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 -58.0346 0) to (29.0158 58.0346 3.1472) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4377 4.4377 3.1472 Created 341 atoms create_atoms CPU = 0.000180006 secs 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4377 4.4377 3.1472 Created 341 atoms create_atoms CPU = 7.48634e-05 secs 341 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 = 10 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 4 atoms, new total = 678 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 = 10 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4509.7361 0 -4509.7361 36716.726 35 0 -4609.5431 0 -4609.5431 -8194.4746 Loop time of 0.0770969 on 1 procs for 35 steps with 678 atoms 103.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4509.73605484 -4609.53897964 -4609.54310465 Force two-norm initial, final = 216.202 0.283504 Force max component initial, final = 73.6913 0.0457658 Final line search alpha, max atom move = 1 0.0457658 Iterations, force evaluations = 35 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.074226 | 0.074226 | 0.074226 | 0.0 | 96.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017033 | 0.0017033 | 0.0017033 | 0.0 | 2.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001167 | | | 1.51 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4717 ave 4717 max 4717 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: 39482 ave 39482 max 39482 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39482 Ave neighs/atom = 58.233 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 : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -4609.5431 0 -4609.5431 -8194.4746 10599.259 38 0 -4609.6189 0 -4609.6189 -1681.414 10575.902 Loop time of 0.00781393 on 1 procs for 3 steps with 678 atoms 128.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4609.54310465 -4609.6171404 -4609.61887542 Force two-norm initial, final = 76.8974 0.299846 Force max component initial, final = 71.1517 0.0460293 Final line search alpha, max atom move = 0.000116027 5.34064e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0071359 | 0.0071359 | 0.0071359 | 0.0 | 91.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016022 | 0.00016022 | 0.00016022 | 0.0 | 2.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005178 | | | 6.63 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4706 ave 4706 max 4706 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: 39650 ave 39650 max 39650 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39650 Ave neighs/atom = 58.4808 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 = 10 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) = 4.652 | 4.652 | 4.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4609.6189 0 -4609.6189 -1681.414 Loop time of 1.19209e-06 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4708 ave 4708 max 4708 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: 39662 ave 39662 max 39662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39662 Ave neighs/atom = 58.4985 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) = 4.652 | 4.652 | 4.652 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 -4609.6189 -4609.6189 29.010417 116.06929 3.1408421 -1681.414 -1681.414 -0.087369108 -5047.1812 3.0265135 2.5271606 228.58008 Loop time of 9.53674e-07 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4708 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19831 ave 19831 max 19831 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39662 ave 39662 max 39662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39662 Ave neighs/atom = 58.4985 Neighbor list builds = 0 Dangerous builds = 0 678 -4609.6188754224 eV 2.52716064055297 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