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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -38.161628 0.0000000) to (46.738258 38.161628 8.9126361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9485056 5.5507822 5.9417574 Created 1320 atoms using lattice units in orthogonal box = (0.0000000 -38.161628 0.0000000) to (46.738258 38.161628 8.9126361) create_atoms CPU = 0.002 seconds 1320 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9485056 5.5507822 5.9417574 Created 1326 atoms using lattice units in orthogonal box = (0.0000000 -38.161628 0.0000000) to (46.738258 38.161628 8.9126361) create_atoms CPU = 0.002 seconds 1326 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2628 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.145 | 8.145 | 8.145 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6731.3431 0 -6731.3431 175403.37 68 0 -8907.4878 0 -8907.4878 -2026.1759 Loop time of 4.89431 on 1 procs for 68 steps with 2628 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6731.34311640047 -8907.47966911048 -8907.48783426042 Force two-norm initial, final = 2828.4755 0.24199073 Force max component initial, final = 375.62947 0.012072225 Final line search alpha, max atom move = 1.0000000 0.012072225 Iterations, force evaluations = 68 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.714 | 4.714 | 4.714 | 0.0 | 96.32 Neigh | 0.14211 | 0.14211 | 0.14211 | 0.0 | 2.90 Comm | 0.019822 | 0.019822 | 0.019822 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01841 | | | 0.38 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12049.0 ave 12049 max 12049 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: 833316.0 ave 833316 max 833316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 833316 Ave neighs/atom = 317.09132 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 8.145 | 8.145 | 8.145 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -8907.4878 0 -8907.4878 -2026.1759 31793.299 71 0 -8907.5739 0 -8907.5739 -162.68443 31751.982 Loop time of 0.214872 on 1 procs for 3 steps with 2628 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8907.4878342604 -8907.57280893053 -8907.5739332819 Force two-norm initial, final = 87.076511 6.2708564 Force max component initial, final = 63.893829 4.6910472 Final line search alpha, max atom move = 0.00011347003 0.00053229329 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21159 | 0.21159 | 0.21159 | 0.0 | 98.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005296 | 0.0005296 | 0.0005296 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002751 | | | 1.28 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12056.0 ave 12056 max 12056 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: 833592.0 ave 833592 max 833592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 833592 Ave neighs/atom = 317.19635 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.283 | 8.283 | 8.283 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8907.5739 0 -8907.5739 -162.68443 Loop time of 2.217e-06 on 1 procs for 0 steps with 2628 atoms 135.3% 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 | | 2.217e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12063.0 ave 12063 max 12063 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: 833628.0 ave 833628 max 833628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 833628 Ave neighs/atom = 317.21005 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 8.283 | 8.283 | 8.283 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 -8907.5739 -8907.5739 46.675666 76.421196 8.9015674 -162.68443 -162.68443 -203.65538 -47.985843 -236.41206 2.2953545 1396.7504 Loop time of 4.931e-06 on 1 procs for 0 steps with 2628 atoms 283.9% 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 | | 4.931e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12063.0 ave 12063 max 12063 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 416814.0 ave 416814 max 416814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 833628.0 ave 833628 max 833628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 833628 Ave neighs/atom = 317.21005 Neighbor list builds = 0 Dangerous builds = 0 2628 -8907.5739332819 eV 2.29535445537649 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06