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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504087 Created 1664 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1664 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504087 Created 1688 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.002 seconds 1688 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 26 3 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3352 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_500937681860_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.696 | 5.696 | 5.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13950.325 0 -13950.325 57849.462 85 0 -14836.604 0 -14836.604 8644.864 Loop time of 20.3679 on 1 procs for 85 steps with 3352 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 = -13950.3246467242 -14836.5906537758 -14836.6035381157 Force two-norm initial, final = 1016.0244 0.43631672 Force max component initial, final = 185.18706 0.066815289 Final line search alpha, max atom move = 1.0000000 0.066815289 Iterations, force evaluations = 85 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.215 | 20.215 | 20.215 | 0.0 | 99.25 Neigh | 0.11121 | 0.11121 | 0.11121 | 0.0 | 0.55 Comm | 0.015739 | 0.015739 | 0.015739 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02568 | | | 0.13 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8794.00 ave 8794 max 8794 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: 294370.0 ave 294370 max 294370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294370 Ave neighs/atom = 87.819212 Neighbor list builds = 4 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -14836.604 0 -14836.604 8644.864 36679.408 92 0 -14837.759 0 -14837.759 -3.123598 36848.76 Loop time of 1.41507 on 1 procs for 7 steps with 3352 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 = -14836.6035381157 -14837.7586274777 -14837.7588784911 Force two-norm initial, final = 430.27368 0.86712671 Force max component initial, final = 404.68591 0.10983226 Final line search alpha, max atom move = 0.00017043029 1.8718743e-05 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4092 | 1.4092 | 1.4092 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0007707 | 0.0007707 | 0.0007707 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005125 | | | 0.36 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9011.00 ave 9011 max 9011 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: 294010.0 ave 294010 max 294010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 294010 Ave neighs/atom = 87.711814 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.837 | 5.837 | 5.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14837.759 0 -14837.759 -3.123598 Loop time of 2.051e-06 on 1 procs for 0 steps with 3352 atoms 195.0% 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 | | 2.051e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9090.00 ave 9090 max 9090 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: 293174.0 ave 293174 max 293174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293174 Ave neighs/atom = 87.462411 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.837 | 5.837 | 5.837 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 -14837.759 -14837.759 51.043017 83.821478 8.6125395 -3.123598 -3.123598 -1.0384955 -4.8035724 -3.5287262 2.2472467 1646.6236 Loop time of 2.495e-06 on 1 procs for 0 steps with 3352 atoms 240.5% 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 | | 2.495e-06 | | |100.00 Nlocal: 3352.00 ave 3352 max 3352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9090.00 ave 9090 max 9090 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146587.0 ave 146587 max 146587 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 293174.0 ave 293174 max 293174 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 293174 Ave neighs/atom = 87.462411 Neighbor list builds = 0 Dangerous builds = 0 3352 -14837.7588784911 eV 2.24724668611316 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22