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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -42.138139 0.0000000) to (21.069070 42.138139 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9574282 4.9574282 3.6133156 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -42.138139 0.0000000) to (21.069070 42.138139 3.6133156) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9574282 4.9574282 3.6133156 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -42.138139 0.0000000) to (21.069070 42.138139 3.6133156) create_atoms CPU = 0.000 seconds 274 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 ghost atom cutoff = 6 binsize = 3, bins = 8 29 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_087820130586_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 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1745.7762 0 -1745.7762 80432.898 34 0 -1923.8741 0 -1923.8741 14575.044 Loop time of 0.711816 on 1 procs for 34 steps with 546 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 = -1745.77622007878 -1923.87241977227 -1923.87414015569 Force two-norm initial, final = 289.03321 0.14416815 Force max component initial, final = 85.110465 0.046578274 Final line search alpha, max atom move = 1.0000000 0.046578274 Iterations, force evaluations = 34 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70681 | 0.70681 | 0.70681 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00267 | 0.00267 | 0.00267 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002338 | | | 0.33 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3869.00 ave 3869 max 3869 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: 42656.0 ave 42656 max 42656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42656 Ave neighs/atom = 78.124542 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 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -1923.8741 0 -1923.8741 14575.044 6415.8856 48 0 -1924.5023 0 -1924.5023 108.26278 6479.8502 Loop time of 0.190729 on 1 procs for 14 steps with 546 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1923.87414015569 -1924.50098691292 -1924.50231134677 Force two-norm initial, final = 118.30777 1.2766010 Force max component initial, final = 107.10490 1.1249747 Final line search alpha, max atom move = 0.00050440864 0.00056744695 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18382 | 0.18382 | 0.18382 | 0.0 | 96.38 Neigh | 0.0032156 | 0.0032156 | 0.0032156 | 0.0 | 1.69 Comm | 0.00070123 | 0.00070123 | 0.00070123 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002989 | | | 1.57 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3845.00 ave 3845 max 3845 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: 42100.0 ave 42100 max 42100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42100 Ave neighs/atom = 77.106227 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 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.616 | 4.616 | 4.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1924.5023 0 -1924.5023 108.26278 Loop time of 2.694e-06 on 1 procs for 0 steps with 546 atoms 148.5% 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 | | 2.694e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3830.00 ave 3830 max 3830 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: 42084.0 ave 42084 max 42084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42084 Ave neighs/atom = 77.076923 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 ghost atom cutoff = 6 binsize = 3, bins = 8 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.616 | 4.616 | 4.616 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 -1924.5023 -1924.5023 21.053594 85.371779 3.6051587 108.26278 108.26278 -30.857292 281.77154 73.874107 2.2979003 316.79413 Loop time of 2.178e-06 on 1 procs for 0 steps with 546 atoms 183.7% 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 | | 2.178e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3830.00 ave 3830 max 3830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21042.0 ave 21042 max 21042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42084.0 ave 42084 max 42084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42084 Ave neighs/atom = 77.076923 Neighbor list builds = 0 Dangerous builds = 0 546 -1924.50231134677 eV 2.29790031209177 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01