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 -40.0605 0) to (9.4416 40.0605 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24533 4.45081 4.45081 Created 110 atoms create_atoms CPU = 0.000228167 secs 110 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24533 4.45081 4.45081 Created 110 atoms create_atoms CPU = 8.10623e-05 secs 110 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 = 4 26 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 = 216 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 = 4 26 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1447.2492 0 -1447.2492 36958.929 35 0 -1461.8802 0 -1461.8802 14814.431 Loop time of 0.0281291 on 1 procs for 35 steps with 216 atoms 106.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1447.2492149 -1461.8788398 -1461.88021114 Force two-norm initial, final = 38.5293 0.140498 Force max component initial, final = 13.4478 0.0259702 Final line search alpha, max atom move = 1 0.0259702 Iterations, force evaluations = 35 66 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.026805 | 0.026805 | 0.026805 | 0.0 | 95.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00086999 | 0.00086999 | 0.00086999 | 0.0 | 3.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004539 | | | 1.61 Nlocal: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2116 ave 2116 max 2116 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: 12652 ave 12652 max 12652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12652 Ave neighs/atom = 58.5741 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -1461.8802 0 -1461.8802 14814.431 3366.9052 38 0 -1461.9102 0 -1461.9102 6503.0103 3376.7881 Loop time of 0.00252295 on 1 procs for 3 steps with 216 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1461.88021114 -1461.91012235 -1461.91018453 Force two-norm initial, final = 28.7365 0.225283 Force max component initial, final = 21.7153 0.0485543 Final line search alpha, max atom move = 0.0017692 8.59021e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0022411 | 0.0022411 | 0.0022411 | 0.0 | 88.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 7.2479e-05 | 7.2479e-05 | 7.2479e-05 | 0.0 | 2.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002093 | | | 8.30 Nlocal: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2116 ave 2116 max 2116 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: 12608 ave 12608 max 12608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12608 Ave neighs/atom = 58.3704 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 = 4 26 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) = 4.544 | 4.544 | 4.544 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1461.9102 0 -1461.9102 6503.0103 Loop time of 9.53674e-07 on 1 procs for 0 steps with 216 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: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2116 ave 2116 max 2116 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: 12608 ave 12608 max 12608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12608 Ave neighs/atom = 58.3704 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) = 4.544 | 4.544 | 4.544 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 -1461.9102 -1461.9102 9.4531361 80.120926 4.4584298 6503.0103 6503.0103 21.433305 19510.674 -23.076883 2.5761888 171.16742 Loop time of 9.53674e-07 on 1 procs for 0 steps with 216 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: 216 ave 216 max 216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2116 ave 2116 max 2116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6304 ave 6304 max 6304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12608 ave 12608 max 12608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12608 Ave neighs/atom = 58.3704 Neighbor list builds = 0 Dangerous builds = 0 216 -1461.91018452681 eV 2.57618875862579 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