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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -71.735333 0.0000000) to (41.416414 71.735333 7.0342281) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3717559 6.4377863 7.0342281 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -71.735333 0.0000000) to (41.416414 71.735333 7.0342281) create_atoms CPU = 0.004 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3717559 6.4377863 7.0342281 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -71.735333 0.0000000) to (41.416414 71.735333 7.0342281) create_atoms CPU = 0.003 seconds 1249 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 30 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2489 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6315.1301 0 -6315.1301 15221.797 104 0 -6690.7096 0 -6690.7096 683.886 Loop time of 4.26878 on 1 procs for 104 steps with 2489 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6315.13012118751 -6690.70360281888 -6690.70963941127 Force two-norm initial, final = 341.57125 0.25331919 Force max component initial, final = 61.346449 0.044979952 Final line search alpha, max atom move = 1.0000000 0.044979952 Iterations, force evaluations = 104 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0691 | 4.0691 | 4.0691 | 0.0 | 95.32 Neigh | 0.1462 | 0.1462 | 0.1462 | 0.0 | 3.42 Comm | 0.029512 | 0.029512 | 0.029512 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02396 | | | 0.56 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14108.0 ave 14108 max 14108 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: 559314.0 ave 559314 max 559314 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559314 Ave neighs/atom = 224.71434 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 104 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 104 0 -6690.7096 0 -6690.7096 683.886 41797.667 106 0 -6690.7187 0 -6690.7187 -3.5710486 41836.096 Loop time of 0.11348 on 1 procs for 2 steps with 2489 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 = -6690.70963941126 -6690.71842330326 -6690.71869669384 Force two-norm initial, final = 31.654460 0.45166993 Force max component initial, final = 23.425725 0.27921330 Final line search alpha, max atom move = 0.00035104978 9.8017768e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11072 | 0.11072 | 0.11072 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005296 | 0.0005296 | 0.0005296 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002232 | | | 1.97 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14075.0 ave 14075 max 14075 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: 559410.0 ave 559410 max 559410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559410 Ave neighs/atom = 224.75291 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 10.35 | 10.35 | 10.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6690.7187 0 -6690.7187 -3.5710486 Loop time of 2.067e-06 on 1 procs for 0 steps with 2489 atoms 193.5% 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 | | 2.067e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14075.0 ave 14075 max 14075 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: 559306.0 ave 559306 max 559306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559306 Ave neighs/atom = 224.71113 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 10.35 | 10.35 | 10.35 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 -6690.7187 -6690.7187 41.423651 143.54541 7.0357998 -3.5710486 -3.5710486 -10.694764 -6.7593679 6.740986 2.5990182 1275.0993 Loop time of 2.407e-06 on 1 procs for 0 steps with 2489 atoms 249.3% 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 | | 2.407e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14075.0 ave 14075 max 14075 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 279653.0 ave 279653 max 279653 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 559306.0 ave 559306 max 559306 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 559306 Ave neighs/atom = 224.71113 Neighbor list builds = 0 Dangerous builds = 0 2489 -6690.71869669384 eV 2.59901822260086 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04