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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -36.948078 0.0000000) to (26.126236 36.948078 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6105123 5.7957769 5.1737657 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -36.948078 0.0000000) to (26.126236 36.948078 5.1737657) create_atoms CPU = 0.002 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6105123 5.7957769 5.1737657 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -36.948078 0.0000000) to (26.126236 36.948078 5.1737657) create_atoms CPU = 0.001 seconds 410 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 810 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_884343146310_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.947 | 4.947 | 4.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2435.9048 0 -2435.9048 169212.8 522 0 -3189.0515 0 -3189.0515 -65939.42 Loop time of 5.76079 on 1 procs for 522 steps with 810 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2435.90480686919 -3189.0487113373 -3189.0515061362 Force two-norm initial, final = 1767.9991 0.15295925 Force max component initial, final = 584.61492 0.019481941 Final line search alpha, max atom move = 1.0000000 0.019481941 Iterations, force evaluations = 522 987 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6038 | 5.6038 | 5.6038 | 0.0 | 97.28 Neigh | 0.075368 | 0.075368 | 0.075368 | 0.0 | 1.31 Comm | 0.045007 | 0.045007 | 0.045007 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03658 | | | 0.64 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4962.00 ave 4962 max 4962 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: 109192.0 ave 109192 max 109192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109192 Ave neighs/atom = 134.80494 Neighbor list builds = 11 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 522 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.945 | 4.945 | 4.945 Mbytes Step Temp E_pair E_mol TotEng Press Volume 522 0 -3189.0515 0 -3189.0515 -65939.42 9988.6191 569 0 -3209.3869 0 -3209.3869 15.108881 9517.1801 Loop time of 0.300002 on 1 procs for 47 steps with 810 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3189.05150613619 -3209.38497099622 -3209.38685403657 Force two-norm initial, final = 814.17801 4.9766331 Force max component initial, final = 666.89832 3.3155478 Final line search alpha, max atom move = 0.00054876915 0.0018194703 Iterations, force evaluations = 47 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28128 | 0.28128 | 0.28128 | 0.0 | 93.76 Neigh | 0.0069207 | 0.0069207 | 0.0069207 | 0.0 | 2.31 Comm | 0.0020885 | 0.0020885 | 0.0020885 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009709 | | | 3.24 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5056.00 ave 5056 max 5056 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: 114432.0 ave 114432 max 114432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114432 Ave neighs/atom = 141.27407 Neighbor list builds = 1 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3209.3869 0 -3209.3869 15.108881 Loop time of 1.764e-06 on 1 procs for 0 steps with 810 atoms 170.1% 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 | | 1.764e-06 | | |100.00 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5116.00 ave 5116 max 5116 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: 114736.0 ave 114736 max 114736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114736 Ave neighs/atom = 141.64938 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 8 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.084 | 5.084 | 5.084 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 -3209.3869 -3209.3869 26.554646 72.42736 4.9484036 15.108881 15.108881 -296.62125 547.06404 -205.11615 2.2466347 2745.9531 Loop time of 2.061e-06 on 1 procs for 0 steps with 810 atoms 242.6% 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 | | 2.061e-06 | | |100.00 Nlocal: 810.000 ave 810 max 810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5116.00 ave 5116 max 5116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57368.0 ave 57368 max 57368 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114736.0 ave 114736 max 114736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114736 Ave neighs/atom = 141.64938 Neighbor list builds = 0 Dangerous builds = 0 810 -3209.38685403657 eV 2.24663466605038 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06