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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -58.019680 0.0000000) to (29.009840 58.019680 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 340 atoms using lattice units in orthogonal box = (0.0000000 -58.019680 0.0000000) to (29.009840 58.019680 3.1465590) create_atoms CPU = 0.001 seconds 340 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.019680 0.0000000) to (29.009840 58.019680 3.1465590) create_atoms CPU = 0.000 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 681 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_805823015127_000#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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.504 | 4.504 | 4.504 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4568.6178 0 -4568.6178 25842.944 12 0 -5501.7751 0 -5501.7751 21247.53 Loop time of 1.71809 on 1 procs for 12 steps with 681 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 = -4568.6177885773 -5501.76991317228 -5501.77512384644 Force two-norm initial, final = 34.263678 559.59077 Force max component initial, final = 11.706395 272.54855 Final line search alpha, max atom move = 2.3961292e-08 6.5306154e-06 Iterations, force evaluations = 12 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7103 | 1.7103 | 1.7103 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0042875 | 0.0042875 | 0.0042875 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003496 | | | 0.20 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4040.00 ave 4040 max 4040 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: 39418.0 ave 39418 max 39418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39418 Ave neighs/atom = 57.882526 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 12 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 12 0 -5501.7751 0 -5501.7751 21247.53 10592.209 13 0 -5501.7757 0 -5501.7757 21098.606 10592.219 Loop time of 0.176395 on 1 procs for 1 steps with 681 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 = -5501.77512384648 -5501.77512384648 -5501.77566837196 Force two-norm initial, final = 612.10112 251.25706 Force max component initial, final = 272.54855 166.42715 Final line search alpha, max atom move = 4.6286015e-08 7.7032496e-06 Iterations, force evaluations = 1 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17441 | 0.17441 | 0.17441 | 0.0 | 98.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036258 | 0.00036258 | 0.00036258 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001627 | | | 0.92 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4052.00 ave 4052 max 4052 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: 39406.0 ave 39406 max 39406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39406 Ave neighs/atom = 57.864905 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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 -5501.7757 0 -5501.7757 21098.606 Loop time of 2.074e-06 on 1 procs for 0 steps with 681 atoms 192.9% 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 | | 2.074e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4052.00 ave 4052 max 4052 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: 39406.0 ave 39406 max 39406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39406 Ave neighs/atom = 57.864905 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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 -5501.7757 -5501.7757 29.009852 116.0394 3.1465597 21098.606 21098.606 25173.74 22609.864 15512.216 0.0056883018 362.68864 Loop time of 1.719e-06 on 1 procs for 0 steps with 681 atoms 232.7% 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 | | 1.719e-06 | | |100.00 Nlocal: 681.000 ave 681 max 681 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4052.00 ave 4052 max 4052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19703.0 ave 19703 max 19703 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39406.0 ave 39406 max 39406 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39406 Ave neighs/atom = 57.864905 Neighbor list builds = 0 Dangerous builds = 0 681 -5501.77566837196 eV 0.00568830176132 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02