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 = 4.0501807 4.0501807 4.0501807 Created orthogonal box = (0.0000000 -50.097969 0.0000000) to (23.616409 50.097969 5.7278205) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9460027 6.8761918 5.7278205 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -50.097969 0.0000000) to (23.616409 50.097969 5.7278205) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9460027 6.8761918 5.7278205 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -50.097969 0.0000000) to (23.616409 50.097969 5.7278205) create_atoms CPU = 0.001 seconds 412 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 6 24 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 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_131650261510_005#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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 4.973 | 4.973 | 4.973 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.7886 0 -2881.7886 8915.5032 93 0 -2917.0829 0 -2917.0829 5528.1893 Loop time of 1.21694 on 1 procs for 93 steps with 816 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 = -2881.78863367448 -2917.08059145962 -2917.08286416882 Force two-norm initial, final = 46.786801 0.094757432 Force max component initial, final = 10.782925 0.0069998571 Final line search alpha, max atom move = 1.0000000 0.0069998571 Iterations, force evaluations = 93 181 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1932 | 1.1932 | 1.1932 | 0.0 | 98.05 Neigh | 0.0073181 | 0.0073181 | 0.0073181 | 0.0 | 0.60 Comm | 0.0090987 | 0.0090987 | 0.0090987 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007319 | | | 0.60 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5310.00 ave 5310 max 5310 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: 114504.0 ave 114504 max 114504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114504 Ave neighs/atom = 140.32353 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.970 | 4.970 | 4.970 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -2917.0829 0 -2917.0829 5528.1893 13553.56 104 0 -2917.4529 0 -2917.4529 9.2054258 13651.647 Loop time of 0.304469 on 1 procs for 11 steps with 816 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -2917.08286416883 -2917.45285242888 -2917.45285242888 Force two-norm initial, final = 93.327422 0.75176869 Force max component initial, final = 84.560445 0.64105541 Final line search alpha, max atom move = 1.1901303e-08 7.6293945e-09 Iterations, force evaluations = 11 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28721 | 0.28721 | 0.28721 | 0.0 | 94.33 Neigh | 0.0072379 | 0.0072379 | 0.0072379 | 0.0 | 2.38 Comm | 0.0019915 | 0.0019915 | 0.0019915 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008029 | | | 2.64 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5302.00 ave 5302 max 5302 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: 113896.0 ave 113896 max 113896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113896 Ave neighs/atom = 139.57843 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 5.108 | 5.108 | 5.108 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2917.4529 0 -2917.4529 9.2054258 Loop time of 1.531e-06 on 1 procs for 0 steps with 816 atoms 130.6% 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 | | 1.531e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5302.00 ave 5302 max 5302 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: 113896.0 ave 113896 max 113896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113896 Ave neighs/atom = 139.57843 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 = 8.4039288 ghost atom cutoff = 8.4039288 binsize = 4.2019644, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928756713867 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) = 5.108 | 5.108 | 5.108 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 -2917.4529 -2917.4529 23.57795 101.1979 5.7214688 9.2054258 9.2054258 -13.394473 75.987515 -34.976764 2.735921 660.85007 Loop time of 1.825e-06 on 1 procs for 0 steps with 816 atoms 164.4% 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 | | 1.825e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5302.00 ave 5302 max 5302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56948.0 ave 56948 max 56948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113896.0 ave 113896 max 113896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113896 Ave neighs/atom = 139.57843 Neighbor list builds = 0 Dangerous builds = 0 816 -2917.45207423064 eV 2.7359210125847 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01