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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0610600 5.9342077 4.9780317 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0610600 5.9342077 4.9780317 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.583315 0.0000000) to (26.575417 37.583315 4.9780317) create_atoms CPU = 0.001 seconds 458 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 904 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_266134052596_000#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.407 | 5.407 | 5.407 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3961.8541 0 -3961.8541 -249.39166 125 0 -4004.7484 0 -4004.7484 -5976.9767 Loop time of 2.91053 on 1 procs for 125 steps with 904 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3961.85406676498 -4004.74479252333 -4004.74838107717 Force two-norm initial, final = 19.855725 0.19684997 Force max component initial, final = 4.4842075 0.028643405 Final line search alpha, max atom move = 1.0000000 0.028643405 Iterations, force evaluations = 125 218 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8468 | 2.8468 | 2.8468 | 0.0 | 97.81 Neigh | 0.037653 | 0.037653 | 0.037653 | 0.0 | 1.29 Comm | 0.014925 | 0.014925 | 0.014925 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01119 | | | 0.38 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7825.00 ave 7825 max 7825 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: 223316.0 ave 223316 max 223316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223316 Ave neighs/atom = 247.03097 Neighbor list builds = 3 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 125 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.410 | 5.410 | 5.410 Mbytes Step Temp E_pair E_mol TotEng Press Volume 125 0 -4004.7484 0 -4004.7484 -5976.9767 9944.0393 130 0 -4004.8831 0 -4004.8831 16.185124 9909.3538 Loop time of 0.105552 on 1 procs for 5 steps with 904 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 = -4004.74838107719 -4004.88296442303 -4004.88312436804 Force two-norm initial, final = 77.374690 0.61445146 Force max component initial, final = 71.783932 0.36542010 Final line search alpha, max atom move = 0.00044219549 0.00016158712 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10317 | 0.10317 | 0.10317 | 0.0 | 97.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045858 | 0.00045858 | 0.00045858 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00192 | | | 1.82 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 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: 223644.0 ave 223644 max 223644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223644 Ave neighs/atom = 247.39381 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.548 | 5.548 | 5.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4004.8831 0 -4004.8831 16.185124 Loop time of 1.881e-06 on 1 procs for 0 steps with 904 atoms 159.5% 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 | | 1.881e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 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: 223980.0 ave 223980 max 223980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223980 Ave neighs/atom = 247.76549 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.548 | 5.548 | 5.548 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 -4004.8831 -4004.8831 26.56458 74.885616 4.9813147 16.185124 16.185124 -51.629926 41.064024 59.121272 2.271095 682.02619 Loop time of 1.94e-06 on 1 procs for 0 steps with 904 atoms 309.3% 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 | | 1.94e-06 | | |100.00 Nlocal: 904.000 ave 904 max 904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7847.00 ave 7847 max 7847 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111990.0 ave 111990 max 111990 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223980.0 ave 223980 max 223980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223980 Ave neighs/atom = 247.76549 Neighbor list builds = 0 Dangerous builds = 0 904 -4004.88312436804 eV 2.27109503801546 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03