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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -42.348635 0.0000000) to (29.945007 42.348635 5.1737092) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8102252 6.3206918 5.1737092 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -42.348635 0.0000000) to (29.945007 42.348635 5.1737092) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8102252 6.3206918 5.1737092 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -42.348635 0.0000000) to (29.945007 42.348635 5.1737092) create_atoms CPU = 0.001 seconds 538 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1066 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.019 | 5.019 | 5.019 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3725.6576 0 -3725.6576 106379.98 861 0 -4339.5008 0 -4339.5008 -77448.409 Loop time of 23.4028 on 1 procs for 861 steps with 1066 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3725.65763271273 -4339.49668708645 -4339.5007643163 Force two-norm initial, final = 1210.8547 0.20549149 Force max component initial, final = 308.52229 0.028119970 Final line search alpha, max atom move = 1.0000000 0.028119970 Iterations, force evaluations = 861 1638 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.71 | 22.71 | 22.71 | 0.0 | 97.04 Neigh | 0.3678 | 0.3678 | 0.3678 | 0.0 | 1.57 Comm | 0.17786 | 0.17786 | 0.17786 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1474 | | | 0.63 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6445.00 ave 6445 max 6445 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: 163592.0 ave 163592 max 163592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163592 Ave neighs/atom = 153.46341 Neighbor list builds = 20 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 861 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.019 | 5.019 | 5.019 Mbytes Step Temp E_pair E_mol TotEng Press Volume 861 0 -4339.5008 0 -4339.5008 -77448.409 13121.873 908 0 -4368.2013 0 -4368.2013 42.960312 12436.352 Loop time of 0.866694 on 1 procs for 47 steps with 1066 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 = -4339.50076431631 -4368.20039982816 -4368.20133674283 Force two-norm initial, final = 1192.4799 3.8466972 Force max component initial, final = 979.48667 2.4827416 Final line search alpha, max atom move = 0.00040396314 0.0010029361 Iterations, force evaluations = 47 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81327 | 0.81327 | 0.81327 | 0.0 | 93.84 Neigh | 0.020552 | 0.020552 | 0.020552 | 0.0 | 2.37 Comm | 0.005427 | 0.005427 | 0.005427 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02744 | | | 3.17 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6651.00 ave 6651 max 6651 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: 173716.0 ave 173716 max 173716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 173716 Ave neighs/atom = 162.96060 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.163 | 5.163 | 5.163 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4368.2013 0 -4368.2013 42.960312 Loop time of 3.725e-06 on 1 procs for 0 steps with 1066 atoms 134.2% 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 | | 3.725e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6759.00 ave 6759 max 6759 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: 175076.0 ave 175076 max 175076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175076 Ave neighs/atom = 164.23640 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.163 | 5.163 | 5.163 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 -4368.2013 -4368.2013 30.12619 83.563193 4.9400777 42.960312 42.960312 -68.037407 315.5691 -118.65076 2.3631446 2662.1113 Loop time of 3.897e-06 on 1 procs for 0 steps with 1066 atoms 205.3% 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 | | 3.897e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6759.00 ave 6759 max 6759 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 87538.0 ave 87538 max 87538 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 175076.0 ave 175076 max 175076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 175076 Ave neighs/atom = 164.23640 Neighbor list builds = 0 Dangerous builds = 0 1066 -4368.20133674283 eV 2.36314456092883 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24