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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -41.728833 0.0000000) to (20.864417 41.728833 2.8659480) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5430141 3.5430141 2.8659480 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -41.728833 0.0000000) to (20.864417 41.728833 2.8659480) create_atoms CPU = 0.001 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5430141 3.5430141 2.8659480 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.728833 0.0000000) to (20.864417 41.728833 2.8659480) create_atoms CPU = 0.001 seconds 213 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 23 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_650279905230_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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1213.7501 0 -1213.7501 272955.2 65 0 -1813.6622 0 -1813.6622 14050.292 Loop time of 1.03873 on 1 procs for 65 steps with 425 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 = -1213.75006764705 -1813.66052240157 -1813.66221465767 Force two-norm initial, final = 1752.9548 0.13904393 Force max component initial, final = 654.53577 0.041842608 Final line search alpha, max atom move = 1.0000000 0.041842608 Iterations, force evaluations = 65 119 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0045 | 1.0045 | 1.0045 | 0.0 | 96.71 Neigh | 0.0088879 | 0.0088879 | 0.0088879 | 0.0 | 0.86 Comm | 0.015168 | 0.015168 | 0.015168 | 0.0 | 1.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01013 | | | 0.98 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4942.00 ave 4942 max 4942 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: 70062.0 ave 70062 max 70062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70062 Ave neighs/atom = 164.85176 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 23 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -1813.6622 0 -1813.6622 14050.292 4990.4624 78 0 -1814.0645 0 -1814.0645 -131.94438 5033.5437 Loop time of 0.144669 on 1 procs for 13 steps with 425 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 = -1813.66221465767 -1814.06446219552 -1814.06454084218 Force two-norm initial, final = 85.637476 0.82555869 Force max component initial, final = 76.286071 0.45753381 Final line search alpha, max atom move = 0.0017951283 0.00082133189 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12837 | 0.12837 | 0.12837 | 0.0 | 88.73 Neigh | 0.0085744 | 0.0085744 | 0.0085744 | 0.0 | 5.93 Comm | 0.0019963 | 0.0019963 | 0.0019963 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005726 | | | 3.96 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4753.00 ave 4753 max 4753 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: 70032.0 ave 70032 max 70032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70032 Ave neighs/atom = 164.78118 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1814.0645 0 -1814.0645 -131.94438 Loop time of 1.0113e-05 on 1 procs for 0 steps with 425 atoms 395.5% 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 | | 1.011e-05 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4753.00 ave 4753 max 4753 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: 70034.0 ave 70034 max 70034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70034 Ave neighs/atom = 164.78588 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 4.614 | 4.614 | 4.614 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 -1814.0645 -1814.0645 20.852362 84.440878 2.858682 -131.94438 -131.94438 -145.54883 -137.40518 -112.87914 2.3621956 199.16454 Loop time of 6.776e-06 on 1 procs for 0 steps with 425 atoms 236.1% 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 | | 6.776e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4753.00 ave 4753 max 4753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35017.0 ave 35017 max 35017 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70034.0 ave 70034 max 70034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70034 Ave neighs/atom = 164.78588 Neighbor list builds = 0 Dangerous builds = 0 425 -1814.06443951428 eV 2.36219556583618 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01