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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -53.079949 0.0000000) to (37.530330 53.079949 5.7233217) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9823870 6.7887781 5.7233217 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -53.079949 0.0000000) to (37.530330 53.079949 5.7233217) create_atoms CPU = 0.002 seconds 693 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9823870 6.7887781 5.7233217 Created 693 atoms using lattice units in orthogonal box = (0.0000000 -53.079949 0.0000000) to (37.530330 53.079949 5.7233217) create_atoms CPU = 0.001 seconds 693 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 30 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 1373 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4539.3939 0 -4539.3939 11260.719 47 0 -4600.5437 0 -4600.5437 1534.3174 Loop time of 4.95179 on 1 procs for 47 steps with 1373 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4539.39393751669 -4600.5404594117 -4600.54366734764 Force two-norm initial, final = 46.800878 0.16629740 Force max component initial, final = 7.0068567 0.044367967 Final line search alpha, max atom move = 0.70266343 0.031175748 Iterations, force evaluations = 47 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9289 | 4.9289 | 4.9289 | 0.0 | 99.54 Neigh | 0.0093497 | 0.0093497 | 0.0093497 | 0.0 | 0.19 Comm | 0.0068116 | 0.0068116 | 0.0068116 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006685 | | | 0.14 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 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: 117378.0 ave 117378 max 117378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117378 Ave neighs/atom = 85.490168 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -4600.5437 0 -4600.5437 1534.3174 22802.95 49 0 -4600.554 0 -4600.554 591.07181 22830.259 Loop time of 0.287526 on 1 procs for 2 steps with 1373 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 = -4600.54366734765 -4600.55337549237 -4600.55397368497 Force two-norm initial, final = 21.689462 0.16996951 Force max component initial, final = 18.281078 0.045283013 Final line search alpha, max atom move = 0.00042178195 1.9099557e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28611 | 0.28611 | 0.28611 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024112 | 0.00024112 | 0.00024112 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001175 | | | 0.41 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 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: 117472.0 ave 117472 max 117472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117472 Ave neighs/atom = 85.558631 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.199 | 5.199 | 5.199 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4600.554 0 -4600.554 591.07181 Loop time of 1.897e-06 on 1 procs for 0 steps with 1373 atoms 158.1% 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 | | 1.897e-06 | | |100.00 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 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: 117460.0 ave 117460 max 117460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117460 Ave neighs/atom = 85.549891 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.199 | 5.199 | 5.199 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 -4600.554 -4600.554 37.537337 106.1599 5.7291064 591.07181 591.07181 0.024673929 1774.633 -1.4422497 2.5263035 910.98876 Loop time of 1.89e-06 on 1 procs for 0 steps with 1373 atoms 211.6% 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 | | 1.89e-06 | | |100.00 Nlocal: 1373.00 ave 1373 max 1373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6139.00 ave 6139 max 6139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58730.0 ave 58730 max 58730 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117460.0 ave 117460 max 117460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117460 Ave neighs/atom = 85.549891 Neighbor list builds = 0 Dangerous builds = 0 1373 -4600.55397368497 eV 2.52630346994079 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05