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 = 2.8665 2.8665 2.8665 Created orthogonal box = (0 -48.9856 0) to (24.4914 48.9856 2.8665) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.69048 3.69048 2.8665 Created 293 atoms create_atoms CPU = 0.000211954 secs 293 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.69048 3.69048 2.8665 Created 293 atoms create_atoms CPU = 8.79765e-05 secs 293 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 9 35 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 578 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2468.4734 0 -2468.4734 -517.1843 23 0 -2482.8248 0 -2482.8248 -7168.0128 Loop time of 0.026746 on 1 procs for 23 steps with 578 atoms 112.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2468.47336269 -2482.82294285 -2482.8248287 Force two-norm initial, final = 27.654 0.150587 Force max component initial, final = 12.6605 0.0267911 Final line search alpha, max atom move = 1 0.0267911 Iterations, force evaluations = 23 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.025328 | 0.025328 | 0.025328 | 0.0 | 94.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083494 | 0.00083494 | 0.00083494 | 0.0 | 3.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005829 | | | 2.18 Nlocal: 578 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3691 ave 3691 max 3691 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: 33430 ave 33430 max 33430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 33430 Ave neighs/atom = 57.8374 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.478 | 4.478 | 4.478 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -2482.8248 0 -2482.8248 -7168.0128 6878.0303 28 0 -2482.9365 0 -2482.9365 1397.9628 6845.1674 Loop time of 0.00553203 on 1 procs for 5 steps with 578 atoms 180.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2482.8248287 -2482.93620155 -2482.93651229 Force two-norm initial, final = 58.8732 1.07107 Force max component initial, final = 48.0428 1.04125 Final line search alpha, max atom move = 0.000339075 0.000353062 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0048599 | 0.0048599 | 0.0048599 | 0.0 | 87.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015712 | 0.00015712 | 0.00015712 | 0.0 | 2.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000515 | | | 9.31 Nlocal: 578 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3683 ave 3683 max 3683 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: 34334 ave 34334 max 34334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34334 Ave neighs/atom = 59.4014 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 9 35 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2482.9365 0 -2482.9365 1397.9628 Loop time of 9.53674e-07 on 1 procs for 0 steps with 578 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: 578 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4631 ave 4631 max 4631 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: 35546 ave 35546 max 35546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35546 Ave neighs/atom = 61.4983 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) = 4.637 | 4.637 | 4.637 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 -2482.9365 -2482.9365 24.471458 97.971279 2.8551272 1397.9628 1397.9628 31.309877 4405.3267 -242.74805 2.3428538 257.06826 Loop time of 1.90735e-06 on 1 procs for 0 steps with 578 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: 578 ave 578 max 578 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4631 ave 4631 max 4631 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17773 ave 17773 max 17773 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 35546 ave 35546 max 35546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 35546 Ave neighs/atom = 61.4983 Neighbor list builds = 0 Dangerous builds = 0 578 -2482.93651229384 eV 2.34285375440412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00