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 -56.998216 0.0000000) to (20.151912 56.998216 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4066107 4.8657013 4.4508129 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -56.998216 0.0000000) to (20.151912 56.998216 4.4508129) create_atoms CPU = 0.001 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4066107 4.8657013 4.4508129 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -56.998216 0.0000000) to (20.151912 56.998216 4.4508129) create_atoms CPU = 0.001 seconds 330 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 = 7 37 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 0 atoms, new total = 658 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 = 7 37 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) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4187.4953 0 -4187.4953 74678.048 46 0 -4464.9586 0 -4464.9586 9320.046 Loop time of 0.284888 on 1 procs for 46 steps with 658 atoms 87.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4187.49528439451 -4464.95513214525 -4464.95856133591 Force two-norm initial, final = 484.77331 0.38717655 Force max component initial, final = 221.32463 0.10671524 Final line search alpha, max atom move = 1.0000000 0.10671524 Iterations, force evaluations = 46 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27988 | 0.27988 | 0.27988 | 0.0 | 98.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024293 | 0.0024293 | 0.0024293 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002583 | | | 0.91 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3475.00 ave 3475 max 3475 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: 38552.0 ave 38552 max 38552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38552 Ave neighs/atom = 58.589666 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 = 7 37 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.509 | 4.509 | 4.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -4464.9586 0 -4464.9586 9320.046 10224.613 53 0 -4465.4672 0 -4465.4672 -135.4446 10256.868 Loop time of 0.030518 on 1 procs for 7 steps with 658 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 = -4464.95856133591 -4465.46289756713 -4465.46719174261 Force two-norm initial, final = 162.27581 1.7954016 Force max component initial, final = 161.72084 1.2072161 Final line search alpha, max atom move = 9.6501224e-05 0.00011649784 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.028777 | 0.028777 | 0.028777 | 0.0 | 94.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030279 | 0.00030279 | 0.00030279 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001438 | | | 4.71 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3472.00 ave 3472 max 3472 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: 38500.0 ave 38500 max 38500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38500 Ave neighs/atom = 58.510638 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 = 7 37 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) = 4.647 | 4.647 | 4.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4465.4672 0 -4465.4672 -135.4446 Loop time of 2.001e-06 on 1 procs for 0 steps with 658 atoms 149.9% 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 | | 2.001e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3472.00 ave 3472 max 3472 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: 38452.0 ave 38452 max 38452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38452 Ave neighs/atom = 58.437690 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 = 7 37 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) = 4.647 | 4.647 | 4.647 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 -4465.4672 -4465.4672 20.107828 114.74693 4.4453763 -135.4446 -135.4446 -188.16097 -141.05152 -77.121324 2.3647493 359.14868 Loop time of 1.85e-06 on 1 procs for 0 steps with 658 atoms 216.2% 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 | | 1.85e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3472.00 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19226.0 ave 19226 max 19226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38452.0 ave 38452 max 38452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38452 Ave neighs/atom = 58.437690 Neighbor list builds = 0 Dangerous builds = 0 658 -4465.46719174261 eV 2.36474930664036 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