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 = 4.0737181 4.0737181 4.0737181 Created orthogonal box = (0.0000000 -52.801422 0.0000000) to (30.484915 52.801422 7.0558868) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5324818 6.2858835 7.0558868 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.801422 0.0000000) to (30.484915 52.801422 7.0558868) create_atoms CPU = 0.004 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5324818 6.2858835 7.0558868 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.801422 0.0000000) to (30.484915 52.801422 7.0558868) create_atoms CPU = 0.004 seconds 676 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 23 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 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_128037485276_003#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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.515 | 5.515 | 5.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3984.4255 0 -3984.4255 60951.861 74 0 -4111.4365 0 -4111.4365 2795.7237 Loop time of 5.23321 on 1 procs for 74 steps with 1344 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 = -3984.42545645811 -4111.43327418689 -4111.4365445215 Force two-norm initial, final = 328.02745 0.13105814 Force max component initial, final = 100.27542 0.012351831 Final line search alpha, max atom move = 1.0000000 0.012351831 Iterations, force evaluations = 74 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1476 | 5.1476 | 5.1476 | 0.0 | 98.36 Neigh | 0.036612 | 0.036612 | 0.036612 | 0.0 | 0.70 Comm | 0.026814 | 0.026814 | 0.026814 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02218 | | | 0.42 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8075.00 ave 8075 max 8075 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: 266672.0 ave 266672 max 266672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266672 Ave neighs/atom = 198.41667 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4111.4365 0 -4111.4365 2795.7237 22714.972 81 0 -4111.7007 0 -4111.7007 22.446386 22842.44 Loop time of 0.34486 on 1 procs for 7 steps with 1344 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 = -4111.43654452149 -4111.69698019173 -4111.70068976072 Force two-norm initial, final = 84.136960 0.71455091 Force max component initial, final = 76.049397 0.52327832 Final line search alpha, max atom move = 0.00018025910 9.4325680e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3378 | 0.3378 | 0.3378 | 0.0 | 97.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015624 | 0.0015624 | 0.0015624 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005494 | | | 1.59 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8076.00 ave 8076 max 8076 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: 266656.0 ave 266656 max 266656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266656 Ave neighs/atom = 198.40476 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.652 | 5.652 | 5.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4111.7007 0 -4111.7007 22.446386 Loop time of 6.806e-06 on 1 procs for 0 steps with 1344 atoms 176.3% 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 | | 6.806e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7999.00 ave 7999 max 7999 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: 266504.0 ave 266504 max 266504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266504 Ave neighs/atom = 198.29167 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 = 9.2864 ghost atom cutoff = 9.2864 binsize = 4.6432, bins = 7 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.2864 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) = 5.652 | 5.652 | 5.652 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 -4111.7007 -4111.7007 30.519506 106.31844 7.0397362 22.446386 22.446386 1.2373225 29.482928 36.618908 2.6471977 1033.464 Loop time of 6.815e-06 on 1 procs for 0 steps with 1344 atoms 234.8% 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 | | 6.815e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7999.00 ave 7999 max 7999 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 133252.0 ave 133252 max 133252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 266504.0 ave 266504 max 266504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 266504 Ave neighs/atom = 198.29167 Neighbor list builds = 0 Dangerous builds = 0 1344 -4304.02092607696 eV 2.64719765048656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07