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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -45.354682 0.0000000) to (16.034001 45.354682 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9072636 4.7737899 5.2021169 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -45.354682 0.0000000) to (16.034001 45.354682 5.2021169) create_atoms CPU = 0.001 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9072636 4.7737899 5.2021169 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -45.354682 0.0000000) to (16.034001 45.354682 5.2021169) create_atoms CPU = 0.001 seconds 306 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 6 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 604 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_024705128470_000#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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2524.4167 0 -2524.4167 8538.7873 28 0 -2542.2813 0 -2542.2813 -6072.6515 Loop time of 0.0761456 on 1 procs for 28 steps with 604 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 = -2524.41671984795 -2542.27914861944 -2542.28127526783 Force two-norm initial, final = 28.420094 0.13806025 Force max component initial, final = 8.3918462 0.022632244 Final line search alpha, max atom move = 1.0000000 0.022632244 Iterations, force evaluations = 28 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073662 | 0.073662 | 0.073662 | 0.0 | 96.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001293 | 0.001293 | 0.001293 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001191 | | | 1.56 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3680.00 ave 3680 max 3680 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: 46800.0 ave 46800 max 46800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46800 Ave neighs/atom = 77.483444 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -2542.2813 0 -2542.2813 -6072.6515 7566.136 30 0 -2542.2944 0 -2542.2944 -3952.9852 7550.9016 Loop time of 0.00705499 on 1 procs for 2 steps with 604 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 = -2542.28127526785 -2542.29265634544 -2542.29436535447 Force two-norm initial, final = 15.999391 0.90299392 Force max component initial, final = 15.069163 0.88917057 Final line search alpha, max atom move = 0.00017871087 0.00015890444 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0065177 | 0.0065177 | 0.0065177 | 0.0 | 92.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011092 | 0.00011092 | 0.00011092 | 0.0 | 1.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004264 | | | 6.04 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 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: 47136.0 ave 47136 max 47136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47136 Ave neighs/atom = 78.039735 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2542.2944 0 -2542.2944 -3952.9852 Loop time of 1.682e-06 on 1 procs for 0 steps with 604 atoms 118.9% 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 | | 1.682e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 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: 47136.0 ave 47136 max 47136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47136 Ave neighs/atom = 78.039735 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.655 | 4.655 | 4.655 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 -2542.2944 -2542.2944 16.027443 90.709365 5.1937669 -3952.9852 -3952.9852 188.59012 -12030.828 -16.717749 2.3924444 230.69786 Loop time of 1.41e-06 on 1 procs for 0 steps with 604 atoms 141.8% 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 | | 1.41e-06 | | |100.00 Nlocal: 604.000 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3687.00 ave 3687 max 3687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23568.0 ave 23568 max 23568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47136.0 ave 47136 max 47136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47136 Ave neighs/atom = 78.039735 Neighbor list builds = 0 Dangerous builds = 0 604 -2542.29430495447 eV 2.39244442410908 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00