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 = 3.5878716 3.5878716 3.5878716 Created orthogonal box = (0.0000000 -43.942273 0.0000000) to (6.2143759 43.942273 5.0740167) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2143759 5.8589698 5.0740167 Created 120 atoms using lattice units in orthogonal box = (0.0000000 -43.942273 0.0000000) to (6.2143759 43.942273 5.0740167) create_atoms CPU = 0.001 seconds 120 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2143759 5.8589698 5.0740167 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -43.942273 0.0000000) to (6.2143759 43.942273 5.0740167) create_atoms CPU = 0.001 seconds 122 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 2 22 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 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 240 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_228059236215_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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 4.494 | 4.494 | 4.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -818.90432 0 -818.90432 36847.89 79 0 -842.85069 0 -842.85069 5065.3421 Loop time of 0.836473 on 1 procs for 79 steps with 240 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 = -818.904322416136 -842.849847943178 -842.850685014735 Force two-norm initial, final = 58.250303 0.087259673 Force max component initial, final = 21.578423 0.019991632 Final line search alpha, max atom move = 1.0000000 0.019991632 Iterations, force evaluations = 79 151 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82401 | 0.82401 | 0.82401 | 0.0 | 98.51 Neigh | 0.0030983 | 0.0030983 | 0.0030983 | 0.0 | 0.37 Comm | 0.0059731 | 0.0059731 | 0.0059731 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003393 | | | 0.41 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4220.00 ave 4220 max 4220 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: 47904.0 ave 47904 max 47904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47904 Ave neighs/atom = 199.60000 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 2 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -842.85069 0 -842.85069 5065.3421 2771.1621 84 0 -842.89064 0 -842.89064 140.69583 2780.6129 Loop time of 0.0422839 on 1 procs for 5 steps with 240 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -842.850685014735 -842.890140225397 -842.89064018092 Force two-norm initial, final = 19.197622 0.47097356 Force max component initial, final = 17.944206 0.38201930 Final line search alpha, max atom move = 0.00076592678 0.00029259881 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040879 | 0.040879 | 0.040879 | 0.0 | 96.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031776 | 0.00031776 | 0.00031776 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001088 | | | 2.57 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3962.00 ave 3962 max 3962 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: 47964.0 ave 47964 max 47964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47964 Ave neighs/atom = 199.85000 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 4.629 | 4.629 | 4.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -842.89064 0 -842.89064 140.69583 Loop time of 2.293e-06 on 1 procs for 0 steps with 240 atoms 130.8% 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 | | 2.293e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3851.00 ave 3851 max 3851 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: 47928.0 ave 47928 max 47928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47928 Ave neighs/atom = 199.70000 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 = 8.2310608 ghost atom cutoff = 8.2310608 binsize = 4.1155304, bins = 2 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.231060792441781 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) = 4.629 | 4.629 | 4.629 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 -842.89064 -842.89064 6.2415001 87.751146 5.0769017 140.69583 140.69583 126.32594 75.518615 220.24294 2.4091314 215.24248 Loop time of 3.383e-06 on 1 procs for 0 steps with 240 atoms 147.8% 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 | | 3.383e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3851.00 ave 3851 max 3851 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23964.0 ave 23964 max 23964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47928.0 ave 47928 max 47928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47928 Ave neighs/atom = 199.70000 Neighbor list builds = 0 Dangerous builds = 0 240 -842.89064018092 eV 2.40913143621775 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01