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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -40.432213 0.0000000) to (28.589892 40.432213 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3190497 5.1715622 4.3599177 Created 343 atoms using lattice units in orthogonal box = (0.0000000 -40.432213 0.0000000) to (28.589892 40.432213 4.3599177) create_atoms CPU = 0.001 seconds 343 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3190497 5.1715622 4.3599177 Created 345 atoms using lattice units in orthogonal box = (0.0000000 -40.432213 0.0000000) to (28.589892 40.432213 4.3599177) create_atoms CPU = 0.001 seconds 345 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 688 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4076.6675 0 -4076.6675 125846.61 98 0 -4465.9836 0 -4465.9836 2952.1504 Loop time of 37.3265 on 1 procs for 98 steps with 688 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 = -4076.66752887783 -4465.97913969896 -4465.98355310545 Force two-norm initial, final = 878.58034 0.31493604 Force max component initial, final = 377.20255 0.10694516 Final line search alpha, max atom move = 1.0000000 0.10694516 Iterations, force evaluations = 98 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.256 | 37.256 | 37.256 | 0.0 | 99.81 Neigh | 0.053813 | 0.053813 | 0.053813 | 0.0 | 0.14 Comm | 0.0088335 | 0.0088335 | 0.0088335 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008098 | | | 0.02 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016.00 ave 4016 max 4016 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: 50936.0 ave 50936 max 50936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50936 Ave neighs/atom = 74.034884 Neighbor list builds = 2 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 98 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.274 | 5.274 | 5.274 Mbytes Step Temp E_pair E_mol TotEng Press Volume 98 0 -4465.9836 0 -4465.9836 2952.1504 10079.717 105 0 -4466.4842 0 -4466.4842 -41.128437 10092.789 Loop time of 1.84007 on 1 procs for 7 steps with 688 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 = -4465.98355310545 -4466.48380011357 -4466.48421124629 Force two-norm initial, final = 145.62677 1.4417023 Force max component initial, final = 133.71991 0.72813992 Final line search alpha, max atom move = 0.00038578325 0.00028090419 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8379 | 1.8379 | 1.8379 | 0.0 | 99.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034198 | 0.00034198 | 0.00034198 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001786 | | | 0.10 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4012.00 ave 4012 max 4012 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: 51600.0 ave 51600 max 51600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51600 Ave neighs/atom = 75.000000 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.412 | 5.412 | 5.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4466.4842 0 -4466.4842 -41.128437 Loop time of 2.386e-06 on 1 procs for 0 steps with 688 atoms 125.7% 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 | | 2.386e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4000.00 ave 4000 max 4000 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: 51362.0 ave 51362 max 51362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51362 Ave neighs/atom = 74.654070 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.412 | 5.412 | 5.412 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 -4466.4842 -4466.4842 28.76102 80.769419 4.3447014 -41.128437 -41.128437 21.509463 -115.45253 -29.442241 2.5134376 1694.1186 Loop time of 1.802e-06 on 1 procs for 0 steps with 688 atoms 166.5% 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 | | 1.802e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4000.00 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25681.0 ave 25681 max 25681 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51362.0 ave 51362 max 51362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51362 Ave neighs/atom = 74.654070 Neighbor list builds = 0 Dangerous builds = 0 688 -4466.48421124629 eV 2.51343758858065 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:40