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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -66.975901 0.0000000) to (23.679557 66.975901 5.1068646) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0575610 6.2303163 5.1068646 Created 688 atoms using lattice units in orthogonal box = (0.0000000 -66.975901 0.0000000) to (23.679557 66.975901 5.1068646) create_atoms CPU = 0.002 seconds 688 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0575610 6.2303163 5.1068646 Created 690 atoms using lattice units in orthogonal box = (0.0000000 -66.975901 0.0000000) to (23.679557 66.975901 5.1068646) create_atoms CPU = 0.002 seconds 690 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 45 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 = 1378 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_162036141261_001#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 45 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) = 5.074 | 5.074 | 5.074 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5743.855 0 -5743.855 23708.898 431 0 -5848.3779 0 -5848.3779 5798.2664 Loop time of 36.5569 on 1 procs for 431 steps with 1378 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 = -5743.85504427611 -5848.37242856043 -5848.37793843567 Force two-norm initial, final = 114.65891 0.23451519 Force max component initial, final = 30.359064 0.062268972 Final line search alpha, max atom move = 1.0000000 0.062268972 Iterations, force evaluations = 431 838 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 36.371 | 36.371 | 36.371 | 0.0 | 99.49 Neigh | 0.083098 | 0.083098 | 0.083098 | 0.0 | 0.23 Comm | 0.051556 | 0.051556 | 0.051556 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05122 | | | 0.14 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6068.00 ave 6068 max 6068 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: 100732.0 ave 100732 max 100732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 100732 Ave neighs/atom = 73.100145 Neighbor list builds = 11 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 45 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 : 431 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 431 0 -5848.3779 0 -5848.3779 5798.2664 16198.562 449 0 -5851.6634 0 -5851.6634 -3.337929 16244.52 Loop time of 0.854291 on 1 procs for 18 steps with 1378 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 = -5848.37793843568 -5851.65820733196 -5851.66336113532 Force two-norm initial, final = 333.50658 0.96063340 Force max component initial, final = 317.35970 0.21497691 Final line search alpha, max atom move = 9.8053366e-05 2.1079210e-05 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84106 | 0.84106 | 0.84106 | 0.0 | 98.45 Neigh | 0.0071617 | 0.0071617 | 0.0071617 | 0.0 | 0.84 Comm | 0.0010639 | 0.0010639 | 0.0010639 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005003 | | | 0.59 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6042.00 ave 6042 max 6042 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: 99464.0 ave 99464 max 99464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99464 Ave neighs/atom = 72.179971 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 = 9 45 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) = 5.214 | 5.214 | 5.214 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5851.6634 0 -5851.6634 -3.337929 Loop time of 1.83e-06 on 1 procs for 0 steps with 1378 atoms 109.3% 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 | | 1.83e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6042.00 ave 6042 max 6042 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: 99456.0 ave 99456 max 99456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99456 Ave neighs/atom = 72.174165 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 = 9 45 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) = 5.214 | 5.214 | 5.214 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 -5851.6634 -5851.6634 24.098275 132.94408 5.070513 -3.337929 -3.337929 -11.393003 21.043392 -19.664176 2.3791498 3252.5646 Loop time of 1.818e-06 on 1 procs for 0 steps with 1378 atoms 110.0% 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 | | 1.818e-06 | | |100.00 Nlocal: 1378.00 ave 1378 max 1378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6042.00 ave 6042 max 6042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49728.0 ave 49728 max 49728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 99456.0 ave 99456 max 99456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 99456 Ave neighs/atom = 72.174165 Neighbor list builds = 0 Dangerous builds = 0 1378 -5851.66336113532 eV 2.37914980741968 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37