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 = 3.6131481 3.6131481 3.6131481 Created orthogonal box = (0.0000000 -65.436896 0.0000000) to (23.135436 65.436896 5.1097631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2070683 5.5860765 5.1097631 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -65.436896 0.0000000) to (23.135436 65.436896 5.1097631) create_atoms CPU = 0.004 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2070683 5.5860765 5.1097631 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -65.436896 0.0000000) to (23.135436 65.436896 5.1097631) create_atoms CPU = 0.004 seconds 658 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 26 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 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_173787283511_004#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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.771 | 6.771 | 6.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4418.8662 0 -4418.8662 22139.317 114 0 -4574.2838 0 -4574.2838 1403.3864 Loop time of 7.7192 on 1 procs for 114 steps with 1312 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 = -4418.866185037 -4574.2799516556 -4574.28381007002 Force two-norm initial, final = 231.59067 0.23250454 Force max component initial, final = 63.573168 0.025209445 Final line search alpha, max atom move = 1.0000000 0.025209445 Iterations, force evaluations = 114 212 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.5321 | 7.5321 | 7.5321 | 0.0 | 97.58 Neigh | 0.10907 | 0.10907 | 0.10907 | 0.0 | 1.41 Comm | 0.048841 | 0.048841 | 0.048841 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02921 | | | 0.38 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13202.0 ave 13202 max 13202 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: 507232.0 ave 507232 max 507232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 507232 Ave neighs/atom = 386.60976 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.772 | 6.772 | 6.772 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -4574.2838 0 -4574.2838 1403.3864 15471.455 118 0 -4574.4058 0 -4574.4058 -67.01196 15487.529 Loop time of 0.35673 on 1 procs for 4 steps with 1312 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 = -4574.28381007002 -4574.40543516249 -4574.40579628715 Force two-norm initial, final = 72.330125 1.4441292 Force max component initial, final = 54.968800 1.3529520 Final line search alpha, max atom move = 0.00023661368 0.00032012694 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34884 | 0.34884 | 0.34884 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014191 | 0.0014191 | 0.0014191 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006474 | | | 1.81 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13262.0 ave 13262 max 13262 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: 506924.0 ave 506924 max 506924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 506924 Ave neighs/atom = 386.37500 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.909 | 6.909 | 6.909 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4574.4058 0 -4574.4058 -67.01196 Loop time of 3.919e-06 on 1 procs for 0 steps with 1312 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 | | 3.919e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13195.0 ave 13195 max 13195 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: 505992.0 ave 505992 max 505992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505992 Ave neighs/atom = 385.66463 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 = 10.45965 ghost atom cutoff = 10.45965 binsize = 5.229825, bins = 5 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.45965 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) = 6.909 | 6.909 | 6.909 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 -4574.4058 -4574.4058 23.181935 131.07141 5.0971156 -67.01196 -67.01196 -140.24345 -21.682608 -39.10982 2.4094348 463.09416 Loop time of 4.565e-06 on 1 procs for 0 steps with 1312 atoms 241.0% 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 | | 4.565e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13195.0 ave 13195 max 13195 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 252996.0 ave 252996 max 252996 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 505992.0 ave 505992 max 505992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505992 Ave neighs/atom = 385.66463 Neighbor list builds = 0 Dangerous builds = 0 1312 -4574.40579628715 eV 2.40943476199939 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09