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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -32.706662 0.0000000) to (7.7090341 32.706662 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1393560 5.4511103 4.4508129 Created 72 atoms using lattice units in orthogonal box = (0.0000000 -32.706662 0.0000000) to (7.7090341 32.706662 4.4508129) create_atoms CPU = 0.001 seconds 72 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1393560 5.4511103 4.4508129 Created 74 atoms using lattice units in orthogonal box = (0.0000000 -32.706662 0.0000000) to (7.7090341 32.706662 4.4508129) create_atoms CPU = 0.000 seconds 74 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 3 21 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 144 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.374 | 4.374 | 4.374 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -940.48213 0 -940.48213 81751.279 12 0 -972.84375 0 -972.84375 15419.733 Loop time of 0.0157269 on 1 procs for 12 steps with 144 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -940.48213376148 -972.843390818029 -972.843750373225 Force two-norm initial, final = 119.18934 0.056288312 Force max component initial, final = 42.130585 0.0086711075 Final line search alpha, max atom move = 1.0000000 0.0086711075 Iterations, force evaluations = 12 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015285 | 0.015285 | 0.015285 | 0.0 | 97.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023552 | 0.00023552 | 0.00023552 | 0.0 | 1.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002067 | | | 1.31 Nlocal: 144.000 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1357.00 ave 1357 max 1357 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: 8408.00 ave 8408 max 8408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8408 Ave neighs/atom = 58.388889 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 3 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.374 | 4.374 | 4.374 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -972.84375 0 -972.84375 15419.733 2244.4271 20 0 -972.98617 0 -972.98617 -309.05061 2255.8716 Loop time of 0.00831713 on 1 procs for 8 steps with 144 atoms 92.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -972.843750373227 -972.98598638972 -972.986168119862 Force two-norm initial, final = 45.755685 0.99303585 Force max component initial, final = 43.107216 0.61276182 Final line search alpha, max atom move = 0.0012359577 0.00075734769 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0077042 | 0.0077042 | 0.0077042 | 0.0 | 92.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013315 | 0.00013315 | 0.00013315 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004798 | | | 5.77 Nlocal: 144.000 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1357.00 ave 1357 max 1357 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: 8408.00 ave 8408 max 8408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8408 Ave neighs/atom = 58.388889 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.513 | 4.513 | 4.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -972.98617 0 -972.98617 -309.05061 Loop time of 1.909e-06 on 1 procs for 0 steps with 144 atoms 104.8% 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 | | 1.909e-06 | | |100.00 Nlocal: 144.000 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1357.00 ave 1357 max 1357 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: 8408.00 ave 8408 max 8408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8408 Ave neighs/atom = 58.388889 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.513 | 4.513 | 4.513 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 -972.98617 -972.98617 7.7007275 65.888783 4.4460171 -309.05061 -309.05061 -244.39488 -438.36206 -244.39488 2.4310079 140.00278 Loop time of 1.508e-06 on 1 procs for 0 steps with 144 atoms 198.9% 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 | | 1.508e-06 | | |100.00 Nlocal: 144.000 ave 144 max 144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1357.00 ave 1357 max 1357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 4204.00 ave 4204 max 4204 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 8408.00 ave 8408 max 8408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 8408 Ave neighs/atom = 58.388889 Neighbor list builds = 0 Dangerous builds = 0 144 -972.986168119863 eV 2.43100793116846 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42