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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -47.296215 0.0000000) to (33.443474 47.296215 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2220417 6.0495159 5.1000820 Created 684 atoms using lattice units in orthogonal box = (0.0000000 -47.296215 0.0000000) to (33.443474 47.296215 5.1000820) create_atoms CPU = 0.002 seconds 684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2220417 6.0495159 5.1000820 Created 692 atoms using lattice units in orthogonal box = (0.0000000 -47.296215 0.0000000) to (33.443474 47.296215 5.1000820) create_atoms CPU = 0.002 seconds 692 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1376 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 11.82 | 11.82 | 11.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5537.0701 0 -5537.0701 37325.744 98 0 -5761.045 0 -5761.045 4518.5001 Loop time of 6.27387 on 1 procs for 98 steps with 1376 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5537.07013076889 -5761.03971779657 -5761.04500712542 Force two-norm initial, final = 241.32034 0.32670980 Force max component initial, final = 56.074227 0.045862841 Final line search alpha, max atom move = 1.0000000 0.045862841 Iterations, force evaluations = 98 171 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1216 | 6.1216 | 6.1216 | 0.0 | 97.57 Neigh | 0.11124 | 0.11124 | 0.11124 | 0.0 | 1.77 Comm | 0.027089 | 0.027089 | 0.027089 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01394 | | | 0.22 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15587.0 ave 15587 max 15587 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: 852708.0 ave 852708 max 852708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 852708 Ave neighs/atom = 619.70058 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.82 | 11.82 | 11.82 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -5761.045 0 -5761.045 4518.5001 16134.107 104 0 -5761.4839 0 -5761.4839 -43.74375 16176.115 Loop time of 0.345705 on 1 procs for 6 steps with 1376 atoms 92.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5761.04500712546 -5761.48378478216 -5761.48385863333 Force two-norm initial, final = 170.85720 0.96745903 Force max component initial, final = 155.54146 0.64260056 Final line search alpha, max atom move = 0.00048107882 0.00030914152 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3407 | 0.3407 | 0.3407 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010075 | 0.0010075 | 0.0010075 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003995 | | | 1.16 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15673.0 ave 15673 max 15673 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: 850606.0 ave 850606 max 850606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 850606 Ave neighs/atom = 618.17297 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 11.33 | 11.33 | 11.33 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5761.4839 0 -5761.4839 -43.74375 Loop time of 1.591e-06 on 1 procs for 0 steps with 1376 atoms 125.7% 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 | | 1.591e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15625.0 ave 15625 max 15625 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: 843802.0 ave 843802 max 843802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 843802 Ave neighs/atom = 613.22820 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 6 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 11.33 | 11.33 | 11.33 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 -5761.4839 -5761.4839 33.59088 94.335103 5.1048091 -43.74375 -43.74375 -63.927428 -50.786629 -16.517192 2.4114099 1330.2053 Loop time of 2.128e-06 on 1 procs for 0 steps with 1376 atoms 282.0% 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 | | 2.128e-06 | | |100.00 Nlocal: 1376.00 ave 1376 max 1376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15625.0 ave 15625 max 15625 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 421901.0 ave 421901 max 421901 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 843802.0 ave 843802 max 843802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 843802 Ave neighs/atom = 613.22820 Neighbor list builds = 0 Dangerous builds = 0 1376 -5761.48385863333 eV 2.41140985881435 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07