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 = 3.6147299 3.6147299 3.6147299 Created orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7300259 5.6712548 6.2608958 Created 623 atoms using lattice units in orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) create_atoms CPU = 0.006 seconds 623 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7300259 5.6712548 6.2608958 Created 630 atoms using lattice units in orthogonal box = (0.0000000 -36.863156 0.0000000) to (31.924430 36.863156 6.2608958) create_atoms CPU = 0.005 seconds 630 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1247 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_887933271505_002#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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4059.6468 0 -4059.6468 60431.632 19 0 -4401.7097 0 -4401.7097 8032.4232 Loop time of 1.29824 on 1 procs for 19 steps with 1247 atoms 52.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = linesearch alpha is zero Energy initial, next-to-last, final = -4059.64680098043 -4401.70973364304 -4401.70973364304 Force two-norm initial, final = 492.55955 0.80445356 Force max component initial, final = 98.948120 0.12346722 Final line search alpha, max atom move = 1.7129428e-08 2.1149228e-09 Iterations, force evaluations = 19 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.266 | 1.266 | 1.266 | 0.0 | 97.52 Neigh | 0.013016 | 0.013016 | 0.013016 | 0.0 | 1.00 Comm | 0.0095605 | 0.0095605 | 0.0095605 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00968 | | | 0.75 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3894.00 ave 3894 max 3894 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: 67816.0 ave 67816 max 67816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67816 Ave neighs/atom = 54.383320 Neighbor list builds = 1 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -4401.7097 0 -4401.7097 8032.4232 14736.086 26 0 -4402.0399 0 -4402.0399 370.75173 14817.502 Loop time of 0.309966 on 1 procs for 7 steps with 1247 atoms 52.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4401.70973364304 -4402.03923676159 -4402.03987031005 Force two-norm initial, final = 148.29538 35.177705 Force max component initial, final = 131.31439 30.585818 Final line search alpha, max atom move = 5.0714222e-07 1.5511359e-05 Iterations, force evaluations = 7 18 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29972 | 0.29972 | 0.29972 | 0.0 | 96.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019976 | 0.0019976 | 0.0019976 | 0.0 | 0.64 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008248 | | | 2.66 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 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: 67832.0 ave 67832 max 67832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67832 Ave neighs/atom = 54.396151 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.716 | 4.716 | 4.716 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 4421.6801 0 4421.6801 370.75173 Loop time of 7.057e-06 on 1 procs for 0 steps with 1247 atoms 0.0% 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 | | 7.057e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 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: 67728.0 ave 67728 max 67728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67728 Ave neighs/atom = 54.312751 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 12 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.716 | 4.716 | 4.716 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 4421.6801 -4402.0399 31.966537 74.050017 6.2597105 370.75173 370.75173 -369.33667 3321.6824 -1840.0905 2.2326357 912.02005 Loop time of 6.956e-06 on 1 procs for 0 steps with 1247 atoms 172.5% 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 | | 6.956e-06 | | |100.00 Nlocal: 1247.00 ave 1247 max 1247 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3897.00 ave 3897 max 3897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33864.0 ave 33864 max 33864 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67728.0 ave 67728 max 67728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67728 Ave neighs/atom = 54.312751 Neighbor list builds = 0 Dangerous builds = 0 1247 4421.68011366402 eV 2.23263565282838 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01