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 -38.801287 0.0000000) to (13.718327 38.801287 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0541203 4.0843460 4.4508129 Created 152 atoms using lattice units in orthogonal box = (0.0000000 -38.801287 0.0000000) to (13.718327 38.801287 4.4508129) create_atoms CPU = 0.001 seconds 152 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0541203 4.0843460 4.4508129 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -38.801287 0.0000000) to (13.718327 38.801287 4.4508129) create_atoms CPU = 0.000 seconds 154 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 = 5 25 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 = 306 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 = 5 25 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) = 4.420 | 4.420 | 4.420 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1835.1503 0 -1835.1503 177961.64 53 0 -2069.7144 0 -2069.7144 27547.538 Loop time of 0.154077 on 1 procs for 53 steps with 306 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 = -1835.15026546152 -2069.71229899549 -2069.71435656673 Force two-norm initial, final = 336.88158 0.17315800 Force max component initial, final = 114.71522 0.022528327 Final line search alpha, max atom move = 1.0000000 0.022528327 Iterations, force evaluations = 53 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14853 | 0.14853 | 0.14853 | 0.0 | 96.40 Neigh | 0.0017485 | 0.0017485 | 0.0017485 | 0.0 | 1.13 Comm | 0.0021049 | 0.0021049 | 0.0021049 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001692 | | | 1.10 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2388.00 ave 2388 max 2388 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: 18184.0 ave 18184 max 18184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18184 Ave neighs/atom = 59.424837 Neighbor list builds = 1 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 = 5 25 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 : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.420 | 4.420 | 4.420 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -2069.7144 0 -2069.7144 27547.538 4738.2351 62 0 -2070.2967 0 -2070.2967 -353.5598 4780.4403 Loop time of 0.0182125 on 1 procs for 9 steps with 306 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 = -2069.71435656673 -2070.29528466053 -2070.29668424053 Force two-norm initial, final = 158.11088 1.9949171 Force max component initial, final = 138.13986 1.2363937 Final line search alpha, max atom move = 0.00023673430 0.00029269681 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016908 | 0.016908 | 0.016908 | 0.0 | 92.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021912 | 0.00021912 | 0.00021912 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001085 | | | 5.96 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2388.00 ave 2388 max 2388 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: 18024.0 ave 18024 max 18024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18024 Ave neighs/atom = 58.901961 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 = 5 26 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) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2070.2967 0 -2070.2967 -353.5598 Loop time of 1.803e-06 on 1 procs for 0 steps with 306 atoms 776.5% 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 | | 1.803e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2388.00 ave 2388 max 2388 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: 17928.0 ave 17928 max 17928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17928 Ave neighs/atom = 58.588235 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 = 5 26 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) = 4.558 | 4.558 | 4.558 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 -2070.2967 -2070.2967 13.702571 78.260636 4.4578192 -353.5598 -353.5598 -413.90453 -302.12818 -344.64668 2.3938091 247.10137 Loop time of 1.795e-06 on 1 procs for 0 steps with 306 atoms 167.1% 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 | | 1.795e-06 | | |100.00 Nlocal: 306.000 ave 306 max 306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2388.00 ave 2388 max 2388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8964.00 ave 8964 max 8964 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17928.0 ave 17928 max 17928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17928 Ave neighs/atom = 58.588235 Neighbor list builds = 0 Dangerous builds = 0 306 -2070.29668424053 eV 2.39380906338063 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