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 -47.521677 0.0000000) to (33.602900 47.521677 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3057211 5.4191387 4.4508129 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -47.521677 0.0000000) to (33.602900 47.521677 4.4508129) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3057211 5.4191387 4.4508129 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -47.521677 0.0000000) to (33.602900 47.521677 4.4508129) create_atoms CPU = 0.001 seconds 458 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 = 11 31 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 = 914 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 = 11 31 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) = 4.556 | 4.556 | 4.556 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5712.4462 0 -5712.4462 129058.54 167 0 -6193.7809 0 -6193.7809 11820.705 Loop time of 1.29941 on 1 procs for 167 steps with 914 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5712.44618588763 -6193.77566477304 -6193.78089137375 Force two-norm initial, final = 500.27267 0.22297356 Force max component initial, final = 119.73576 0.040684703 Final line search alpha, max atom move = 0.90351798 0.036759361 Iterations, force evaluations = 167 322 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.27 | 1.27 | 1.27 | 0.0 | 97.74 Neigh | 0.0044524 | 0.0044524 | 0.0044524 | 0.0 | 0.34 Comm | 0.012344 | 0.012344 | 0.012344 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0126 | | | 0.97 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4037.00 ave 4037 max 4037 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: 53536.0 ave 53536 max 53536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53536 Ave neighs/atom = 58.573304 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 = 11 31 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 : 167 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press Volume 167 0 -6193.7809 0 -6193.7809 11820.705 14214.705 172 0 -6194.2018 0 -6194.2018 -622.62734 14274.061 Loop time of 0.0276924 on 1 procs for 5 steps with 914 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 = -6193.78089137375 -6194.1969169992 -6194.20177634916 Force two-norm initial, final = 207.77422 10.257921 Force max component initial, final = 176.17555 8.1305609 Final line search alpha, max atom move = 6.8869429e-05 0.00055994708 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026447 | 0.026447 | 0.026447 | 0.0 | 95.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020666 | 0.00020666 | 0.00020666 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001038 | | | 3.75 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4030.00 ave 4030 max 4030 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: 53492.0 ave 53492 max 53492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53492 Ave neighs/atom = 58.525164 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 = 11 31 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) = 4.689 | 4.689 | 4.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6194.2018 0 -6194.2018 -622.62734 Loop time of 1.791e-06 on 1 procs for 0 steps with 914 atoms 167.5% 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 | | 1.791e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4036.00 ave 4036 max 4036 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: 53444.0 ave 53444 max 53444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53444 Ave neighs/atom = 58.472648 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 = 11 31 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) = 4.689 | 4.689 | 4.689 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 -6194.2018 -6194.2018 33.550307 95.45017 4.4573254 -622.62734 -622.62734 -911.17762 -351.86611 -604.83828 2.4427812 658.13371 Loop time of 2.027e-06 on 1 procs for 0 steps with 914 atoms 197.3% 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 | | 2.027e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4036.00 ave 4036 max 4036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26722.0 ave 26722 max 26722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53444.0 ave 53444 max 53444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53444 Ave neighs/atom = 58.472648 Neighbor list builds = 0 Dangerous builds = 0 914 -6194.20177634916 eV 2.44278120103308 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