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 -37.447178 0.0000000) to (17.652769 37.447178 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7163725 4.5987763 4.0498230 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -37.447178 0.0000000) to (17.652769 37.447178 4.0498230) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7163725 4.5987763 4.0498230 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.447178 0.0000000) to (17.652769 37.447178 4.0498230) create_atoms CPU = 0.000 seconds 229 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 452 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1859.7386 0 -1859.7386 29810.194 44 0 -1927.9126 0 -1927.9126 -5671.8794 Loop time of 0.893809 on 1 procs for 44 steps with 452 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 = -1859.73860237715 -1927.91085403503 -1927.91256232968 Force two-norm initial, final = 162.23997 0.13803020 Force max component initial, final = 56.421907 0.036139646 Final line search alpha, max atom move = 1.0000000 0.036139646 Iterations, force evaluations = 44 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.88665 | 0.88665 | 0.88665 | 0.0 | 99.20 Neigh | 0.0025685 | 0.0025685 | 0.0025685 | 0.0 | 0.29 Comm | 0.0023792 | 0.0023792 | 0.0023792 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002211 | | | 0.25 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3060.00 ave 3060 max 3060 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: 29094.0 ave 29094 max 29094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29094 Ave neighs/atom = 64.367257 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -1927.9126 0 -1927.9126 -5671.8794 5354.2418 48 0 -1927.952 0 -1927.952 -0.80186842 5336.3188 Loop time of 0.0946027 on 1 procs for 4 steps with 452 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 = -1927.91256232968 -1927.95183449322 -1927.95203925861 Force two-norm initial, final = 33.954519 0.15402053 Force max component initial, final = 25.662284 0.037134400 Final line search alpha, max atom move = 0.00073129121 2.7156061e-05 Iterations, force evaluations = 4 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.093618 | 0.093618 | 0.093618 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019081 | 0.00019081 | 0.00019081 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007939 | | | 0.84 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3068.00 ave 3068 max 3068 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: 29112.0 ave 29112 max 29112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29112 Ave neighs/atom = 64.407080 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1927.952 0 -1927.952 -0.80186842 Loop time of 1.749e-06 on 1 procs for 0 steps with 452 atoms 171.5% 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 | | 1.749e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3068.00 ave 3068 max 3068 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: 29128.0 ave 29128 max 29128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29128 Ave neighs/atom = 64.442478 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 ghost atom cutoff = 6 binsize = 3, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.595 | 4.595 | 4.595 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 -1927.952 -1927.952 17.6573 74.719487 4.0446745 -0.80186842 -0.80186842 -3.4379165 -1.9598634 2.9921746 2.2842217 320.16714 Loop time of 1.452e-06 on 1 procs for 0 steps with 452 atoms 137.7% 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 | | 1.452e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3068.00 ave 3068 max 3068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14564.0 ave 14564 max 14564 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29128.0 ave 29128 max 29128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29128 Ave neighs/atom = 64.442478 Neighbor list builds = 0 Dangerous builds = 0 452 -1927.95203925861 eV 2.28422165857015 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01