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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -52.805883 0.0000000) to (26.401510 52.805883 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0378779 4.0378779 2.8636458 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -52.805883 0.0000000) to (26.401510 52.805883 2.8636458) create_atoms CPU = 0.002 seconds 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0378779 4.0378779 2.8636458 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -52.805883 0.0000000) to (26.401510 52.805883 2.8636458) create_atoms CPU = 0.001 seconds 341 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 34 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 678 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2853.056 0 -2853.056 19092.808 25 0 -2901.5779 0 -2901.5779 -1730.7968 Loop time of 6.45457 on 1 procs for 25 steps with 678 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 = -2853.05604610228 -2901.57535889798 -2901.57792596757 Force two-norm initial, final = 101.54564 0.15711462 Force max component initial, final = 35.312618 0.025129477 Final line search alpha, max atom move = 1.0000000 0.025129477 Iterations, force evaluations = 25 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4435 | 6.4435 | 6.4435 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0061439 | 0.0061439 | 0.0061439 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004954 | | | 0.08 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5510.00 ave 5510 max 5510 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: 59630.0 ave 59630 max 59630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59630 Ave neighs/atom = 87.949853 Neighbor list builds = 0 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -2901.5779 0 -2901.5779 -1730.7968 7984.7323 29 0 -2901.6139 0 -2901.6139 788.60594 7972.9255 Loop time of 1.15779 on 1 procs for 4 steps with 678 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 = -2901.57792596757 -2901.61378006333 -2901.61393556108 Force two-norm initial, final = 24.558322 0.16111938 Force max component initial, final = 24.506223 0.025605378 Final line search alpha, max atom move = 0.00042404355 1.0857796e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1534 | 1.1534 | 1.1534 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097958 | 0.00097958 | 0.00097958 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00338 | | | 0.29 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5486.00 ave 5486 max 5486 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: 65116.0 ave 65116 max 65116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65116 Ave neighs/atom = 96.041298 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.674 | 4.674 | 4.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2901.6139 0 -2901.6139 788.60594 Loop time of 7.668e-06 on 1 procs for 0 steps with 678 atoms 182.6% 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 | | 7.668e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5500.00 ave 5500 max 5500 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: 67118.0 ave 67118 max 67118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67118 Ave neighs/atom = 98.994100 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 4.674 | 4.674 | 4.674 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 -2901.6139 -2901.6139 26.437514 105.61177 2.8555173 788.60594 788.60594 -0.41486139 2365.3196 0.91306472 2.3229256 133.72143 Loop time of 6.445e-06 on 1 procs for 0 steps with 678 atoms 325.8% 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 | | 6.445e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5500.00 ave 5500 max 5500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33559.0 ave 33559 max 33559 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67118.0 ave 67118 max 67118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67118 Ave neighs/atom = 98.994100 Neighbor list builds = 0 Dangerous builds = 0 678 -2901.61393556108 eV 2.32292555434458 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08