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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -72.803714 0.0000000) to (51.480000 72.803714 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9911111 6.7410846 5.7200000 Created 1294 atoms using lattice units in orthogonal box = (0.0000000 -72.803714 0.0000000) to (51.480000 72.803714 5.7200000) create_atoms CPU = 0.004 seconds 1294 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9911111 6.7410846 5.7200000 Created 1298 atoms using lattice units in orthogonal box = (0.0000000 -72.803714 0.0000000) to (51.480000 72.803714 5.7200000) create_atoms CPU = 0.004 seconds 1298 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 43 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2584 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_131642768288_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.701 | 5.701 | 5.701 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8373.2573 0 -8373.2573 15956.875 81 0 -8665.9425 0 -8665.9425 98.202876 Loop time of 12.9217 on 1 procs for 81 steps with 2584 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8373.25727186957 -8665.93444819909 -8665.94245264755 Force two-norm initial, final = 323.32503 0.21073254 Force max component initial, final = 54.732982 0.019898645 Final line search alpha, max atom move = 1.0000000 0.019898645 Iterations, force evaluations = 81 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.851 | 12.851 | 12.851 | 0.0 | 99.45 Neigh | 0.030674 | 0.030674 | 0.030674 | 0.0 | 0.24 Comm | 0.018643 | 0.018643 | 0.018643 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02172 | | | 0.17 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9287.00 ave 9287 max 9287 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: 200632.0 ave 200632 max 200632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200632 Ave neighs/atom = 77.643963 Neighbor list builds = 2 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.708 | 5.708 | 5.708 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -8665.9425 0 -8665.9425 98.202876 42876.378 83 0 -8665.9669 0 -8665.9669 167.57935 42872.716 Loop time of 0.377561 on 1 procs for 2 steps with 2584 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 = -8665.94245264755 -8665.96417733745 -8665.96694863306 Force two-norm initial, final = 29.248788 9.0364899 Force max component initial, final = 26.215327 8.2415247 Final line search alpha, max atom move = 0.00011728943 0.00096664372 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3755 | 0.3755 | 0.3755 | 0.0 | 99.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034407 | 0.00034407 | 0.00034407 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001719 | | | 0.46 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9897.00 ave 9897 max 9897 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: 200416.0 ave 200416 max 200416 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200416 Ave neighs/atom = 77.560372 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.846 | 5.846 | 5.846 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8665.9669 0 -8665.9669 167.57935 Loop time of 2.261e-06 on 1 procs for 0 steps with 2584 atoms 221.1% 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 | | 2.261e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9897.00 ave 9897 max 9897 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: 200404.0 ave 200404 max 200404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200404 Ave neighs/atom = 77.555728 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.846 | 5.846 | 5.846 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 -8665.9669 -8665.9669 51.448825 145.77922 5.7162329 167.57935 167.57935 107.22547 308.3536 87.158962 2.6944985 1523.0947 Loop time of 2.412e-06 on 1 procs for 0 steps with 2584 atoms 290.2% 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 | | 2.412e-06 | | |100.00 Nlocal: 2584.00 ave 2584 max 2584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9897.00 ave 9897 max 9897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100202.0 ave 100202 max 100202 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200404.0 ave 200404 max 200404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200404 Ave neighs/atom = 77.555728 Neighbor list builds = 0 Dangerous builds = 0 2584 -8665.96694863306 eV 2.69449853278011 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14