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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5713292 6.7587366 5.5400000 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) create_atoms CPU = 0.008 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5713292 6.7587366 5.5400000 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -72.656419 0.0000000) to (25.687923 72.656419 5.5400000) create_atoms CPU = 0.007 seconds 690 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1378 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7686.1132 0 -7686.1132 37701.768 67 0 -7934.0294 0 -7934.0294 6887.653 Loop time of 7.29518 on 1 procs for 67 steps with 1378 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 = -7686.11316217262 -7934.02178128131 -7934.0294116184 Force two-norm initial, final = 329.54933 0.31329973 Force max component initial, final = 75.609317 0.058294068 Final line search alpha, max atom move = 1.0000000 0.058294068 Iterations, force evaluations = 67 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2559 | 7.2559 | 7.2559 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019124 | 0.019124 | 0.019124 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02014 | | | 0.28 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5991.00 ave 5991 max 5991 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: 107416.0 ave 107416 max 107416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107416 Ave neighs/atom = 77.950653 Neighbor list builds = 0 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -7934.0294 0 -7934.0294 6887.653 20679.629 71 0 -7934.304 0 -7934.304 291.09043 20756.527 Loop time of 0.337795 on 1 procs for 4 steps with 1378 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 = -7934.0294116184 -7934.29909943741 -7934.30395413813 Force two-norm initial, final = 174.12133 7.3536713 Force max component initial, final = 155.27193 6.3924179 Final line search alpha, max atom move = 7.5875527e-05 0.00048502808 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.33395 | 0.33395 | 0.33395 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082289 | 0.00082289 | 0.00082289 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003023 | | | 0.89 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 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: 106976.0 ave 106976 max 106976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106976 Ave neighs/atom = 77.631350 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.213 | 5.213 | 5.213 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7934.304 0 -7934.304 291.09043 Loop time of 6.385e-06 on 1 procs for 0 steps with 1378 atoms 187.9% 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 | | 6.385e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 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: 106960.0 ave 106960 max 106960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106960 Ave neighs/atom = 77.619739 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 8 45 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.213 | 5.213 | 5.213 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 -7934.304 -7934.304 25.69518 145.78305 5.5411001 291.09043 291.09043 246.3122 495.02129 131.93781 2.5819897 435.68728 Loop time of 6.766e-06 on 1 procs for 0 steps with 1378 atoms 280.8% 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 | | 6.766e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5999.00 ave 5999 max 5999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53480.0 ave 53480 max 53480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106960.0 ave 106960 max 106960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106960 Ave neighs/atom = 77.619739 Neighbor list builds = 0 Dangerous builds = 0 1378 -7934.30395413813 eV 2.58198974060729 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08