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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721388 41.251551 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4115313 6.3457702 7.0055406 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721388 41.251551 7.0055406) create_atoms CPU = 0.004 seconds 628 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4115313 6.3457702 7.0055406 Created 629 atoms using lattice units in orthogonal box = (0.0000000 -41.251551 0.0000000) to (35.721388 41.251551 7.0055406) create_atoms CPU = 0.004 seconds 629 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 25 atoms, new total = 1232 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_618133763375_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4097.3087 0 -4097.3087 2386.2496 67 0 -4120.0858 0 -4120.0858 -4028.9243 Loop time of 12.6803 on 1 procs for 67 steps with 1232 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 = -4097.30869189586 -4120.0821303305 -4120.08581983152 Force two-norm initial, final = 28.295125 0.14928674 Force max component initial, final = 6.4579369 0.034182821 Final line search alpha, max atom move = 1.0000000 0.034182821 Iterations, force evaluations = 67 118 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.616 | 12.616 | 12.616 | 0.0 | 99.49 Neigh | 0.032272 | 0.032272 | 0.032272 | 0.0 | 0.25 Comm | 0.01385 | 0.01385 | 0.01385 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01849 | | | 0.15 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4693.00 ave 4693 max 4693 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: 95134.0 ave 95134 max 95134 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95134 Ave neighs/atom = 77.219156 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4120.0858 0 -4120.0858 -4028.9243 20646.207 70 0 -4120.1981 0 -4120.1981 -580.33971 20554.336 Loop time of 0.498159 on 1 procs for 3 steps with 1232 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4120.08581983152 -4120.19499507332 -4120.1981097056 Force two-norm initial, final = 70.909409 1.5587739 Force max component initial, final = 53.137738 1.2903428 Final line search alpha, max atom move = 0.00010130663 0.00013072029 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49557 | 0.49557 | 0.49557 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052632 | 0.00052632 | 0.00052632 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002067 | | | 0.41 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4708.00 ave 4708 max 4708 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: 95182.0 ave 95182 max 95182 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95182 Ave neighs/atom = 77.258117 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.777 | 4.777 | 4.777 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4120.1981 0 -4120.1981 -580.33971 Loop time of 6.695e-06 on 1 procs for 0 steps with 1232 atoms 164.3% 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 | | 6.695e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4708.00 ave 4708 max 4708 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: 95206.0 ave 95206 max 95206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95206 Ave neighs/atom = 77.277597 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.777 | 4.777 | 4.777 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 -4120.1981 -4120.1981 35.649594 82.503102 6.9884133 -580.33971 -580.33971 100.37794 -1774.5923 -66.804771 2.5230553 1060.721 Loop time of 7.508e-06 on 1 procs for 0 steps with 1232 atoms 253.1% 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 | | 7.508e-06 | | |100.00 Nlocal: 1232.00 ave 1232 max 1232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4708.00 ave 4708 max 4708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47603.0 ave 47603 max 47603 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95206.0 ave 95206 max 95206 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95206 Ave neighs/atom = 77.277597 Neighbor list builds = 0 Dangerous builds = 0 1232 -4120.1981097056 eV 2.52305533357407 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13