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 -47.5248 0) to (33.6029 47.5248 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.30572 4.58543 4.45081 Created 458 atoms create_atoms CPU = 0.000411034 secs 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.30572 4.58543 4.45081 Created 458 atoms create_atoms CPU = 0.000266075 secs 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: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 = 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 8 atoms, new total = 908 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 = 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) = 4.555 | 4.555 | 4.555 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6074.2277 0 -6074.2277 31971.419 40 0 -6149.3435 0 -6149.3435 -4437.2432 Loop time of 0.118362 on 1 procs for 40 steps with 908 atoms 92.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6074.22770999 -6149.33818498 -6149.34352005 Force two-norm initial, final = 155.996 0.267922 Force max component initial, final = 36.1351 0.0509512 Final line search alpha, max atom move = 0.884734 0.0450783 Iterations, force evaluations = 40 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11447 | 0.11447 | 0.11447 | 0.0 | 96.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021296 | 0.0021296 | 0.0021296 | 0.0 | 1.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001761 | | | 1.49 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692 ave 4692 max 4692 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: 52796 ave 52796 max 52796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52796 Ave neighs/atom = 58.1454 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.555 | 4.555 | 4.555 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -6149.3435 0 -6149.3435 -4437.2432 14215.647 42 0 -6149.3935 0 -6149.3935 816.72275 14189.807 Loop time of 0.00652909 on 1 procs for 2 steps with 908 atoms 153.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6149.34352005 -6149.39051006 -6149.39346501 Force two-norm initial, final = 73.6127 5.9219 Force max component initial, final = 63.6265 5.41163 Final line search alpha, max atom move = 8.58058e-05 0.000464349 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0060723 | 0.0060723 | 0.0060723 | 0.0 | 93.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010419 | 0.00010419 | 0.00010419 | 0.0 | 1.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003526 | | | 5.40 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4736 ave 4736 max 4736 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: 52956 ave 52956 max 52956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52956 Ave neighs/atom = 58.3216 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/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) = 4.693 | 4.693 | 4.693 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6149.3935 0 -6149.3935 816.72275 Loop time of 1.19209e-06 on 1 procs for 0 steps with 908 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 | | 1.192e-06 | | |100.00 Nlocal: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4736 ave 4736 max 4736 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: 52976 ave 52976 max 52976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52976 Ave neighs/atom = 58.3436 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) = 4.693 | 4.693 | 4.693 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 -6149.3935 -6149.3935 33.55507 95.049649 4.4490553 816.72275 816.72275 268.28914 1571.0912 610.78791 2.4031483 680.17602 Loop time of 9.53674e-07 on 1 procs for 0 steps with 908 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: 908 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4736 ave 4736 max 4736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26488 ave 26488 max 26488 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 52976 ave 52976 max 52976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 52976 Ave neighs/atom = 58.3436 Neighbor list builds = 0 Dangerous builds = 0 908 -6149.39346500751 eV 2.40314832731505 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