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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5889210 4.3910710 5.0449565 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449565) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5889210 4.3910710 5.0449565 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.962138 0.0000000) to (20.492710 57.962138 5.0449565) create_atoms CPU = 0.001 seconds 530 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1052 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4284.0522 0 -4284.0522 27918.393 83 0 -4439.2729 0 -4439.2729 33254.98 Loop time of 4.88883 on 1 procs for 83 steps with 1052 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 = -4284.05216730033 -4439.26916905361 -4439.27288074503 Force two-norm initial, final = 301.93949 0.24536683 Force max component initial, final = 98.618393 0.020128319 Final line search alpha, max atom move = 1.0000000 0.020128319 Iterations, force evaluations = 83 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8635 | 4.8635 | 4.8635 | 0.0 | 99.48 Neigh | 0.0048499 | 0.0048499 | 0.0048499 | 0.0 | 0.10 Comm | 0.0096974 | 0.0096974 | 0.0096974 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01074 | | | 0.22 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 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: 59752.0 ave 59752 max 59752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59752 Ave neighs/atom = 56.798479 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -4439.2729 0 -4439.2729 33254.98 11984.812 90 0 -4440.4996 0 -4440.4996 1.557131 12097.168 Loop time of 0.352544 on 1 procs for 7 steps with 1052 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 = -4439.27288074502 -4440.49931941722 -4440.49955418113 Force two-norm initial, final = 436.12494 1.7881813 Force max component initial, final = 303.32785 0.95052906 Final line search alpha, max atom move = 0.00093966442 0.00089317834 Iterations, force evaluations = 7 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34931 | 0.34931 | 0.34931 | 0.0 | 99.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048509 | 0.00048509 | 0.00048509 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002748 | | | 0.78 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4722.00 ave 4722 max 4722 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: 60452.0 ave 60452 max 60452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60452 Ave neighs/atom = 57.463878 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.753 | 4.753 | 4.753 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4440.4996 0 -4440.4996 1.557131 Loop time of 2.508e-06 on 1 procs for 0 steps with 1052 atoms 199.4% 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 | | 2.508e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4715.00 ave 4715 max 4715 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: 59208.0 ave 59208 max 59208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59208 Ave neighs/atom = 56.281369 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.753 | 4.753 | 4.753 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 -4440.4996 -4440.4996 20.524753 116.51392 5.058572 1.557131 1.557131 96.835753 34.065635 -126.22999 2.3558276 546.22179 Loop time of 2.254e-06 on 1 procs for 0 steps with 1052 atoms 221.8% 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 | | 2.254e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4715.00 ave 4715 max 4715 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29604.0 ave 29604 max 29604 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59208.0 ave 59208 max 59208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59208 Ave neighs/atom = 56.281369 Neighbor list builds = 0 Dangerous builds = 0 1052 -4440.49955418113 eV 2.35582762002337 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05