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 -44.2882 0) to (10.4381 44.2882 4.45081) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.74458 5.36788 4.45081 Created 134 atoms create_atoms CPU = 0.000193119 secs 134 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.74458 5.36788 4.45081 Created 134 atoms create_atoms CPU = 8.39233e-05 secs 134 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 29 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 = 264 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 29 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) = 4.419 | 4.419 | 4.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1767.4875 0 -1767.4875 40869.772 25 0 -1791.3189 0 -1791.3189 195.70836 Loop time of 0.0169678 on 1 procs for 25 steps with 264 atoms 58.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1767.48752372 -1791.31760486 -1791.3189384 Force two-norm initial, final = 68.01 0.14968 Force max component initial, final = 17.5729 0.0363813 Final line search alpha, max atom move = 1 0.0363813 Iterations, force evaluations = 25 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016173 | 0.016173 | 0.016173 | 0.0 | 95.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052714 | 0.00052714 | 0.00052714 | 0.0 | 3.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002677 | | | 1.58 Nlocal: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 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: 15472 ave 15472 max 15472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15472 Ave neighs/atom = 58.6061 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 : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.419 | 4.419 | 4.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -1791.3189 0 -1791.3189 195.70836 4115.0755 28 0 -1791.3312 0 -1791.3312 3041.3589 4110.9187 Loop time of 0.00227308 on 1 procs for 3 steps with 264 atoms 439.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1791.3189384 -1791.33120078 -1791.33122654 Force two-norm initial, final = 15.8239 0.185497 Force max component initial, final = 15.8153 0.0439479 Final line search alpha, max atom move = 0.00130518 5.73599e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0020418 | 0.0020418 | 0.0020418 | 0.0 | 89.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.3896e-05 | 6.3896e-05 | 6.3896e-05 | 0.0 | 2.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001674 | | | 7.36 Nlocal: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 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: 15416 ave 15416 max 15416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15416 Ave neighs/atom = 58.3939 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 29 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) = 4.557 | 4.557 | 4.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1791.3312 0 -1791.3312 3041.3589 Loop time of 9.53674e-07 on 1 procs for 0 steps with 264 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: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 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: 15440 ave 15440 max 15440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15440 Ave neighs/atom = 58.4848 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) = 4.557 | 4.557 | 4.557 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 -1791.3312 -1791.3312 10.443936 88.576353 4.4438245 3041.3589 3041.3589 1.7185245 9108.6537 13.704418 2.5613233 184.49846 Loop time of 0 on 1 procs for 0 steps with 264 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 | | 0 | | | 0.00 Nlocal: 264 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2368 ave 2368 max 2368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7720 ave 7720 max 7720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15440 ave 15440 max 15440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15440 Ave neighs/atom = 58.4848 Neighbor list builds = 0 Dangerous builds = 0 264 -1791.33122653714 eV 2.56132331729443 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