LAMMPS (19 Mar 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -40.3249 0) to (20.1604 40.3249 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.64492 5.64492 4.03208 Created 202 atoms create_atoms CPU = 0.000319958 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.64492 5.64492 4.03208 Created 202 atoms create_atoms CPU = 0.000170946 secs 202 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1146) 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 22 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 396 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.45 | 4.45 | 4.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1317.2624 0 -1317.2624 3756.5004 18 0 -1326.6316 0 -1326.6316 -4066.0201 Loop time of 0.0525749 on 1 procs for 18 steps with 396 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1317.26235281 -1326.63044652 -1326.63163288 Force two-norm initial, final = 20.2991 0.0997971 Force max component initial, final = 7.06266 0.0322457 Final line search alpha, max atom move = 1 0.0322457 Iterations, force evaluations = 18 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051705 | 0.051705 | 0.051705 | 0.0 | 98.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055075 | 0.00055075 | 0.00055075 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000319 | | | 0.61 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298 ave 3298 max 3298 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: 51640 ave 51640 max 51640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51640 Ave neighs/atom = 130.404 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.45 | 4.45 | 4.45 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -1326.6316 0 -1326.6316 -4066.0201 6555.891 23 0 -1326.6788 0 -1326.6788 -493.31765 6526.4706 Loop time of 0.0122359 on 1 procs for 5 steps with 396 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1326.63163288 -1326.67839101 -1326.67881252 Force two-norm initial, final = 25.0273 0.125674 Force max component initial, final = 21.8182 0.0291977 Final line search alpha, max atom move = 0.000408115 1.1916e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011733 | 0.011733 | 0.011733 | 0.0 | 95.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012088 | 0.00012088 | 0.00012088 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003819 | | | 3.12 Nlocal: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298 ave 3298 max 3298 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: 47096 ave 47096 max 47096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47096 Ave neighs/atom = 118.929 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 6 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.588 | 4.588 | 4.588 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1326.6788 0 -1326.6788 -493.31765 Loop time of 1.19209e-06 on 1 procs for 0 steps with 396 atoms 167.8% 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298 ave 3298 max 3298 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: 48104 ave 48104 max 48104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48104 Ave neighs/atom = 121.475 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) = 4.588 | 4.588 | 4.588 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 -1326.6788 -1326.6788 20.078442 80.649718 4.0303755 -493.31765 -493.31765 -1.6289399 -1476.1932 -2.1308014 2.5850681 202.96192 Loop time of 9.53674e-07 on 1 procs for 0 steps with 396 atoms 209.7% 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: 396 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3298 ave 3298 max 3298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24052 ave 24052 max 24052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48104 ave 48104 max 48104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48104 Ave neighs/atom = 121.475 Neighbor list builds = 0 Dangerous builds = 0 396 -1326.67881252171 eV 2.58506813561522 Angstroms This indicates that LAMMPS ran successfully Please see the log.cite file for references relevant to this simulation Total wall time: 0:00:00