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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -52.586368 0.0000000) to (26.293184 52.586368 3.4524642) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5333076 4.5333076 3.4524642 Created 463 atoms using lattice units in orthogonal box = (0.0000000 -52.586368 0.0000000) to (26.293184 52.586368 3.4524642) create_atoms CPU = 0.002 seconds 463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5333076 4.5333076 3.4524642 Created 465 atoms using lattice units in orthogonal box = (0.0000000 -52.586368 0.0000000) to (26.293184 52.586368 3.4524642) create_atoms CPU = 0.002 seconds 465 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 928 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3973.9072 0 -3973.9072 60896.614 93 0 -4164.2183 0 -4164.2183 21711.866 Loop time of 3.98591 on 1 procs for 93 steps with 928 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3973.90717459413 -4164.21472187014 -4164.21832537635 Force two-norm initial, final = 296.93326 0.21414865 Force max component initial, final = 66.839478 0.054224212 Final line search alpha, max atom move = 1.0000000 0.054224212 Iterations, force evaluations = 93 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8772 | 3.8772 | 3.8772 | 0.0 | 97.27 Neigh | 0.047449 | 0.047449 | 0.047449 | 0.0 | 1.19 Comm | 0.037055 | 0.037055 | 0.037055 | 0.0 | 0.93 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0242 | | | 0.61 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8485.00 ave 8485 max 8485 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: 184944.0 ave 184944 max 184944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184944 Ave neighs/atom = 199.29310 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -4164.2183 0 -4164.2183 21711.866 9547.1893 102 0 -4165.0421 0 -4165.0421 -82.98031 9598.344 Loop time of 0.282745 on 1 procs for 9 steps with 928 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 = -4164.21832537635 -4165.04204275481 -4165.04206443671 Force two-norm initial, final = 259.24133 1.0765241 Force max component initial, final = 234.87919 0.74299390 Final line search alpha, max atom move = 0.0010606964 0.00078809098 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27229 | 0.27229 | 0.27229 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022988 | 0.0022988 | 0.0022988 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008155 | | | 2.88 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8475.00 ave 8475 max 8475 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: 184918.0 ave 184918 max 184918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184918 Ave neighs/atom = 199.26509 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.167 | 5.167 | 5.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4165.0421 0 -4165.0421 -82.98031 Loop time of 6.716e-06 on 1 procs for 0 steps with 928 atoms 193.6% 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 | | 6.716e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8475.00 ave 8475 max 8475 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: 184716.0 ave 184716 max 184716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184716 Ave neighs/atom = 199.04741 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 7 27 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.167 | 5.167 | 5.167 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 -4165.0421 -4165.0421 26.272767 106.0063 3.4463456 -82.98031 -82.98031 -123.92586 -83.218457 -41.796618 2.1689069 361.82429 Loop time of 6.635e-06 on 1 procs for 0 steps with 928 atoms 316.5% 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 | | 6.635e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8475.00 ave 8475 max 8475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92358.0 ave 92358 max 92358 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184716.0 ave 184716 max 184716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184716 Ave neighs/atom = 199.04741 Neighbor list builds = 0 Dangerous builds = 0 928 -4165.04206443901 eV 2.168906919883 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05