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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5820674 5.5248140 6.0992295 Created 624 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992295) create_atoms CPU = 0.002 seconds 624 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5820674 5.5248140 6.0992295 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -35.911291 0.0000000) to (31.100090 35.911291 6.0992295) create_atoms CPU = 0.001 seconds 629 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1251 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_500937681860_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4723.2961 0 -4723.2961 135584.23 80 0 -5526.5327 0 -5526.5327 20479.056 Loop time of 8.59058 on 1 procs for 80 steps with 1251 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4723.29607013191 -5526.52741162821 -5526.53273864979 Force two-norm initial, final = 897.11421 0.28665512 Force max component initial, final = 172.47470 0.098483155 Final line search alpha, max atom move = 0.39926684 0.039321058 Iterations, force evaluations = 80 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.538 | 8.538 | 8.538 | 0.0 | 99.39 Neigh | 0.029083 | 0.029083 | 0.029083 | 0.0 | 0.34 Comm | 0.011522 | 0.011522 | 0.011522 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01196 | | | 0.14 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5709.00 ave 5709 max 5709 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: 112134.0 ave 112134 max 112134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112134 Ave neighs/atom = 89.635492 Neighbor list builds = 3 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 80 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.041 | 5.041 | 5.041 Mbytes Step Temp E_pair E_mol TotEng Press Volume 80 0 -5526.5327 0 -5526.5327 20479.056 13623.78 92 0 -5528.3097 0 -5528.3097 -86.559674 13771.679 Loop time of 0.913121 on 1 procs for 12 steps with 1251 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 = -5526.53273864981 -5528.30951833213 -5528.30968781986 Force two-norm initial, final = 356.51920 1.6641065 Force max component initial, final = 323.21476 1.0021642 Final line search alpha, max atom move = 0.00042741020 0.00042833518 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90796 | 0.90796 | 0.90796 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079698 | 0.00079698 | 0.00079698 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004362 | | | 0.48 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5714.00 ave 5714 max 5714 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: 111586.0 ave 111586 max 111586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111586 Ave neighs/atom = 89.197442 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.179 | 5.179 | 5.179 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5528.3097 0 -5528.3097 -86.559674 Loop time of 2.201e-06 on 1 procs for 0 steps with 1251 atoms 181.7% 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 | | 2.201e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5720.00 ave 5720 max 5720 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: 110200.0 ave 110200 max 110200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110200 Ave neighs/atom = 88.089528 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.179 | 5.179 | 5.179 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 -5528.3097 -5528.3097 31.132892 72.613526 6.0918599 -86.559674 -86.559674 -116.71325 -93.779936 -49.18584 2.2403987 828.01463 Loop time of 2.372e-06 on 1 procs for 0 steps with 1251 atoms 210.8% 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 | | 2.372e-06 | | |100.00 Nlocal: 1251.00 ave 1251 max 1251 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5720.00 ave 5720 max 5720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55100.0 ave 55100 max 55100 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 110200.0 ave 110200 max 110200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110200 Ave neighs/atom = 88.089528 Neighbor list builds = 0 Dangerous builds = 0 1251 -5528.30968781986 eV 2.240398667849 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10