LAMMPS (18 Jun 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:88) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -41.1234 0) to (20.5597 41.1234 4.03208) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.74454 4.74454 4.03208 Created 209 atoms create_atoms CPU = 0.000168085 secs 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.74454 4.74454 4.03208 Created 209 atoms create_atoms CPU = 4.19617e-05 secs 209 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1089) 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 9 atoms, new total = 409 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 = 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1362.5653 0 -1362.5653 1229.0634 342 0 -1368.1355 0 -1368.1355 -6239.0102 Loop time of 1.02215 on 1 procs for 342 steps with 409 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 = -1362.56531004 -1368.1354541 -1368.1354541 Force two-norm initial, final = 12.7087 1.6032e-06 Force max component initial, final = 4.4497 2.75347e-07 Final line search alpha, max atom move = 1 2.75347e-07 Iterations, force evaluations = 342 680 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0002 | 1.0002 | 1.0002 | 0.0 | 97.85 Neigh | 0.0012641 | 0.0012641 | 0.0012641 | 0.0 | 0.12 Comm | 0.013494 | 0.013494 | 0.013494 | 0.0 | 1.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007195 | | | 0.70 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3549 ave 3549 max 3549 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: 44574 ave 44574 max 44574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44574 Ave neighs/atom = 108.983 Neighbor list builds = 1 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 : 342 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 342 0 -1368.1355 0 -1368.1355 -6239.0102 6818.1134 1205 0 -1368.1966 0 -1368.1966 -1881.5326 6779.4999 Loop time of 2.63261 on 1 procs for 863 steps with 409 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1368.1354541 -1368.19659884 -1368.19659884 Force two-norm initial, final = 29.7597 1.94265e-05 Force max component initial, final = 22.7355 1.39972e-05 Final line search alpha, max atom move = 1 1.39972e-05 Iterations, force evaluations = 863 1723 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4994 | 2.4994 | 2.4994 | 0.0 | 94.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.03174 | 0.03174 | 0.03174 | 0.0 | 1.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1014 | | | 3.85 Nlocal: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3552 ave 3552 max 3552 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: 44532 ave 44532 max 44532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44532 Ave neighs/atom = 108.88 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1368.1966 0 -1368.1966 -1881.5326 Loop time of 9.53674e-07 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3570 ave 3570 max 3570 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: 46296 ave 46296 max 46296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46296 Ave neighs/atom = 113.193 Neighbor list builds = 0 Dangerous builds = 0 WARNING: No fixes defined, atoms won't move (src/verlet.cpp:55) Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.592 | 4.592 | 4.592 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 -1368.1966 -1368.1966 20.484253 82.246738 4.024008 -1881.5326 -1881.5326 -0.0032957725 -5644.5963 0.0017896237 2.5414163 329.46901 Loop time of 9.53674e-07 on 1 procs for 0 steps with 409 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: 409 ave 409 max 409 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3570 ave 3570 max 3570 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23148 ave 23148 max 23148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46296 ave 46296 max 46296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46296 Ave neighs/atom = 113.193 Neighbor list builds = 0 Dangerous builds = 0 409 -1368.19659883864 eV 2.54141628995489 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03