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 -69.404896 0.0000000) to (34.702448 69.404896 3.6784521) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0688969 5.0688969 3.6784521 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -69.404896 0.0000000) to (34.702448 69.404896 3.6784521) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0688969 5.0688969 3.6784521 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -69.404896 0.0000000) to (34.702448 69.404896 3.6784521) create_atoms CPU = 0.002 seconds 714 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 = 12 46 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 0 atoms, new total = 1426 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 = 12 46 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) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5820.7533 0 -5820.7533 24982.821 62 0 -6007.7041 0 -6007.7041 1309.7447 Loop time of 1.07579 on 1 procs for 62 steps with 1426 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 = -5820.75331367662 -6007.69891237447 -6007.70414270875 Force two-norm initial, final = 165.76456 0.26854314 Force max component initial, final = 31.574039 0.035535114 Final line search alpha, max atom move = 1.0000000 0.035535114 Iterations, force evaluations = 62 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0358 | 1.0358 | 1.0358 | 0.0 | 96.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020609 | 0.020609 | 0.020609 | 0.0 | 1.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01934 | | | 1.80 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8065.00 ave 8065 max 8065 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: 111392.0 ave 111392 max 111392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111392 Ave neighs/atom = 78.115007 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 = 12 46 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -6007.7041 0 -6007.7041 1309.7447 17719.25 79 0 -6008.3867 0 -6008.3867 -5.827824 17727.153 Loop time of 0.210099 on 1 procs for 17 steps with 1426 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 = -6007.70414270875 -6008.38456412153 -6008.38673417881 Force two-norm initial, final = 66.106396 1.1478522 Force max component initial, final = 64.408008 0.31239343 Final line search alpha, max atom move = 0.00033576259 0.00010489003 Iterations, force evaluations = 17 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17621 | 0.17621 | 0.17621 | 0.0 | 83.87 Neigh | 0.017598 | 0.017598 | 0.017598 | 0.0 | 8.38 Comm | 0.0036791 | 0.0036791 | 0.0036791 | 0.0 | 1.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01261 | | | 6.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8096.00 ave 8096 max 8096 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: 110996.0 ave 110996 max 110996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110996 Ave neighs/atom = 77.837307 Neighbor list builds = 1 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 = 12 45 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) = 5.222 | 5.222 | 5.222 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6008.3867 0 -6008.3867 -5.827824 Loop time of 6.334e-06 on 1 procs for 0 steps with 1426 atoms 189.5% 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 | | 6.334e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8096.00 ave 8096 max 8096 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: 111008.0 ave 111008 max 111008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111008 Ave neighs/atom = 77.845722 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 = 12 45 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) = 5.222 | 5.222 | 5.222 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 -6008.3867 -6008.3867 34.41569 137.7066 3.7404838 -5.827824 -5.827824 5.8957495 5.3309579 -28.710179 2.2919649 416.24372 Loop time of 7.236e-06 on 1 procs for 0 steps with 1426 atoms 262.6% 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 | | 7.236e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8096.00 ave 8096 max 8096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55504.0 ave 55504 max 55504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111008.0 ave 111008 max 111008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111008 Ave neighs/atom = 77.845722 Neighbor list builds = 0 Dangerous builds = 0 1426 -6008.38659157882 eV 2.2919648570808 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01