LAMMPS (24 Jan 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 = 2.86883 2.86883 2.86883 Created orthogonal box = (0 -46.6158 0) to (16.4802 46.6158 4.05714) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.49459 4.9438 4.05714 Created 265 atoms create_atoms CPU = 0.000607014 secs 265 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.49459 4.9438 4.05714 Created 265 atoms create_atoms CPU = 0.00041604 secs 265 atoms in group lower Displacing atoms ... 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 523 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.361 | 5.361 | 5.361 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2099.0231 0 -2099.0231 14840.374 295 0 -2155.3234 0 -2155.3234 -12532.355 Loop time of 3.92605 on 1 procs for 295 steps with 523 atoms 85.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2099.02307427 -2155.32128588 -2155.32336976 Force two-norm initial, final = 80.4986 0.194478 Force max component initial, final = 25.4921 0.0171602 Final line search alpha, max atom move = 1 0.0171602 Iterations, force evaluations = 295 549 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8103 | 3.8103 | 3.8103 | 0.0 | 97.05 Neigh | 0.055759 | 0.055759 | 0.055759 | 0.0 | 1.42 Comm | 0.048693 | 0.048693 | 0.048693 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01131 | | | 0.29 Nlocal: 523 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8849 ave 8849 max 8849 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: 199748 ave 199748 max 199748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199748 Ave neighs/atom = 381.927 Neighbor list builds = 10 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 295 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.363 | 5.363 | 5.363 Mbytes Step Temp E_pair E_mol TotEng Press Volume 295 0 -2155.3234 0 -2155.3234 -12532.355 6233.69 315 0 -2157.5253 0 -2157.5253 -1431.4425 6188.3569 Loop time of 0.344133 on 1 procs for 20 steps with 523 atoms 43.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2155.32336976 -2157.52438807 -2157.52534517 Force two-norm initial, final = 188.873 1.33333 Force max component initial, final = 171.852 0.354757 Final line search alpha, max atom move = 0.000378602 0.000134312 Iterations, force evaluations = 20 21 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30553 | 0.30553 | 0.30553 | 0.0 | 88.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.034487 | 0.034487 | 0.034487 | 0.0 | 10.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004117 | | | 1.20 Nlocal: 523 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8850 ave 8850 max 8850 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: 199884 ave 199884 max 199884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199884 Ave neighs/atom = 382.187 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 4 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 5.501 | 5.501 | 5.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2157.5253 0 -2157.5253 -1431.4425 Loop time of 9.53674e-07 on 1 procs for 0 steps with 523 atoms 314.6% 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: 523 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8928 ave 8928 max 8928 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: 200272 ave 200272 max 200272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200272 Ave neighs/atom = 382.929 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) = 5.501 | 5.501 | 5.501 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 -2157.5253 -2157.5253 16.161416 93.231686 4.1070728 -1431.4425 -1431.4425 64.503311 -4265.8532 -92.977584 2.3363492 903.89269 Loop time of 2.14577e-06 on 1 procs for 0 steps with 523 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 523 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8928 ave 8928 max 8928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100136 ave 100136 max 100136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200272 ave 200272 max 200272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200272 Ave neighs/atom = 382.929 Neighbor list builds = 0 Dangerous builds = 0 523 -2157.52534516627 eV 2.33634917260293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04