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 = 3.6390851 3.6390851 3.6390851 Created orthogonal box = (0.0000000 -44.121562 0.0000000) to (36.025105 44.121562 8.9139016) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1464435 5.1024936 5.9426011 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -44.121562 0.0000000) to (36.025105 44.121562 8.9139016) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1464435 5.1024936 5.9426011 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -44.121562 0.0000000) to (36.025105 44.121562 8.9139016) create_atoms CPU = 0.002 seconds 1184 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2336 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_600021860456_005#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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.713 | 7.713 | 7.713 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6745.9812 0 -6745.9812 88882.675 79 0 -7628.7679 0 -7628.7679 -1878.9943 Loop time of 5.22795 on 1 procs for 79 steps with 2336 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6745.98118023017 -7628.76132462308 -7628.76789823323 Force two-norm initial, final = 1317.9898 0.19776535 Force max component initial, final = 229.39901 0.0082102242 Final line search alpha, max atom move = 1.0000000 0.0082102242 Iterations, force evaluations = 79 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1126 | 5.1126 | 5.1126 | 0.0 | 97.79 Neigh | 0.076527 | 0.076527 | 0.076527 | 0.0 | 1.46 Comm | 0.020162 | 0.020162 | 0.020162 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01861 | | | 0.36 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11494.0 ave 11494 max 11494 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: 740448.0 ave 740448 max 740448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740448 Ave neighs/atom = 316.97260 Neighbor list builds = 2 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.713 | 7.713 | 7.713 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -7628.7679 0 -7628.7679 -1878.9943 28337.006 82 0 -7628.8422 0 -7628.8422 223.41291 28295.945 Loop time of 0.175715 on 1 procs for 3 steps with 2336 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7628.76789823316 -7628.84000153845 -7628.84221308013 Force two-norm initial, final = 74.468283 9.2551555 Force max component initial, final = 64.641130 8.8072784 Final line search alpha, max atom move = 9.2907217e-05 0.00081825973 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17298 | 0.17298 | 0.17298 | 0.0 | 98.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042983 | 0.00042983 | 0.00042983 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002302 | | | 1.31 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11075.0 ave 11075 max 11075 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: 739568.0 ave 739568 max 739568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739568 Ave neighs/atom = 316.59589 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.851 | 7.851 | 7.851 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7628.8422 0 -7628.8422 223.41291 Loop time of 2.27e-06 on 1 procs for 0 steps with 2336 atoms 176.2% 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 | | 2.27e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11081.0 ave 11081 max 11081 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: 739520.0 ave 739520 max 739520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739520 Ave neighs/atom = 316.57534 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.851 | 7.851 | 7.851 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 -7628.8422 -7628.8422 35.995285 88.339939 8.8985959 223.41291 223.41291 11.069863 499.23394 159.93492 2.2558569 1435.9223 Loop time of 2.266e-06 on 1 procs for 0 steps with 2336 atoms 264.8% 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 | | 2.266e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11081.0 ave 11081 max 11081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 369760.0 ave 369760 max 369760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 739520.0 ave 739520 max 739520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739520 Ave neighs/atom = 316.57534 Neighbor list builds = 0 Dangerous builds = 0 2336 -7628.84221308013 eV 2.25585689303686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06