LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8688302 2.8688302 2.8688302 Created orthogonal box = (0.0000000 -28.688302 0.0000000) to (4.0571386 28.688302 4.0571386) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0571386 2.8688302 4.0571386 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -28.688302 0.0000000) to (4.0571386 28.688302 4.0571386) create_atoms CPU = 0.001 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0571386 2.8688302 4.0571386 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -28.688302 0.0000000) to (4.0571386 28.688302 4.0571386) create_atoms CPU = 0.000 seconds 42 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 = 1 12 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 0 atoms, new total = 82 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_984358344196_004#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) 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 = 1 12 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) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -143.40787 0 -143.40787 314170.69 44 0 -334.84064 0 -334.84064 58026.051 Loop time of 0.124453 on 1 procs for 44 steps with 82 atoms 89.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -143.407867002312 -334.840381681668 -334.840636214152 Force two-norm initial, final = 547.96755 0.070548689 Force max component initial, final = 193.59657 0.013963126 Final line search alpha, max atom move = 1.0000000 0.013963126 Iterations, force evaluations = 44 72 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1193 | 0.1193 | 0.1193 | 0.0 | 95.86 Neigh | 0.0014841 | 0.0014841 | 0.0014841 | 0.0 | 1.19 Comm | 0.0025695 | 0.0025695 | 0.0025695 | 0.0 | 2.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001095 | | | 0.88 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3950.00 ave 3950 max 3950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 32468.0 ave 32468 max 32468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 32468 Ave neighs/atom = 395.95122 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) 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 = 1 12 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 : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -334.84064 0 -334.84064 58026.051 944.44036 367 0 -339.35069 0 -339.35069 -1121.9447 969.93953 Loop time of 0.57464 on 1 procs for 323 steps with 82 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -334.840636214152 -339.350353782552 -339.350685721467 Force two-norm initial, final = 59.992292 1.3371457 Force max component initial, final = 41.914668 0.78408749 Final line search alpha, max atom move = 0.0054993235 0.0043119508 Iterations, force evaluations = 323 332 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49335 | 0.49335 | 0.49335 | 0.0 | 85.85 Neigh | 0.024546 | 0.024546 | 0.024546 | 0.0 | 4.27 Comm | 0.012747 | 0.012747 | 0.012747 | 0.0 | 2.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.044 | | | 7.66 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4893.00 ave 4893 max 4893 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31000.0 ave 31000 max 31000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31000 Ave neighs/atom = 378.04878 Neighbor list builds = 16 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 = 1 15 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -339.35069 0 -339.35069 -1121.9447 Loop time of 1.939e-06 on 1 procs for 0 steps with 82 atoms 154.7% 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 | | 1.939e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4974.00 ave 4974 max 4974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30984.0 ave 30984 max 30984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30984 Ave neighs/atom = 377.85366 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 = 1 15 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.600 | 4.600 | 4.600 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 -339.35069 -339.35069 3.6022927 74.745778 3.6022927 -1121.9447 -1121.9447 -1149.9776 -1065.8788 -1149.9776 2.5146038 66.460052 Loop time of 1.866e-06 on 1 procs for 0 steps with 82 atoms 160.8% 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 | | 1.866e-06 | | |100.00 Nlocal: 82.0000 ave 82 max 82 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4974.00 ave 4974 max 4974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15492.0 ave 15492 max 15492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30984.0 ave 30984 max 30984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30984 Ave neighs/atom = 377.85366 Neighbor list builds = 0 Dangerous builds = 0 82 -339.350685721467 eV 2.51460378860392 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00