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 -49.164 0) to (24.5804 49.164 3.1472) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.43253 4.43253 3.1472 Created 245 atoms create_atoms CPU = 0.000174046 secs 245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.43253 4.43253 3.1472 Created 245 atoms create_atoms CPU = 5.29289e-05 secs 245 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 = 8 32 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 4 atoms, new total = 486 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 = 8 32 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3225.7923 0 -3225.7923 39343.028 55 0 -3301.12 0 -3301.12 -11142.519 Loop time of 0.0895979 on 1 procs for 55 steps with 486 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3225.79229412 -3301.11760593 -3301.12002015 Force two-norm initial, final = 184.543 0.204076 Force max component initial, final = 69.4005 0.0354152 Final line search alpha, max atom move = 1 0.0354152 Iterations, force evaluations = 55 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.08602 | 0.08602 | 0.08602 | 0.0 | 96.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022242 | 0.0022242 | 0.0022242 | 0.0 | 2.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001354 | | | 1.51 Nlocal: 486 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3639 ave 3639 max 3639 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: 28286 ave 28286 max 28286 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28286 Ave neighs/atom = 58.2016 Neighbor list builds = 0 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -3301.12 0 -3301.12 -11142.519 7606.6012 59 0 -3301.2173 0 -3301.2173 -2266.7234 7584.1994 Loop time of 0.00639606 on 1 procs for 4 steps with 486 atoms 156.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3301.12002015 -3301.21666056 -3301.21729659 Force two-norm initial, final = 74.7971 0.290546 Force max component initial, final = 68.7994 0.169369 Final line search alpha, max atom move = 0.000178532 3.02379e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.00582 | 0.00582 | 0.00582 | 0.0 | 90.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014353 | 0.00014353 | 0.00014353 | 0.0 | 2.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004325 | | | 6.76 Nlocal: 486 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3648 ave 3648 max 3648 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: 28456 ave 28456 max 28456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28456 Ave neighs/atom = 58.5514 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 32 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/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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3301.2173 0 -3301.2173 -2266.7234 Loop time of 9.53674e-07 on 1 procs for 0 steps with 486 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: 486 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3648 ave 3648 max 3648 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: 28464 ave 28464 max 28464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28464 Ave neighs/atom = 58.5679 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) = 4.595 | 4.595 | 4.595 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 -3301.2173 -3301.2173 24.572626 98.327965 3.1389263 -2266.7234 -2266.7234 -9.3891738 -6755.0957 -35.685453 2.5283779 222.11858 Loop time of 9.53674e-07 on 1 procs for 0 steps with 486 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: 486 ave 486 max 486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3648 ave 3648 max 3648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14232 ave 14232 max 14232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28464 ave 28464 max 28464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28464 Ave neighs/atom = 58.5679 Neighbor list builds = 0 Dangerous builds = 0 486 -3301.21729658668 eV 2.52837787707007 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