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 = 2.8675702 2.8675702 2.8675702 Created orthogonal box = (0.0000000 -41.755319 0.0000000) to (20.876226 41.755319 2.8675702) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5450195 3.5450195 2.8675702 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.755319 0.0000000) to (20.876226 41.755319 2.8675702) create_atoms CPU = 0.000 seconds 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5450195 3.5450195 2.8675702 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.755319 0.0000000) to (20.876226 41.755319 2.8675702) create_atoms CPU = 0.000 seconds 213 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 420 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1769.99 0 -1769.99 8857.1054 54 0 -1789.7472 0 -1789.7472 -8237.1068 Loop time of 4.64256 on 1 procs for 54 steps with 420 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 = -1769.98997675296 -1789.74586746834 -1789.7472179633 Force two-norm initial, final = 65.590287 0.10315959 Force max component initial, final = 28.787646 0.030703766 Final line search alpha, max atom move = 1.0000000 0.030703766 Iterations, force evaluations = 54 99 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6323 | 4.6323 | 4.6323 | 0.0 | 99.78 Neigh | 0.0032344 | 0.0032344 | 0.0032344 | 0.0 | 0.07 Comm | 0.0043185 | 0.0043185 | 0.0043185 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002752 | | | 0.06 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4488.00 ave 4488 max 4488 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: 48680.0 ave 48680 max 48680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48680 Ave neighs/atom = 115.90476 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.470 | 4.470 | 4.470 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1789.7472 0 -1789.7472 -8237.1068 4999.2845 58 0 -1789.8327 0 -1789.8327 723.62429 4972.1194 Loop time of 0.350368 on 1 procs for 4 steps with 420 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 = -1789.7472179633 -1789.83255635094 -1789.83272367885 Force two-norm initial, final = 44.249348 0.14312229 Force max component initial, final = 31.429221 0.047672105 Final line search alpha, max atom move = 0.0013885124 6.6193309e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34899 | 0.34899 | 0.34899 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027143 | 0.00027143 | 0.00027143 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001105 | | | 0.32 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4488.00 ave 4488 max 4488 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: 47976.0 ave 47976 max 47976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47976 Ave neighs/atom = 114.22857 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1789.8327 0 -1789.8327 723.62429 Loop time of 2.189e-06 on 1 procs for 0 steps with 420 atoms 182.7% 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 | | 2.189e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4488.00 ave 4488 max 4488 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: 48616.0 ave 48616 max 48616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48616 Ave neighs/atom = 115.75238 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 ghost atom cutoff = 7 binsize = 3.5, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.608 | 4.608 | 4.608 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 -1789.8327 -1789.8327 20.82598 83.510639 2.8588692 723.62429 723.62429 -6.8815447 2175.0779 2.6765161 2.2996601 207.02824 Loop time of 1.671e-06 on 1 procs for 0 steps with 420 atoms 179.5% 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 | | 1.671e-06 | | |100.00 Nlocal: 420.000 ave 420 max 420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4488.00 ave 4488 max 4488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24308.0 ave 24308 max 24308 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48616.0 ave 48616 max 48616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48616 Ave neighs/atom = 115.75238 Neighbor list builds = 0 Dangerous builds = 0 420 -1789.83272367885 eV 2.29966012532064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05