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 -58.375 0) to (20.6376 58.375 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.27938 5.42994 4.45081 Created 346 atoms create_atoms CPU = 0.00031805 secs 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.27938 5.42994 4.45081 Created 346 atoms create_atoms CPU = 0.000189066 secs 346 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 = 7 38 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 = 684 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 = 7 38 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) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4619.4278 0 -4619.4278 8693.0314 28 0 -4640.7433 0 -4640.7433 -9318.0259 Loop time of 0.0425401 on 1 procs for 28 steps with 684 atoms 94.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4619.42779966 -4640.73869869 -4640.74332795 Force two-norm initial, final = 54.5658 0.239127 Force max component initial, final = 14.9726 0.0469715 Final line search alpha, max atom move = 1 0.0469715 Iterations, force evaluations = 28 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.040961 | 0.040961 | 0.040961 | 0.0 | 96.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00090671 | 0.00090671 | 0.00090671 | 0.0 | 2.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006721 | | | 1.58 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567 ave 3567 max 3567 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: 39632 ave 39632 max 39632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39632 Ave neighs/atom = 57.9415 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -4640.7433 0 -4640.7433 -9318.0259 10723.952 30 0 -4640.805 0 -4640.805 -2677.4738 10697.97 Loop time of 0.00364709 on 1 procs for 2 steps with 684 atoms 274.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4640.74332795 -4640.80231592 -4640.80499778 Force two-norm initial, final = 71.8086 1.4167 Force max component initial, final = 52.7413 1.07438 Final line search alpha, max atom move = 8.34176e-05 8.96223e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.003355 | 0.003355 | 0.003355 | 0.0 | 91.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.987e-05 | 7.987e-05 | 7.987e-05 | 0.0 | 2.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002122 | | | 5.82 Nlocal: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567 ave 3567 max 3567 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: 39776 ave 39776 max 39776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39776 Ave neighs/atom = 58.152 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 = 7 38 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4640.805 0 -4640.805 -2677.4738 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567 ave 3567 max 3567 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: 39812 ave 39812 max 39812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39812 Ave neighs/atom = 58.2047 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) = 4.656 | 4.656 | 4.656 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 -4640.805 -4640.805 20.610996 116.75002 4.4457539 -2677.4738 -2677.4738 -131.40258 -8061.7401 160.72128 2.4846331 349.92151 Loop time of 9.53674e-07 on 1 procs for 0 steps with 684 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: 684 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3567 ave 3567 max 3567 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19906 ave 19906 max 19906 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39812 ave 39812 max 39812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39812 Ave neighs/atom = 58.2047 Neighbor list builds = 0 Dangerous builds = 0 684 -4640.80499777769 eV 2.48463308856683 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