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 = 2.8667458 2.8667458 2.8667458 Created orthogonal box = (0.0000000 -53.170213 0.0000000) to (18.798509 53.170213 4.0541907) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8089209 4.9460663 4.0541907 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -53.170213 0.0000000) to (18.798509 53.170213 4.0541907) create_atoms CPU = 0.009 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8089209 4.9460663 4.0541907 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.170213 0.0000000) to (18.798509 53.170213 4.0541907) create_atoms CPU = 0.007 seconds 346 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 688 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2440.9678 0 -2440.9678 115034.71 97 0 -2930.0692 0 -2930.0692 2860.6087 Loop time of 2.2772 on 1 procs for 97 steps with 688 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 = -2440.9677502894 -2930.06665721978 -2930.06924843803 Force two-norm initial, final = 1084.2576 0.21764425 Force max component initial, final = 377.20975 0.030985028 Final line search alpha, max atom move = 1.0000000 0.030985028 Iterations, force evaluations = 97 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1966 | 2.1966 | 2.1966 | 0.0 | 96.46 Neigh | 0.033565 | 0.033565 | 0.033565 | 0.0 | 1.47 Comm | 0.027306 | 0.027306 | 0.027306 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01969 | | | 0.86 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6442.00 ave 6442 max 6442 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: 114680.0 ave 114680 max 114680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114680 Ave neighs/atom = 166.68605 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -2930.0692 0 -2930.0692 2860.6087 8104.4953 102 0 -2930.2039 0 -2930.2039 -31.430342 8114.9364 Loop time of 0.101698 on 1 procs for 5 steps with 688 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 = -2930.06924843803 -2930.20384104714 -2930.20386246156 Force two-norm initial, final = 70.864973 0.48737383 Force max component initial, final = 68.588262 0.28040127 Final line search alpha, max atom move = 0.0012399486 0.00034768317 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.096971 | 0.096971 | 0.096971 | 0.0 | 95.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011493 | 0.0011493 | 0.0011493 | 0.0 | 1.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003577 | | | 3.52 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6412.00 ave 6412 max 6412 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: 114788.0 ave 114788 max 114788 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114788 Ave neighs/atom = 166.84302 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2930.2039 0 -2930.2039 -31.430342 Loop time of 7.948e-06 on 1 procs for 0 steps with 688 atoms 176.1% 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 | | 7.948e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6412.00 ave 6412 max 6412 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: 114784.0 ave 114784 max 114784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114784 Ave neighs/atom = 166.83721 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 5.085 | 5.085 | 5.085 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 -2930.2039 -2930.2039 18.778581 106.71784 4.0493501 -31.430342 -31.430342 3.196892 -42.192855 -55.295063 2.3413598 427.65171 Loop time of 7.468e-06 on 1 procs for 0 steps with 688 atoms 254.4% 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 | | 7.468e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6412.00 ave 6412 max 6412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57392.0 ave 57392 max 57392 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114784.0 ave 114784 max 114784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114784 Ave neighs/atom = 166.83721 Neighbor list builds = 0 Dangerous builds = 0 688 -2930.20386246156 eV 2.34135980752751 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03