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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -34.639021 0.0000000) to (42.423963 34.639021 7.0220643) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0680512 4.2705642 4.6813762 Created 874 atoms using lattice units in orthogonal box = (0.0000000 -34.639021 0.0000000) to (42.423963 34.639021 7.0220643) create_atoms CPU = 0.006 seconds 874 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0680512 4.2705642 4.6813762 Created 880 atoms using lattice units in orthogonal box = (0.0000000 -34.639021 0.0000000) to (42.423963 34.639021 7.0220643) create_atoms CPU = 0.003 seconds 880 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 18 2 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1752 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4996.1873 0 -4996.1873 221475.97 83 0 -7439.9326 0 -7439.9326 9543.4111 Loop time of 4.09469 on 1 procs for 83 steps with 1752 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 = -4996.18734615226 -7439.92634635902 -7439.93263038439 Force two-norm initial, final = 2544.0015 0.31826049 Force max component initial, final = 330.27279 0.077716769 Final line search alpha, max atom move = 0.68368092 0.053133472 Iterations, force evaluations = 83 144 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9168 | 3.9168 | 3.9168 | 0.0 | 95.66 Neigh | 0.11987 | 0.11987 | 0.11987 | 0.0 | 2.93 Comm | 0.028708 | 0.028708 | 0.028708 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02932 | | | 0.72 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7538.00 ave 7538 max 7538 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: 291176.0 ave 291176 max 291176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 291176 Ave neighs/atom = 166.19635 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.565 | 5.565 | 5.565 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -7439.9326 0 -7439.9326 9543.4111 20638.192 89 0 -7440.5732 0 -7440.5732 25.574701 20732.551 Loop time of 0.225188 on 1 procs for 6 steps with 1752 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 = -7439.93263038439 -7440.56614553841 -7440.57321624204 Force two-norm initial, final = 257.28874 1.8663220 Force max component initial, final = 238.11200 1.4707962 Final line search alpha, max atom move = 6.0442186e-05 8.8898136e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21818 | 0.21818 | 0.21818 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014099 | 0.0014099 | 0.0014099 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005603 | | | 2.49 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7884.00 ave 7884 max 7884 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: 290994.0 ave 290994 max 290994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290994 Ave neighs/atom = 166.09247 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.703 | 5.703 | 5.703 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7440.5732 0 -7440.5732 25.574701 Loop time of 6.836e-06 on 1 procs for 0 steps with 1752 atoms 160.9% 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 | | 6.836e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7862.00 ave 7862 max 7862 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: 290758.0 ave 290758 max 290758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290758 Ave neighs/atom = 165.95776 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.703 | 5.703 | 5.703 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 -7440.5732 -7440.5732 42.416964 69.663961 7.0162492 25.574701 25.574701 -45.875865 9.0334543 113.56652 2.3391928 1660.7186 Loop time of 7.207e-06 on 1 procs for 0 steps with 1752 atoms 263.6% 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 | | 7.207e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7862.00 ave 7862 max 7862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 145379.0 ave 145379 max 145379 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 290758.0 ave 290758 max 290758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290758 Ave neighs/atom = 165.95776 Neighbor list builds = 0 Dangerous builds = 0 1752 -7440.57321624204 eV 2.33919283553234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05