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 = 3.9173716 3.9173716 3.9173716 Created orthogonal box = (0.0000000 -61.195217 0.0000000) to (30.595650 61.195217 3.9173716) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5172484 5.5172484 3.9173716 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -61.195217 0.0000000) to (30.595650 61.195217 3.9173716) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5172484 5.5172484 3.9173716 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -61.195217 0.0000000) to (30.595650 61.195217 3.9173716) create_atoms CPU = 0.002 seconds 490 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 972 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_020840179467_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5513.9112 0 -5513.9112 19318.092 83 0 -5594.2119 0 -5594.2119 -2118.1464 Loop time of 5.68407 on 1 procs for 83 steps with 972 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 = -5513.91116989095 -5594.20709500026 -5594.2119441629 Force two-norm initial, final = 68.759575 0.30947416 Force max component initial, final = 17.718526 0.095614674 Final line search alpha, max atom move = 1.0000000 0.095614674 Iterations, force evaluations = 83 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6335 | 5.6335 | 5.6335 | 0.0 | 99.11 Neigh | 0.012372 | 0.012372 | 0.012372 | 0.0 | 0.22 Comm | 0.019669 | 0.019669 | 0.019669 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01851 | | | 0.33 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5920.00 ave 5920 max 5920 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: 75108.0 ave 75108 max 75108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75108 Ave neighs/atom = 77.271605 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -5594.2119 0 -5594.2119 -2118.1464 14669.048 85 0 -5594.2195 0 -5594.2195 -562.91249 14656.017 Loop time of 0.20479 on 1 procs for 2 steps with 972 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 = -5594.21194416289 -5594.21943881511 -5594.2194596006 Force two-norm initial, final = 24.108287 0.36927639 Force max component initial, final = 18.492386 0.20540021 Final line search alpha, max atom move = 0.0022436794 0.00046085221 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20208 | 0.20208 | 0.20208 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00062133 | 0.00062133 | 0.00062133 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002085 | | | 1.02 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5946.00 ave 5946 max 5946 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: 75384.0 ave 75384 max 75384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75384 Ave neighs/atom = 77.555556 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.733 | 4.733 | 4.733 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5594.2195 0 -5594.2195 -562.91249 Loop time of 6.264e-06 on 1 procs for 0 steps with 972 atoms 191.6% 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 | | 6.264e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5946.00 ave 5946 max 5946 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: 75384.0 ave 75384 max 75384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75384 Ave neighs/atom = 77.555556 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 10 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.733 | 4.733 | 4.733 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 -5594.2195 -5594.2195 30.582107 122.39043 3.9156249 -562.91249 -562.91249 -1.367339 -1709.8142 22.444069 2.4891212 183.122 Loop time of 6.906e-06 on 1 procs for 0 steps with 972 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 972.000 ave 972 max 972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5946.00 ave 5946 max 5946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37692.0 ave 37692 max 37692 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75384.0 ave 75384 max 75384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75384 Ave neighs/atom = 77.555556 Neighbor list builds = 0 Dangerous builds = 0 972 -5594.2194596006 eV 2.4891212153302 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06