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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -41.801487 0.0000000) to (29.558115 41.801487 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7351567 6.2390280 5.1068645 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.801487 0.0000000) to (29.558115 41.801487 5.1068645) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7351567 6.2390280 5.1068645 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.801487 0.0000000) to (29.558115 41.801487 5.1068645) create_atoms CPU = 0.001 seconds 538 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1066 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_115454747503_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4117.1145 0 -4117.1145 63367.259 363 0 -4536.6456 0 -4536.6456 -4100.0216 Loop time of 52.2418 on 1 procs for 363 steps with 1066 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 = -4117.11445976774 -4536.64261786116 -4536.64564015598 Force two-norm initial, final = 629.98093 0.18764170 Force max component initial, final = 167.33542 0.030959883 Final line search alpha, max atom move = 1.0000000 0.030959883 Iterations, force evaluations = 363 677 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 52.065 | 52.065 | 52.065 | 0.0 | 99.66 Neigh | 0.093811 | 0.093811 | 0.093811 | 0.0 | 0.18 Comm | 0.043545 | 0.043545 | 0.043545 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0392 | | | 0.08 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5220.00 ave 5220 max 5220 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: 109426.0 ave 109426 max 109426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 109426 Ave neighs/atom = 102.65103 Neighbor list builds = 13 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 363 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.995 | 4.995 | 4.995 Mbytes Step Temp E_pair E_mol TotEng Press Volume 363 0 -4536.6456 0 -4536.6456 -4100.0216 12619.81 390 0 -4545.1704 0 -4545.1704 -19.934636 12569.803 Loop time of 2.40545 on 1 procs for 27 steps with 1066 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 = -4536.64564015598 -4545.16960850972 -4545.17044069014 Force two-norm initial, final = 526.07032 1.4537353 Force max component initial, final = 451.07324 0.67359191 Final line search alpha, max atom move = 0.00025202513 0.00016976209 Iterations, force evaluations = 27 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3896 | 2.3896 | 2.3896 | 0.0 | 99.34 Neigh | 0.0072251 | 0.0072251 | 0.0072251 | 0.0 | 0.30 Comm | 0.0015192 | 0.0015192 | 0.0015192 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007091 | | | 0.29 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5303.00 ave 5303 max 5303 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: 111398.0 ave 111398 max 111398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111398 Ave neighs/atom = 104.50094 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.134 | 5.134 | 5.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4545.1704 0 -4545.1704 -19.934636 Loop time of 1.882e-06 on 1 procs for 0 steps with 1066 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5321.00 ave 5321 max 5321 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: 111538.0 ave 111538 max 111538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111538 Ave neighs/atom = 104.63227 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.134 | 5.134 | 5.134 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 -4545.1704 -4545.1704 29.749032 84.962216 4.9731299 -19.934636 -19.934636 -86.412158 -21.383999 47.992248 2.35734 2227.8325 Loop time of 1.898e-06 on 1 procs for 0 steps with 1066 atoms 210.7% 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 | | 1.898e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5321.00 ave 5321 max 5321 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55769.0 ave 55769 max 55769 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111538.0 ave 111538 max 111538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111538 Ave neighs/atom = 104.63227 Neighbor list builds = 0 Dangerous builds = 0 1066 -4545.17044069014 eV 2.35733999526687 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:55