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 -43.266846 0.0000000) to (11.775744 43.266846 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0467474 4.8074274 5.1393560 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -43.266846 0.0000000) to (11.775744 43.266846 7.7090341) create_atoms CPU = 0.002 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0467474 4.8074274 5.1393560 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -43.266846 0.0000000) to (11.775744 43.266846 7.7090341) create_atoms CPU = 0.002 seconds 254 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 = 4 28 3 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 0 atoms, new total = 506 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 = 4 28 3 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) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3223.2559 0 -3223.2559 112616.61 107 0 -3426.5444 0 -3426.5444 15981.08 Loop time of 1.08682 on 1 procs for 107 steps with 506 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3223.25586239187 -3426.54109381717 -3426.54443265699 Force two-norm initial, final = 331.61048 0.28855335 Force max component initial, final = 101.41899 0.052536742 Final line search alpha, max atom move = 1.0000000 0.052536742 Iterations, force evaluations = 107 209 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0608 | 1.0608 | 1.0608 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012189 | 0.012189 | 0.012189 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0138 | | | 1.27 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2695.00 ave 2695 max 2695 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: 29728.0 ave 29728 max 29728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29728 Ave neighs/atom = 58.750988 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 = 4 28 3 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 : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.462 | 4.462 | 4.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -3426.5444 0 -3426.5444 15981.08 7855.495 115 0 -3427.0408 0 -3427.0408 -115.12854 7897.0347 Loop time of 0.0532831 on 1 procs for 8 steps with 506 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 = -3426.54443265699 -3427.04078457829 -3427.04081780766 Force two-norm initial, final = 164.86027 1.2744683 Force max component initial, final = 154.41933 0.61379501 Final line search alpha, max atom move = 0.0018597879 0.0011415285 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.050472 | 0.050472 | 0.050472 | 0.0 | 94.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057177 | 0.00057177 | 0.00057177 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00224 | | | 4.20 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2690.00 ave 2690 max 2690 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: 29624.0 ave 29624 max 29624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29624 Ave neighs/atom = 58.545455 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 = 4 28 3 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) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3427.0408 0 -3427.0408 -115.12854 Loop time of 6.194e-06 on 1 procs for 0 steps with 506 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2690.00 ave 2690 max 2690 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: 29580.0 ave 29580 max 29580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29580 Ave neighs/atom = 58.458498 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 = 4 28 3 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) = 4.600 | 4.600 | 4.600 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 -3427.0408 -3427.0408 11.760688 87.141612 7.7055868 -115.12854 -115.12854 -110.85583 -110.05673 -124.47307 2.4572643 436.91617 Loop time of 6.455e-06 on 1 procs for 0 steps with 506 atoms 247.9% 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: 506.000 ave 506 max 506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2690.00 ave 2690 max 2690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14790.0 ave 14790 max 14790 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29580.0 ave 29580 max 29580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29580 Ave neighs/atom = 58.458498 Neighbor list builds = 0 Dangerous builds = 0 506 -3427.04081780766 eV 2.45726428760609 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42