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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -49.367658 0.0000000) to (20.154262 49.367658 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8370229 4.2785304 4.6544275 Created 599 atoms using lattice units in orthogonal box = (0.0000000 -49.367658 0.0000000) to (20.154262 49.367658 6.9816412) create_atoms CPU = 0.001 seconds 599 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8370229 4.2785304 4.6544275 Created 601 atoms using lattice units in orthogonal box = (0.0000000 -49.367658 0.0000000) to (20.154262 49.367658 6.9816412) create_atoms CPU = 0.001 seconds 601 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 33 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1197 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3334.9729 0 -3334.9729 275884.82 109 0 -5115.5377 0 -5115.5377 1195.9462 Loop time of 15.5736 on 1 procs for 109 steps with 1197 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3334.97293781934 -5115.53281620065 -5115.53769942036 Force two-norm initial, final = 4465.8956 0.22139375 Force max component initial, final = 1301.7193 0.060110671 Final line search alpha, max atom move = 0.93355083 0.056116367 Iterations, force evaluations = 109 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.531 | 15.531 | 15.531 | 0.0 | 99.73 Neigh | 0.015583 | 0.015583 | 0.015583 | 0.0 | 0.10 Comm | 0.011855 | 0.011855 | 0.011855 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01523 | | | 0.10 Nlocal: 1197.00 ave 1197 max 1197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4613.00 ave 4613 max 4613 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: 78280.0 ave 78280 max 78280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78280 Ave neighs/atom = 65.396825 Neighbor list builds = 2 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.631 | 4.631 | 4.631 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -5115.5377 0 -5115.5377 1195.9462 13893.029 112 0 -5115.5629 0 -5115.5629 -0.26139641 13903.07 Loop time of 0.480351 on 1 procs for 3 steps with 1197 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 = -5115.53769942036 -5115.56201777794 -5115.56289322648 Force two-norm initial, final = 31.244157 0.30103230 Force max component initial, final = 30.631862 0.15645965 Final line search alpha, max atom move = 0.00012338489 1.9304757e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47867 | 0.47867 | 0.47867 | 0.0 | 99.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024368 | 0.00024368 | 0.00024368 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001434 | | | 0.30 Nlocal: 1197.00 ave 1197 max 1197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4611.00 ave 4611 max 4611 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: 78186.0 ave 78186 max 78186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78186 Ave neighs/atom = 65.318296 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.769 | 4.769 | 4.769 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5115.5629 0 -5115.5629 -0.26139641 Loop time of 2.122e-06 on 1 procs for 0 steps with 1197 atoms 188.5% 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 | | 2.122e-06 | | |100.00 Nlocal: 1197.00 ave 1197 max 1197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4604.00 ave 4604 max 4604 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: 78166.0 ave 78166 max 78166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78166 Ave neighs/atom = 65.301587 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 7 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.769 | 4.769 | 4.769 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 -5115.5629 -5115.5629 20.15202 98.889998 6.9765346 -0.26139641 -0.26139641 18.028255 -8.0590542 -10.75339 2.2436389 725.50974 Loop time of 2.486e-06 on 1 procs for 0 steps with 1197 atoms 201.1% 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 | | 2.486e-06 | | |100.00 Nlocal: 1197.00 ave 1197 max 1197 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4604.00 ave 4604 max 4604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39083.0 ave 39083 max 39083 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78166.0 ave 78166 max 78166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78166 Ave neighs/atom = 65.301587 Neighbor list builds = 0 Dangerous builds = 0 1197 -5115.56289322648 eV 2.24363890185398 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16