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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -46.318021 0.0000000) to (32.751787 46.318021 5.1464468) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0651457 6.2901016 5.1464468 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -46.318021 0.0000000) to (32.751787 46.318021 5.1464468) create_atoms CPU = 0.005 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0651457 6.2901016 5.1464468 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -46.318021 0.0000000) to (32.751787 46.318021 5.1464468) create_atoms CPU = 0.005 seconds 650 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 = 7 20 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 0 atoms, new total = 1298 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_609260676108_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 = 7 20 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) = 6.292 | 6.292 | 6.292 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4088.544 0 -4088.544 53868.281 47 0 -4251.5018 0 -4251.5018 6533.143 Loop time of 4.28369 on 1 procs for 47 steps with 1298 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 = -4088.54402968333 -4251.4985405307 -4251.50182088559 Force two-norm initial, final = 350.60116 0.14951426 Force max component initial, final = 83.994386 0.0077883533 Final line search alpha, max atom move = 1.0000000 0.0077883533 Iterations, force evaluations = 47 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2493 | 4.2493 | 4.2493 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.020261 | 0.020261 | 0.020261 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01413 | | | 0.33 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10518.0 ave 10518 max 10518 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: 414224.0 ave 414224 max 414224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 414224 Ave neighs/atom = 319.12481 Neighbor list builds = 0 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 = 7 20 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.287 | 6.287 | 6.287 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -4251.5018 0 -4251.5018 6533.143 15614.298 53 0 -4251.7644 0 -4251.7644 -6.5008567 15685.114 Loop time of 0.44392 on 1 procs for 6 steps with 1298 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4251.50182088558 -4251.76398672832 -4251.76438056898 Force two-norm initial, final = 126.77614 0.60107790 Force max component initial, final = 114.55257 0.40463639 Final line search alpha, max atom move = 0.00018871391 7.6360516e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43607 | 0.43607 | 0.43607 | 0.0 | 98.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018867 | 0.0018867 | 0.0018867 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005963 | | | 1.34 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9871.00 ave 9871 max 9871 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: 412816.0 ave 412816 max 412816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412816 Ave neighs/atom = 318.04006 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 = 7 20 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) = 6.425 | 6.425 | 6.425 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4251.7644 0 -4251.7644 -6.5008567 Loop time of 6.225e-06 on 1 procs for 0 steps with 1298 atoms 192.8% 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 | | 6.225e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9871.00 ave 9871 max 9871 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: 412584.0 ave 412584 max 412584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412584 Ave neighs/atom = 317.86133 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 = 7 20 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) = 6.425 | 6.425 | 6.425 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 -4251.7644 -4251.7644 32.76127 93.063759 5.1445377 -6.5008567 -6.5008567 36.477289 -14.663078 -41.316782 2.3456927 491.56996 Loop time of 7.026e-06 on 1 procs for 0 steps with 1298 atoms 284.7% 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 | | 7.026e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9871.00 ave 9871 max 9871 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 206292.0 ave 206292 max 206292 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412584.0 ave 412584 max 412584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412584 Ave neighs/atom = 317.86133 Neighbor list builds = 0 Dangerous builds = 0 1298 -4251.76438056898 eV 2.34569266848952 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05