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 -44.508129 0.0000000) to (22.254064 44.508129 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5606503 3.5606503 3.1472000 Created 200 atoms using lattice units in orthogonal box = (0.0000000 -44.508129 0.0000000) to (22.254064 44.508129 3.1472000) create_atoms CPU = 0.002 seconds 200 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5606503 3.5606503 3.1472000 Created 202 atoms using lattice units in orthogonal box = (0.0000000 -44.508129 0.0000000) to (22.254064 44.508129 3.1472000) create_atoms CPU = 0.001 seconds 202 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 = 8 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 402 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 = 8 29 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) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2556.8971 0 -2556.8971 109360.01 33 0 -2727.7995 0 -2727.7995 17501.441 Loop time of 0.260442 on 1 procs for 33 steps with 402 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 = -2556.89708761221 -2727.79687330488 -2727.79947661235 Force two-norm initial, final = 317.37104 0.21818095 Force max component initial, final = 139.80883 0.064189466 Final line search alpha, max atom move = 1.0000000 0.064189466 Iterations, force evaluations = 33 58 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25308 | 0.25308 | 0.25308 | 0.0 | 97.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037778 | 0.0037778 | 0.0037778 | 0.0 | 1.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003581 | | | 1.37 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3183.00 ave 3183 max 3183 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: 23636.0 ave 23636 max 23636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23636 Ave neighs/atom = 58.796020 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 = 8 29 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.436 | 4.436 | 4.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -2727.7995 0 -2727.7995 17501.441 6234.5199 42 0 -2728.3218 0 -2728.3218 -284.05828 6271.3648 Loop time of 0.0505741 on 1 procs for 9 steps with 402 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 = -2727.79947661235 -2728.32172784527 -2728.3218215416 Force two-norm initial, final = 151.20337 2.2053727 Force max component initial, final = 145.21509 1.1416332 Final line search alpha, max atom move = 0.0026568623 0.0030331622 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047407 | 0.047407 | 0.047407 | 0.0 | 93.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00066861 | 0.00066861 | 0.00066861 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002498 | | | 4.94 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3188.00 ave 3188 max 3188 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: 23588.0 ave 23588 max 23588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23588 Ave neighs/atom = 58.676617 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 = 8 29 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) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2728.3218 0 -2728.3218 -284.05828 Loop time of 6.645e-06 on 1 procs for 0 steps with 402 atoms 135.4% 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 | | 6.645e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3158.00 ave 3158 max 3158 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: 23476.0 ave 23476 max 23476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23476 Ave neighs/atom = 58.398010 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 = 8 29 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) = 4.574 | 4.574 | 4.574 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 -2728.3218 -2728.3218 22.223152 89.732528 3.1448976 -284.05828 -284.05828 -290.83096 -269.8986 -291.4453 2.5682338 223.94284 Loop time of 6.495e-06 on 1 procs for 0 steps with 402 atoms 184.8% 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 | | 6.495e-06 | | |100.00 Nlocal: 402.000 ave 402 max 402 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3158.00 ave 3158 max 3158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11738.0 ave 11738 max 11738 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23476.0 ave 23476 max 23476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23476 Ave neighs/atom = 58.398010 Neighbor list builds = 0 Dangerous builds = 0 402 -2728.3218215416 eV 2.56823384953605 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