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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -49.270501 0.0000000) to (24.635250 49.270501 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6607231 4.6607231 4.0500102 Created 296 atoms using lattice units in orthogonal box = (0.0000000 -49.270501 0.0000000) to (24.635250 49.270501 4.0500102) create_atoms CPU = 0.002 seconds 296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6607231 4.6607231 4.0500102 Created 298 atoms using lattice units in orthogonal box = (0.0000000 -49.270501 0.0000000) to (24.635250 49.270501 4.0500102) create_atoms CPU = 0.001 seconds 298 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 588 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1896.8038 0 -1896.8038 21926.272 51 0 -1986.8475 0 -1986.8475 -1338.1508 Loop time of 0.807592 on 1 procs for 51 steps with 588 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 = -1896.80379643653 -1986.84620642799 -1986.84754742846 Force two-norm initial, final = 198.26277 0.078953243 Force max component initial, final = 67.649548 0.0088505239 Final line search alpha, max atom move = 1.0000000 0.0088505239 Iterations, force evaluations = 51 94 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7794 | 0.7794 | 0.7794 | 0.0 | 96.51 Neigh | 0.0090305 | 0.0090305 | 0.0090305 | 0.0 | 1.12 Comm | 0.010448 | 0.010448 | 0.010448 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008718 | | | 1.08 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4359.00 ave 4359 max 4359 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: 68648.0 ave 68648 max 68648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68648 Ave neighs/atom = 116.74830 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 51 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press Volume 51 0 -1986.8475 0 -1986.8475 -1338.1508 9831.7329 54 0 -1986.8629 0 -1986.8629 -330.21604 9818.7199 Loop time of 0.0493059 on 1 procs for 3 steps with 588 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 = -1986.84754742846 -1986.86162481803 -1986.86294412488 Force two-norm initial, final = 15.250104 3.7704943 Force max component initial, final = 11.381312 2.7603337 Final line search alpha, max atom move = 0.00035470841 0.00097911359 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.046699 | 0.046699 | 0.046699 | 0.0 | 94.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00060086 | 0.00060086 | 0.00060086 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002006 | | | 4.07 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4350.00 ave 4350 max 4350 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: 67248.0 ave 67248 max 67248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67248 Ave neighs/atom = 114.36735 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.642 | 4.642 | 4.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1986.8629 0 -1986.8629 -330.21604 Loop time of 6.665e-06 on 1 procs for 0 steps with 588 atoms 180.0% 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 | | 6.665e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4350.00 ave 4350 max 4350 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: 69656.0 ave 69656 max 69656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69656 Ave neighs/atom = 118.46259 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 7 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 4.642 | 4.642 | 4.642 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 -1986.8629 -1986.8629 24.610884 98.356936 4.0562309 -330.21604 -330.21604 -390.53675 -449.57805 -150.53332 2.6278769 255.56717 Loop time of 7.066e-06 on 1 procs for 0 steps with 588 atoms 283.0% 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 | | 7.066e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4350.00 ave 4350 max 4350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34828.0 ave 34828 max 34828 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69656.0 ave 69656 max 69656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69656 Ave neighs/atom = 118.46259 Neighbor list builds = 0 Dangerous builds = 0 588 -1986.86294412488 eV 2.62787689659464 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01