LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.1472 3.1472 3.1472 Created orthogonal box = (0 -38.0309 0) to (46.5743 38.0309 7.70903) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.46603 4.68835 5.13936 Created 878 atoms create_atoms CPU = 0.000319958 secs 878 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.46603 4.68835 5.13936 Created 878 atoms create_atoms CPU = 0.000200033 secs 878 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 15 25 3 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 6 atoms, new total = 1750 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) 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 = 15 25 3 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11220.375 0 -11220.375 107155.13 296 0 -11839.977 0 -11839.977 2617.2349 Loop time of 1.49274 on 1 procs for 296 steps with 1750 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 = -11220.3753379 -11839.9677905 -11839.9772143 Force two-norm initial, final = 531.167 0.384932 Force max component initial, final = 66.3343 0.0722844 Final line search alpha, max atom move = 0.546353 0.0394928 Iterations, force evaluations = 296 585 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4513 | 1.4513 | 1.4513 | 0.0 | 97.22 Neigh | 0.0044632 | 0.0044632 | 0.0044632 | 0.0 | 0.30 Comm | 0.016996 | 0.016996 | 0.016996 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02001 | | | 1.34 Nlocal: 1750 ave 1750 max 1750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5109 ave 5109 max 5109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102662 ave 102662 max 102662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102662 Ave neighs/atom = 58.664 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 296 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press Volume 296 0 -11839.977 0 -11839.977 2617.2349 27309.457 297 0 -11839.986 0 -11839.986 4222.7439 27294.495 Loop time of 0.00875497 on 1 procs for 1 steps with 1750 atoms 114.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11839.9772143 -11839.9772143 -11839.9860326 Force two-norm initial, final = 45.1825 0.833172 Force max component initial, final = 32.5496 0.678555 Final line search alpha, max atom move = 3.07223e-05 2.08468e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0083365 | 0.0083365 | 0.0083365 | 0.0 | 95.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.1076e-05 | 9.1076e-05 | 9.1076e-05 | 0.0 | 1.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003273 | | | 3.74 Nlocal: 1750 ave 1750 max 1750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5117 ave 5117 max 5117 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102780 ave 102780 max 102780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102780 Ave neighs/atom = 58.7314 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 = 15 25 3 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11839.986 0 -11839.986 4222.7439 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1750 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1750 ave 1750 max 1750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5117 ave 5117 max 5117 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102798 ave 102798 max 102798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102798 Ave neighs/atom = 58.7417 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 5.187 | 5.187 | 5.187 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 -11839.986 -11839.986 46.56179 76.061818 7.7068819 4222.7439 4222.7439 16.607136 12691.444 -39.819789 2.4784117 1843.2041 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1750 atoms 0.0% 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 | | 9.537e-07 | | |100.00 Nlocal: 1750 ave 1750 max 1750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5117 ave 5117 max 5117 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51399 ave 51399 max 51399 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102798 ave 102798 max 102798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102798 Ave neighs/atom = 58.7417 Neighbor list builds = 0 Dangerous builds = 0 1750 -11839.9860326032 eV 2.47841165235812 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