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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7941953 5.5194308 5.9005197 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7941953 5.5194308 5.9005197 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.674877 0.0000000) to (13.519789 49.674877 8.8507796) create_atoms CPU = 0.001 seconds 507 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1007 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3463.5836 0 -3463.5836 29094.015 44 0 -3551.3386 0 -3551.3386 5351.9085 Loop time of 1.36736 on 1 procs for 44 steps with 1007 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3463.58362806454 -3551.33661662395 -3551.33863190135 Force two-norm initial, final = 153.17908 0.14362040 Force max component initial, final = 36.016287 0.054437715 Final line search alpha, max atom move = 1.0000000 0.054437715 Iterations, force evaluations = 44 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3584 | 1.3584 | 1.3584 | 0.0 | 99.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036954 | 0.0036954 | 0.0036954 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005248 | | | 0.38 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3996.00 ave 3996 max 3996 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: 78326.0 ave 78326 max 78326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78326 Ave neighs/atom = 77.781529 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.543 | 4.543 | 4.543 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3551.3386 0 -3551.3386 5351.9085 11888.259 49 0 -3551.5028 0 -3551.5028 -297.55053 11935.591 Loop time of 0.114582 on 1 procs for 5 steps with 1007 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 = -3551.33863190136 -3551.50081363495 -3551.50278502669 Force two-norm initial, final = 80.046301 4.0562611 Force max component initial, final = 69.484983 2.8122289 Final line search alpha, max atom move = 0.00016227994 0.00045636832 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11294 | 0.11294 | 0.11294 | 0.0 | 98.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026046 | 0.00026046 | 0.00026046 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001383 | | | 1.21 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4153.00 ave 4153 max 4153 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: 77882.0 ave 77882 max 77882 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77882 Ave neighs/atom = 77.340616 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.680 | 4.680 | 4.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3551.5028 0 -3551.5028 -297.55053 Loop time of 1.935e-06 on 1 procs for 0 steps with 1007 atoms 206.7% 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 | | 1.935e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4133.00 ave 4133 max 4133 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: 77824.0 ave 77824 max 77824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77824 Ave neighs/atom = 77.283019 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 ghost atom cutoff = 6 binsize = 3, bins = 5 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.680 | 4.680 | 4.680 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 -3551.5028 -3551.5028 13.53244 99.802787 8.8374133 -297.55053 -297.55053 -359.54932 -156.17226 -376.93001 2.2926274 425.84622 Loop time of 1.652e-06 on 1 procs for 0 steps with 1007 atoms 242.1% 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 | | 1.652e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4133.00 ave 4133 max 4133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38912.0 ave 38912 max 38912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77824.0 ave 77824 max 77824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77824 Ave neighs/atom = 77.283019 Neighbor list builds = 0 Dangerous builds = 0 1007 -3551.50278502669 eV 2.29262742836207 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01