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 -38.287340 0.0000000) to (19.143670 38.287340 3.1472000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.6217754 3.6217754 3.1472000 Created 148 atoms using lattice units in orthogonal box = (0.0000000 -38.287340 0.0000000) to (19.143670 38.287340 3.1472000) create_atoms CPU = 0.002 seconds 148 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.6217754 3.6217754 3.1472000 Created 149 atoms using lattice units in orthogonal box = (0.0000000 -38.287340 0.0000000) to (19.143670 38.287340 3.1472000) create_atoms CPU = 0.001 seconds 149 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 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 = 297 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 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1888.9208 0 -1888.9208 128652.91 55 0 -2013.0234 0 -2013.0234 15994.924 Loop time of 0.355448 on 1 procs for 55 steps with 297 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 = -1888.92079174538 -2013.02166879657 -2013.02341012981 Force two-norm initial, final = 187.63396 0.19008633 Force max component initial, final = 58.182455 0.036860307 Final line search alpha, max atom move = 1.0000000 0.036860307 Iterations, force evaluations = 55 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34567 | 0.34567 | 0.34567 | 0.0 | 97.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005355 | 0.005355 | 0.005355 | 0.0 | 1.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004423 | | | 1.24 Nlocal: 297.000 ave 297 max 297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2270.00 ave 2270 max 2270 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: 17454.0 ave 17454 max 17454 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17454 Ave neighs/atom = 58.767677 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 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -2013.0234 0 -2013.0234 15994.924 4613.5447 64 0 -2013.4022 0 -2013.4022 -388.97924 4638.0272 Loop time of 0.0425853 on 1 procs for 9 steps with 297 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 = -2013.02341012981 -2013.40199263174 -2013.40218296445 Force two-norm initial, final = 107.85805 2.4186522 Force max component initial, final = 105.24653 1.9687075 Final line search alpha, max atom move = 0.0036997542 0.0072837337 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040056 | 0.040056 | 0.040056 | 0.0 | 94.06 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057418 | 0.00057418 | 0.00057418 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001955 | | | 4.59 Nlocal: 297.000 ave 297 max 297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2270.00 ave 2270 max 2270 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: 17456.0 ave 17456 max 17456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17456 Ave neighs/atom = 58.774411 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 25 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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2013.4022 0 -2013.4022 -388.97924 Loop time of 6.385e-06 on 1 procs for 0 steps with 297 atoms 172.3% 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 | | 6.385e-06 | | |100.00 Nlocal: 297.000 ave 297 max 297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2278.00 ave 2278 max 2278 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: 17364.0 ave 17364 max 17364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17364 Ave neighs/atom = 58.464646 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 25 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) = 4.544 | 4.544 | 4.544 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 -2013.4022 -2013.4022 19.121198 77.183648 3.1426274 -388.97924 -388.97924 -88.888723 -398.95984 -679.08917 2.5550213 244.89208 Loop time of 6.595e-06 on 1 procs for 0 steps with 297 atoms 227.4% 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 | | 6.595e-06 | | |100.00 Nlocal: 297.000 ave 297 max 297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2278.00 ave 2278 max 2278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8682.00 ave 8682 max 8682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17364.0 ave 17364 max 17364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17364 Ave neighs/atom = 58.464646 Neighbor list builds = 0 Dangerous builds = 0 297 -2013.40218296445 eV 2.555021337688 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