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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -40.904847 0.0000000) to (28.921578 40.904847 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3820572 5.5774483 5.0346005 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.904847 0.0000000) to (28.921578 40.904847 5.0346005) create_atoms CPU = 0.001 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3820572 5.5774483 5.0346005 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.904847 0.0000000) to (28.921578 40.904847 5.0346005) create_atoms CPU = 0.001 seconds 532 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1044 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4519.3707 0 -4519.3707 -258.70582 43 0 -4571.7529 0 -4571.7529 -3247.1282 Loop time of 0.699723 on 1 procs for 43 steps with 1044 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 = -4519.37074582781 -4571.74944447431 -4571.75294074905 Force two-norm initial, final = 45.033776 0.29053975 Force max component initial, final = 9.6747751 0.042635687 Final line search alpha, max atom move = 1.0000000 0.042635687 Iterations, force evaluations = 43 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.69226 | 0.69226 | 0.69226 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041067 | 0.0041067 | 0.0041067 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003358 | | | 0.48 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7088.00 ave 7088 max 7088 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: 181400.0 ave 181400 max 181400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181400 Ave neighs/atom = 173.75479 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.033 | 5.033 | 5.033 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -4571.7529 0 -4571.7529 -3247.1282 11912.194 45 0 -4571.778 0 -4571.778 -289.93493 11895.782 Loop time of 0.0363293 on 1 procs for 2 steps with 1044 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 = -4571.75294074905 -4571.77382073638 -4571.7780338333 Force two-norm initial, final = 35.419869 1.2453069 Force max component initial, final = 31.533792 0.89260192 Final line search alpha, max atom move = 0.00016401524 0.00014640032 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035356 | 0.035356 | 0.035356 | 0.0 | 97.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020215 | 0.00020215 | 0.00020215 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007709 | | | 2.12 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7078.00 ave 7078 max 7078 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: 181776.0 ave 181776 max 181776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181776 Ave neighs/atom = 174.11494 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.171 | 5.171 | 5.171 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4571.778 0 -4571.778 -289.93493 Loop time of 7.95e-06 on 1 procs for 0 steps with 1044 atoms 113.2% 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 | | 7.95e-06 | | |100.00 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7078.00 ave 7078 max 7078 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: 181840.0 ave 181840 max 181840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181840 Ave neighs/atom = 174.17625 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.171 | 5.171 | 5.171 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 -4571.778 -4571.778 28.872792 81.809695 5.0361593 -289.93493 -289.93493 -120.01678 -643.60494 -106.18307 2.3462024 763.33513 Loop time of 1.67e-06 on 1 procs for 0 steps with 1044 atoms 179.6% 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 | | 1.67e-06 | | |100.00 Nlocal: 1044.00 ave 1044 max 1044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7078.00 ave 7078 max 7078 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90920.0 ave 90920 max 90920 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181840.0 ave 181840 max 181840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181840 Ave neighs/atom = 174.17625 Neighbor list builds = 0 Dangerous builds = 0 1044 -4571.7780338333 eV 2.34620243741048 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01