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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -43.617753 0.0000000) to (21.808877 43.617753 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7601512 3.7601512 2.8636458 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -43.617753 0.0000000) to (21.808877 43.617753 2.8636458) create_atoms CPU = 0.001 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7601512 3.7601512 2.8636458 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.617753 0.0000000) to (21.808877 43.617753 2.8636458) create_atoms CPU = 0.001 seconds 234 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 27 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 466 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1921.0423 0 -1921.0423 51086.37 32 0 -1988.9405 0 -1988.9405 15588.534 Loop time of 6.05315 on 1 procs for 32 steps with 466 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 = -1921.04227780342 -1988.9391415864 -1988.94053242628 Force two-norm initial, final = 109.50503 0.11859987 Force max component initial, final = 32.189279 0.022010127 Final line search alpha, max atom move = 1.0000000 0.022010127 Iterations, force evaluations = 32 56 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0421 | 6.0421 | 6.0421 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0063034 | 0.0063034 | 0.0063034 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004712 | | | 0.08 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4634.00 ave 4634 max 4634 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: 51896.0 ave 51896 max 51896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51896 Ave neighs/atom = 111.36481 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.476 | 4.476 | 4.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -1988.9405 0 -1988.9405 15588.534 5448.1102 47 0 -1989.6387 0 -1989.6387 3.5344679 5496.0037 Loop time of 1.79678 on 1 procs for 15 steps with 466 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 = -1988.94053242628 -1989.63734269715 -1989.63868127791 Force two-norm initial, final = 113.19178 0.43902260 Force max component initial, final = 106.59322 0.11749086 Final line search alpha, max atom move = 0.00040892664 4.8045144e-05 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7821 | 1.7821 | 1.7821 | 0.0 | 99.18 Neigh | 0.0070867 | 0.0070867 | 0.0070867 | 0.0 | 0.39 Comm | 0.0019532 | 0.0019532 | 0.0019532 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005667 | | | 0.32 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4598.00 ave 4598 max 4598 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: 50944.0 ave 50944 max 50944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50944 Ave neighs/atom = 109.32189 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1989.6387 0 -1989.6387 3.5344679 Loop time of 6.485e-06 on 1 procs for 0 steps with 466 atoms 185.0% 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 | | 6.485e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4598.00 ave 4598 max 4598 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: 50920.0 ave 50920 max 50920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50920 Ave neighs/atom = 109.27039 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.614 | 4.614 | 4.614 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 -1989.6387 -1989.6387 21.839984 88.462991 2.8446778 3.5344679 3.5344679 5.3560086 -11.32937 16.576766 2.2994598 293.68242 Loop time of 6.546e-06 on 1 procs for 0 steps with 466 atoms 290.3% 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 | | 6.546e-06 | | |100.00 Nlocal: 466.000 ave 466 max 466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4598.00 ave 4598 max 4598 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25460.0 ave 25460 max 25460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50920.0 ave 50920 max 50920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50920 Ave neighs/atom = 109.27039 Neighbor list builds = 0 Dangerous builds = 0 466 -1989.63868127791 eV 2.29945982835373 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09