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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -55.955175 0.0000000) to (39.563514 55.955175 5.5400000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2060414 4.9368757 5.5400000 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -55.955175 0.0000000) to (39.563514 55.955175 5.5400000) create_atoms CPU = 0.004 seconds 821 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2060414 4.9368757 5.5400000 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -55.955175 0.0000000) to (39.563514 55.955175 5.5400000) create_atoms CPU = 0.004 seconds 821 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 = 13 35 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 1629 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_070797404269_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 = 13 35 2 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) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9247.7164 0 -9247.7164 20580.493 21 0 -9363.4133 0 -9363.4133 5099.0663 Loop time of 2.00134 on 1 procs for 21 steps with 1629 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 = -9247.71640483141 -9363.40406894874 -9363.41332823828 Force two-norm initial, final = 109.33537 0.37435004 Force max component initial, final = 20.557922 0.091848698 Final line search alpha, max atom move = 1.0000000 0.091848698 Iterations, force evaluations = 21 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9899 | 1.9899 | 1.9899 | 0.0 | 99.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0050187 | 0.0050187 | 0.0050187 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006377 | | | 0.32 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 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: 126922.0 ave 126922 max 126922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126922 Ave neighs/atom = 77.914058 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 = 13 35 2 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 : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.112 | 5.112 | 5.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -9363.4133 0 -9363.4133 5099.0663 24528.72 24 0 -9363.5348 0 -9363.5348 157.38174 24595.599 Loop time of 0.440619 on 1 procs for 3 steps with 1629 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9363.41332823827 -9363.53407671974 -9363.5347744941 Force two-norm initial, final = 119.25632 0.38820007 Force max component initial, final = 100.63172 0.090752218 Final line search alpha, max atom move = 0.00017279612 1.5681631e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43512 | 0.43512 | 0.43512 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010437 | 0.0010437 | 0.0010437 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004452 | | | 1.01 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 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: 126308.0 ave 126308 max 126308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126308 Ave neighs/atom = 77.537139 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 = 13 35 2 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) = 5.250 | 5.250 | 5.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9363.5348 0 -9363.5348 157.38174 Loop time of 8.76e-06 on 1 procs for 0 steps with 1629 atoms 159.8% 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 | | 8.76e-06 | | |100.00 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 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: 126266.0 ave 126266 max 126266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126266 Ave neighs/atom = 77.511357 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 = 13 35 2 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) = 5.250 | 5.250 | 5.250 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 -9363.5348 -9363.5348 39.63824 111.91035 5.5446328 157.38174 157.38174 -1.7873961 475.31183 -1.3792126 2.5427093 683.98971 Loop time of 9.141e-06 on 1 procs for 0 steps with 1629 atoms 240.7% 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 | | 9.141e-06 | | |100.00 Nlocal: 1629.00 ave 1629 max 1629 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6202.00 ave 6202 max 6202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63133.0 ave 63133 max 63133 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126266.0 ave 126266 max 126266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126266 Ave neighs/atom = 77.511357 Neighbor list builds = 0 Dangerous builds = 0 1629 -9363.5347744941 eV 2.54270930296716 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03