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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -52.791559 0.0000000) to (43.104128 52.791559 8.7381211) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3142075 5.0622043 5.8254141 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -52.791559 0.0000000) to (43.104128 52.791559 8.7381211) create_atoms CPU = 0.002 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3142075 5.0622043 5.8254141 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -52.791559 0.0000000) to (43.104128 52.791559 8.7381211) create_atoms CPU = 0.002 seconds 1755 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 = 16 38 4 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 27 atoms, new total = 3475 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_058735400462_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 = 16 38 4 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) = 5.255 | 5.255 | 5.255 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14158.235 0 -14158.235 22876.272 112 0 -14642.888 0 -14642.888 32983.581 Loop time of 17.8355 on 1 procs for 112 steps with 3475 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14158.2352192134 -14642.8762020878 -14642.8881311753 Force two-norm initial, final = 502.45737 0.67233172 Force max component initial, final = 87.645711 0.23895516 Final line search alpha, max atom move = 0.65445140 0.15638454 Iterations, force evaluations = 112 205 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.722 | 17.722 | 17.722 | 0.0 | 99.36 Neigh | 0.056672 | 0.056672 | 0.056672 | 0.0 | 0.32 Comm | 0.021185 | 0.021185 | 0.021185 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03613 | | | 0.20 Nlocal: 3475.00 ave 3475 max 3475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7687.00 ave 7687 max 7687 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: 199420.0 ave 199420 max 199420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 199420 Ave neighs/atom = 57.387050 Neighbor list builds = 3 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 = 16 38 4 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 : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -14642.888 0 -14642.888 32983.581 39767.786 117 0 -14646.874 0 -14646.874 -18.961486 40156.839 Loop time of 0.65595 on 1 procs for 5 steps with 3475 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 = -14642.8881311753 -14646.8666435148 -14646.8742444218 Force two-norm initial, final = 1419.0913 3.5734440 Force max component initial, final = 863.89251 1.5246846 Final line search alpha, max atom move = 4.2508186e-05 6.4811577e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65187 | 0.65187 | 0.65187 | 0.0 | 99.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048937 | 0.00048937 | 0.00048937 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003589 | | | 0.55 Nlocal: 3475.00 ave 3475 max 3475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7645.00 ave 7645 max 7645 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: 200814.0 ave 200814 max 200814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200814 Ave neighs/atom = 57.788201 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 = 16 38 4 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) = 5.392 | 5.392 | 5.392 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14646.874 0 -14646.874 -18.961486 Loop time of 2.4e-06 on 1 procs for 0 steps with 3475 atoms 166.7% 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 | | 2.4e-06 | | |100.00 Nlocal: 3475.00 ave 3475 max 3475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7620.00 ave 7620 max 7620 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: 195386.0 ave 195386 max 195386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195386 Ave neighs/atom = 56.226187 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 = 16 38 4 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) = 5.392 | 5.392 | 5.392 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 -14646.874 -14646.874 43.278108 105.89095 8.7625887 -18.961486 -18.961486 -47.461843 51.579545 -61.002161 2.2030325 2453.4145 Loop time of 2.596e-06 on 1 procs for 0 steps with 3475 atoms 231.1% 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 | | 2.596e-06 | | |100.00 Nlocal: 3475.00 ave 3475 max 3475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7620.00 ave 7620 max 7620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 97693.0 ave 97693 max 97693 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 195386.0 ave 195386 max 195386 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 195386 Ave neighs/atom = 56.226187 Neighbor list builds = 0 Dangerous builds = 0 3475 -14646.8742444218 eV 2.20303246373096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19