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 -38.9319 0) to (18.3512 38.9319 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3974 5.34316 4.45081 Created 205 atoms create_atoms CPU = 0.000280857 secs 205 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3974 5.34316 4.45081 Created 205 atoms create_atoms CPU = 0.000154018 secs 205 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 = 6 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 3 atoms, new total = 407 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 = 6 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) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2685.4948 0 -2685.4948 58914.879 43 0 -2756.5768 0 -2756.5768 -384.37449 Loop time of 0.0593989 on 1 procs for 43 steps with 407 atoms 101.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2685.49483398 -2756.57477397 -2756.57678587 Force two-norm initial, final = 164.391 0.191907 Force max component initial, final = 56.2365 0.0417981 Final line search alpha, max atom move = 1 0.0417981 Iterations, force evaluations = 43 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057235 | 0.057235 | 0.057235 | 0.0 | 96.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013242 | 0.0013242 | 0.0013242 | 0.0 | 2.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008395 | | | 1.41 Nlocal: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2765 ave 2765 max 2765 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: 23746 ave 23746 max 23746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23746 Ave neighs/atom = 58.344 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 : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -2756.5768 0 -2756.5768 -384.37449 6359.7244 45 0 -2756.5839 0 -2756.5839 670.98023 6357.5148 Loop time of 0.003896 on 1 procs for 2 steps with 407 atoms 256.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2756.57678587 -2756.58288229 -2756.58390868 Force two-norm initial, final = 13.372 0.205793 Force max component initial, final = 12.8955 0.0404903 Final line search alpha, max atom move = 0.000145353 5.88537e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0035782 | 0.0035782 | 0.0035782 | 0.0 | 91.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.7963e-05 | 7.7963e-05 | 7.7963e-05 | 0.0 | 2.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002398 | | | 6.16 Nlocal: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2765 ave 2765 max 2765 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: 23870 ave 23870 max 23870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23870 Ave neighs/atom = 58.6486 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 = 6 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/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) = 4.579 | 4.579 | 4.579 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2756.5839 0 -2756.5839 670.98023 Loop time of 9.53674e-07 on 1 procs for 0 steps with 407 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: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2765 ave 2765 max 2765 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: 23876 ave 23876 max 23876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23876 Ave neighs/atom = 58.6634 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) = 4.579 | 4.579 | 4.579 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 -2756.5839 -2756.5839 18.333905 77.863722 4.4534567 670.98023 670.98023 0.8555404 2012.5208 -0.43563686 2.4262145 282.11861 Loop time of 1.19209e-06 on 1 procs for 0 steps with 407 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: 407 ave 407 max 407 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2765 ave 2765 max 2765 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11938 ave 11938 max 11938 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23876 ave 23876 max 23876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23876 Ave neighs/atom = 58.6634 Neighbor list builds = 0 Dangerous builds = 0 407 -2756.58390867821 eV 2.42621445613267 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