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 = 2.8510002 2.8510002 2.8510002 Created orthogonal box = (0.0000000 -41.511189 0.0000000) to (20.755594 41.511189 2.8510002) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5245349 3.5245349 2.8510002 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -41.511189 0.0000000) to (20.755594 41.511189 2.8510002) create_atoms CPU = 0.001 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5245349 3.5245349 2.8510002 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.511189 0.0000000) to (20.755594 41.511189 2.8510002) create_atoms CPU = 0.001 seconds 213 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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_492310898779_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 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1741.5929 0 -1741.5929 65150.012 46 0 -1814.5818 0 -1814.5818 11460.901 Loop time of 2.75056 on 1 procs for 46 steps with 425 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1741.59290187626 -1814.58026376708 -1814.58184445631 Force two-norm initial, final = 274.61965 0.12002941 Force max component initial, final = 131.70179 0.038313301 Final line search alpha, max atom move = 1.0000000 0.038313301 Iterations, force evaluations = 46 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7404 | 2.7404 | 2.7404 | 0.0 | 99.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0054733 | 0.0054733 | 0.0054733 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004695 | | | 0.17 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3435.00 ave 3435 max 3435 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: 27686.0 ave 27686 max 27686 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27686 Ave neighs/atom = 65.143529 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -1814.5818 0 -1814.5818 11460.901 4912.783 60 0 -1815.0468 0 -1815.0468 0.46091045 4946.0656 Loop time of 0.440682 on 1 procs for 14 steps with 425 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 = -1814.58184445631 -1815.04635067972 -1815.04678280666 Force two-norm initial, final = 78.501557 0.40357220 Force max component initial, final = 74.779948 0.093617743 Final line search alpha, max atom move = 0.00081824861 7.6602588e-05 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43051 | 0.43051 | 0.43051 | 0.0 | 97.69 Neigh | 0.0047741 | 0.0047741 | 0.0047741 | 0.0 | 1.08 Comm | 0.0010879 | 0.0010879 | 0.0010879 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004307 | | | 0.98 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3395.00 ave 3395 max 3395 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: 27282.0 ave 27282 max 27282 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27282 Ave neighs/atom = 64.192941 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 7 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1815.0468 0 -1815.0468 0.46091045 Loop time of 3.465e-06 on 1 procs for 0 steps with 425 atoms 173.2% 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 | | 3.465e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3395.00 ave 3395 max 3395 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: 27278.0 ave 27278 max 27278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27278 Ave neighs/atom = 64.183529 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 ghost atom cutoff = 6 binsize = 3, bins = 7 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.594 | 4.594 | 4.594 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 -1815.0468 -1815.0468 20.762912 84.121766 2.8318043 0.46091045 0.46091045 6.442847 -27.456642 22.396526 2.2940148 239.88703 Loop time of 4.561e-06 on 1 procs for 0 steps with 425 atoms 175.4% 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 | | 4.561e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3395.00 ave 3395 max 3395 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13639.0 ave 13639 max 13639 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27278.0 ave 27278 max 27278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27278 Ave neighs/atom = 64.183529 Neighbor list builds = 0 Dangerous builds = 0 425 -1815.04678280666 eV 2.29401477799211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03