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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -52.960615 0.0000000) to (24.965873 52.960615 5.7275641) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2559733 6.5039352 5.7275641 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -52.960615 0.0000000) to (24.965873 52.960615 5.7275641) create_atoms CPU = 0.001 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2559733 6.5039352 5.7275641 Created 463 atoms using lattice units in orthogonal box = (0.0000000 -52.960615 0.0000000) to (24.965873 52.960615 5.7275641) create_atoms CPU = 0.001 seconds 463 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 912 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_117656786760_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.011 | 5.011 | 5.011 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3041.1996 0 -3041.1996 3896.6731 40 0 -3057.0083 0 -3057.0083 4934.7151 Loop time of 0.642562 on 1 procs for 40 steps with 912 atoms 97.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3041.19964817094 -3057.00614484877 -3057.00825254435 Force two-norm initial, final = 16.256674 0.096462926 Force max component initial, final = 3.1415638 0.0076815116 Final line search alpha, max atom move = 1.0000000 0.0076815116 Iterations, force evaluations = 40 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63515 | 0.63515 | 0.63515 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0040799 | 0.0040799 | 0.0040799 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003333 | | | 0.52 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6823.00 ave 6823 max 6823 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: 159840.0 ave 159840 max 159840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159840 Ave neighs/atom = 175.26316 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.012 | 5.012 | 5.012 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -3057.0083 0 -3057.0083 4934.7151 15146.062 50 0 -3057.3793 0 -3057.3793 43.166571 15237.732 Loop time of 0.111709 on 1 procs for 10 steps with 912 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 = -3057.00825254434 -3057.37900641896 -3057.37928837958 Force two-norm initial, final = 96.529045 0.74563416 Force max component initial, final = 89.667063 0.45795710 Final line search alpha, max atom move = 0.00079223761 0.00036281084 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.098762 | 0.098762 | 0.098762 | 0.0 | 88.41 Neigh | 0.0095512 | 0.0095512 | 0.0095512 | 0.0 | 8.55 Comm | 0.00075677 | 0.00075677 | 0.00075677 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002638 | | | 2.36 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 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: 158272.0 ave 158272 max 158272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158272 Ave neighs/atom = 173.54386 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.150 | 5.150 | 5.150 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3057.3793 0 -3057.3793 43.166571 Loop time of 1.677e-06 on 1 procs for 0 steps with 912 atoms 178.9% 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 | | 1.677e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 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: 158272.0 ave 158272 max 158272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158272 Ave neighs/atom = 173.54386 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 5.150 | 5.150 | 5.150 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 -3057.3793 -3057.3793 24.907774 106.89692 5.7229537 43.166571 43.166571 34.673367 46.713052 48.113293 2.6128526 677.58632 Loop time of 8.554e-06 on 1 procs for 0 steps with 912 atoms 128.6% 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 | | 8.554e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6760.00 ave 6760 max 6760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79136.0 ave 79136 max 79136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 158272.0 ave 158272 max 158272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158272 Ave neighs/atom = 173.54386 Neighbor list builds = 0 Dangerous builds = 0 912 -3001.53413746144 eV 2.61285260490357 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01