1056.4159 0.48218853 Force max component initial, final = 206.21045 0.067103397 Final line search alpha, max atom move = 1.0000000 0.067103397 Iterations, force evaluations = 103 190 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.06 | 22.06 | 22.06 | 0.0 | 99.47 Neigh | 0.064557 | 0.064557 | 0.064557 | 0.0 | 0.29 Comm | 0.020547 | 0.020547 | 0.020547 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03177 | | | 0.14 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8544.00 ave 8544 max 8544 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: 273744.0 ave 273744 max 273744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273744 Ave neighs/atom = 77.945330 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 = 15 35 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 : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.689 | 5.689 | 5.689 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -14864.826 0 -14864.826 8311.7866 41018.769 110 0 -14865.915 0 -14865.915 -151.1206 41231.237 Loop time of 1.03198 on 1 procs for 7 steps with 3512 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 = -14864.8260324459 -14865.9133612717 -14865.9145105471 Force two-norm initial, final = 418.57573 7.6100717 Force max component initial, final = 374.40244 5.6600097 Final line search alpha, max atom move = 9.1122791e-05 0.00051575588 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0269 | 1.0269 | 1.0269 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064638 | 0.00064638 | 0.00064638 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00445 | | | 0.43 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8537.00 ave 8537 max 8537 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: 273936.0 ave 273936 max 273936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273936 Ave neighs/atom = 78.000000 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 = 15 35 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) = 5.826 | 5.826 | 5.826 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14865.915 0 -14865.915 -151.1206 Loop time of 2.298e-06 on 1 procs for 0 steps with 3512 atoms 174.1% 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 | | 2.298e-06 | | |100.00 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8473.00 ave 8473 max 8473 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: 273488.0 ave 273488 max 273488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273488 Ave neighs/atom = 77.872437 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 = 15 35 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) = 5.826 | 5.826 | 5.826 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 -14865.915 -14865.915 43.538369 106.6021 8.8835889 -151.1206 -151.1206 -219.8724 -191.62426 -41.865134 2.211303 2264.2854 Loop time of 2.15e-06 on 1 procs for 0 steps with 3512 atoms 325.6% 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 | | 2.15e-06 | | |100.00 Nlocal: 3512.00 ave 3512 max 3512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8473.00 ave 8473 max 8473 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136744.0 ave 136744 max 136744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 273488.0 ave 273488 max 273488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 273488 Ave neighs/atom = 77.872437 Neighbor list builds = 0 Dangerous builds = 0 3512 -14865.9145105471 eV 2.21130298948388 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24