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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -40.363220 0.0000000) to (5.0449566 40.363220 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0449566 5.0449566 3.5673230 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.363220 0.0000000) to (5.0449566 40.363220 3.5673230) create_atoms CPU = 0.002 seconds 66 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0449566 5.0449566 3.5673230 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.363220 0.0000000) to (5.0449566 40.363220 3.5673230) create_atoms CPU = 0.001 seconds 66 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 124 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.388 | 4.388 | 4.388 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -517.55355 0 -517.55355 -17902.451 46 0 -523.66778 0 -523.66778 -18549.214 Loop time of 0.682149 on 1 procs for 46 steps with 124 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 = -517.553549918448 -523.667450483025 -523.667783568102 Force two-norm initial, final = 1.7765080 0.37550645 Force max component initial, final = 0.43374145 0.084176660 Final line search alpha, max atom move = 1.0000000 0.084176660 Iterations, force evaluations = 46 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67635 | 0.67635 | 0.67635 | 0.0 | 99.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033058 | 0.0033058 | 0.0033058 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002497 | | | 0.37 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1556.00 ave 1556 max 1556 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: 6584.00 ave 6584 max 6584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6584 Ave neighs/atom = 53.096774 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.388 | 4.388 | 4.388 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -523.66778 0 -523.66778 -18549.214 1452.8329 228 0 -525.7039 0 -525.7039 48443.699 1423.4804 Loop time of 1.47092 on 1 procs for 182 steps with 124 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 = -523.667783568102 -525.703576745505 -525.70390271711 Force two-norm initial, final = 83.613257 1.1525351 Force max component initial, final = 75.905850 0.95494602 Final line search alpha, max atom move = 0.0012969273 0.0012384955 Iterations, force evaluations = 182 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4428 | 1.4428 | 1.4428 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0065733 | 0.0065733 | 0.0065733 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02155 | | | 1.47 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1556.00 ave 1556 max 1556 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: 6696.00 ave 6696 max 6696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 6696 Ave neighs/atom = 54.000000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.522 | 4.522 | 4.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -525.7039 0 -525.7039 48443.699 Loop time of 6.855e-06 on 1 procs for 0 steps with 124 atoms 175.1% 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 | | 6.855e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1976.00 ave 1976 max 1976 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: 7440.00 ave 7440 max 7440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7440 Ave neighs/atom = 60.000000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 3 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.522 | 4.522 | 4.522 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 -525.7039 -525.7039 5.9207334 80.72644 2.9782434 48443.699 48443.699 1261.4085 143517.58 552.11011 2.4611186 0.013889103 Loop time of 6.455e-06 on 1 procs for 0 steps with 124 atoms 216.9% 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 | | 6.455e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1976.00 ave 1976 max 1976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3720.00 ave 3720 max 3720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7440.00 ave 7440 max 7440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7440 Ave neighs/atom = 60.000000 Neighbor list builds = 0 Dangerous builds = 0 124 -525.70390271711 eV 2.4611186101948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02