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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -35.424349 0.0000000) to (11.807162 35.424349 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4726946 3.4726946 2.8636573 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -35.424349 0.0000000) to (11.807162 35.424349 2.8636573) create_atoms CPU = 0.001 seconds 103 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4726946 3.4726946 2.8636573 Created 103 atoms using lattice units in orthogonal box = (0.0000000 -35.424349 0.0000000) to (11.807162 35.424349 2.8636573) create_atoms CPU = 0.001 seconds 103 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 202 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_856956178669_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.386 | 4.386 | 4.386 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -855.2089 0 -855.2089 5102.8711 22 0 -861.72959 0 -861.72959 -8268.6385 Loop time of 0.47355 on 1 procs for 22 steps with 202 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 = -855.208899972203 -861.72894769461 -861.729590202473 Force two-norm initial, final = 16.606610 0.10045983 Force max component initial, final = 7.4273892 0.029087512 Final line search alpha, max atom move = 1.0000000 0.029087512 Iterations, force evaluations = 22 37 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4702 | 0.4702 | 0.4702 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017399 | 0.0017399 | 0.0017399 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001611 | | | 0.34 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1837.00 ave 1837 max 1837 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: 11656.0 ave 11656 max 11656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11656 Ave neighs/atom = 57.702970 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.386 | 4.386 | 4.386 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -861.72959 0 -861.72959 -8268.6385 2395.5124 30 0 -861.79828 0 -861.79828 1376.5707 2381.7935 Loop time of 0.140943 on 1 procs for 8 steps with 202 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -861.729590202473 -861.798265936794 -861.798283861707 Force two-norm initial, final = 23.524847 0.41718373 Force max component initial, final = 21.613630 0.27999926 Final line search alpha, max atom move = 0.021891275 0.0061295406 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13886 | 0.13886 | 0.13886 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047569 | 0.00047569 | 0.00047569 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001608 | | | 1.14 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841.00 ave 1841 max 1841 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: 11694.0 ave 11694 max 11694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11694 Ave neighs/atom = 57.891089 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -861.79828 0 -861.79828 1376.5707 Loop time of 6.064e-06 on 1 procs for 0 steps with 202 atoms 181.4% 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 | | 6.064e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841.00 ave 1841 max 1841 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: 11698.0 ave 11698 max 11698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11698 Ave neighs/atom = 57.910891 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.524 | 4.524 | 4.524 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 -861.79828 -861.79828 11.820657 70.848697 2.8440067 1376.5707 1376.5707 180.11022 3762.5455 187.05645 2.351479 159.76338 Loop time of 6.615e-06 on 1 procs for 0 steps with 202 atoms 226.8% 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 | | 6.615e-06 | | |100.00 Nlocal: 202.000 ave 202 max 202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1841.00 ave 1841 max 1841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 5849.00 ave 5849 max 5849 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 11698.0 ave 11698 max 11698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 11698 Ave neighs/atom = 57.910891 Neighbor list builds = 0 Dangerous builds = 0 202 -861.798283861707 eV 2.35147896264948 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00