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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -44.989258 0.0000000) to (31.809784 44.989258 4.8509466) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9180993 5.7540012 4.8509466 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -44.989258 0.0000000) to (31.809784 44.989258 4.8509466) create_atoms CPU = 0.002 seconds 691 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9180993 5.7540012 4.8509466 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -44.989258 0.0000000) to (31.809784 44.989258 4.8509466) create_atoms CPU = 0.002 seconds 691 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 ghost atom cutoff = 8 binsize = 4, bins = 8 23 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 25 atoms, new total = 1357 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_044341472608_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.520 | 5.520 | 5.520 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5387.2226 0 -5387.2226 -3187.5099 134 0 -5407.7954 0 -5407.7954 -6324.5737 Loop time of 3.42614 on 1 procs for 134 steps with 1357 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 = -5387.22263900994 -5407.79065869188 -5407.79537914655 Force two-norm initial, final = 16.365743 0.29495513 Force max component initial, final = 2.4174407 0.095673869 Final line search alpha, max atom move = 1.0000000 0.095673869 Iterations, force evaluations = 134 259 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.374 | 3.374 | 3.374 | 0.0 | 98.48 Neigh | 0.016321 | 0.016321 | 0.016321 | 0.0 | 0.48 Comm | 0.020157 | 0.020157 | 0.020157 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01569 | | | 0.46 Nlocal: 1357.00 ave 1357 max 1357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9362.00 ave 9362 max 9362 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: 269798.0 ave 269798 max 269798 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269798 Ave neighs/atom = 198.81945 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 ghost atom cutoff = 8 binsize = 4, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.516 | 5.516 | 5.516 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -5407.7954 0 -5407.7954 -6324.5737 13884.365 136 0 -5407.8323 0 -5407.8323 -757.63981 13866.49 Loop time of 0.0666293 on 1 procs for 2 steps with 1357 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 = -5407.79537914652 -5407.83229160666 -5407.8322987723 Force two-norm initial, final = 81.067093 0.35568414 Force max component initial, final = 58.748774 0.17257310 Final line search alpha, max atom move = 0.0021244168 0.00036661719 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065029 | 0.065029 | 0.065029 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031885 | 0.00031885 | 0.00031885 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001281 | | | 1.92 Nlocal: 1357.00 ave 1357 max 1357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8866.00 ave 8866 max 8866 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: 269750.0 ave 269750 max 269750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269750 Ave neighs/atom = 198.78408 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 ghost atom cutoff = 8 binsize = 4, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.654 | 5.654 | 5.654 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5407.8323 0 -5407.8323 -757.63981 Loop time of 1.67e-06 on 1 procs for 0 steps with 1357 atoms 119.8% 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: 1357.00 ave 1357 max 1357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8866.00 ave 8866 max 8866 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: 269824.0 ave 269824 max 269824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269824 Ave neighs/atom = 198.83861 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 ghost atom cutoff = 8 binsize = 4, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.654 | 5.654 | 5.654 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 -5407.8323 -5407.8323 31.790231 89.978516 4.847681 -757.63981 -757.63981 -3.75232 -2289.0933 19.926198 2.2569435 833.74711 Loop time of 2.068e-06 on 1 procs for 0 steps with 1357 atoms 193.4% 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 | | 2.068e-06 | | |100.00 Nlocal: 1357.00 ave 1357 max 1357 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8866.00 ave 8866 max 8866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 134912.0 ave 134912 max 134912 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 269824.0 ave 269824 max 269824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 269824 Ave neighs/atom = 198.83861 Neighbor list builds = 0 Dangerous builds = 0 1357 -5407.8322987723 eV 2.25694346801178 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03