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 = 3.52264 3.52264 3.52264 Created orthogonal box = (0 -53.1943 0) to (37.6115 53.1943 4.98177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.93866 5.13244 4.98177 Created 916 atoms create_atoms CPU = 0.000586033 secs 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.93866 5.13244 4.98177 Created 916 atoms create_atoms CPU = 0.00045085 secs 916 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 19 1 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 11.7548 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1808 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 13.11 | 13.11 | 13.11 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7567.3556 0 -7567.3556 5612.2226 56 0 -7636.027 0 -7636.027 -10811.376 Loop time of 2.88817 on 1 procs for 56 steps with 1808 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7567.35562473 -7636.02034649 -7636.02700517 Force two-norm initial, final = 57.1848 0.36008 Force max component initial, final = 11.2922 0.0348125 Final line search alpha, max atom move = 1 0.0348125 Iterations, force evaluations = 56 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8698 | 2.8698 | 2.8698 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.013231 | 0.013231 | 0.013231 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005141 | | | 0.18 Nlocal: 1808 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18831 ave 18831 max 18831 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: 1.12145e+06 ave 1.12145e+06 max 1.12145e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1121448 Ave neighs/atom = 620.27 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.11 | 13.11 | 13.11 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -7636.027 0 -7636.027 -10811.376 19934.223 60 0 -7636.3202 0 -7636.3202 -2698.4495 19845.651 Loop time of 0.143607 on 1 procs for 4 steps with 1808 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7636.02700517 -7636.31912488 -7636.32019754 Force two-norm initial, final = 171.169 1.00399 Force max component initial, final = 152.308 0.858958 Final line search alpha, max atom move = 0.000112369 9.652e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1413 | 0.1413 | 0.1413 | 0.0 | 98.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061798 | 0.00061798 | 0.00061798 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001688 | | | 1.18 Nlocal: 1808 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18836 ave 18836 max 18836 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: 1.12189e+06 ave 1.12189e+06 max 1.12189e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1121888 Ave neighs/atom = 620.513 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 12.63 | 12.63 | 12.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7636.3202 0 -7636.3202 -2698.4495 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1808 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: 1808 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18836 ave 18836 max 18836 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: 1.1237e+06 ave 1.1237e+06 max 1.1237e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1123696 Ave neighs/atom = 621.513 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) = 12.63 | 12.63 | 12.63 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 -7636.3202 -7636.3202 37.565044 106.38852 4.9657711 -2698.4495 -2698.4495 69.259564 -8188.5585 23.950353 2.3130508 547.43873 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1808 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 | | 1.907e-06 | | |100.00 Nlocal: 1808 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18836 ave 18836 max 18836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 561848 ave 561848 max 561848 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.1237e+06 ave 1.1237e+06 max 1.1237e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1123696 Ave neighs/atom = 621.513 Neighbor list builds = 0 Dangerous builds = 0 1808 -7636.32019754063 eV 2.31305080166313 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03