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 = 4.0409265 4.0409265 4.0409265 Created orthogonal box = (0.0000000 -43.145288 0.0000000) to (24.909944 43.145288 6.9990900) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5552483 6.0554790 6.9990900 Created 455 atoms using lattice units in orthogonal box = (0.0000000 -43.145288 0.0000000) to (24.909944 43.145288 6.9990900) create_atoms CPU = 0.001 seconds 455 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5552483 6.0554790 6.9990900 Created 457 atoms using lattice units in orthogonal box = (0.0000000 -43.145288 0.0000000) to (24.909944 43.145288 6.9990900) create_atoms CPU = 0.001 seconds 457 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 18 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 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_338600200739_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3359.7924 0 -3359.7924 33825.374 96 0 -3549.5674 0 -3549.5674 7646.5752 Loop time of 2.31874 on 1 procs for 96 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 = -3359.79241337041 -3549.56394504929 -3549.56738014965 Force two-norm initial, final = 301.49031 0.14501287 Force max component initial, final = 93.645154 0.028572964 Final line search alpha, max atom move = 1.0000000 0.028572964 Iterations, force evaluations = 96 175 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2595 | 2.2595 | 2.2595 | 0.0 | 97.45 Neigh | 0.040673 | 0.040673 | 0.040673 | 0.0 | 1.75 Comm | 0.010766 | 0.010766 | 0.010766 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007766 | | | 0.33 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7200.00 ave 7200 max 7200 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: 224754.0 ave 224754 max 224754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224754 Ave neighs/atom = 246.44079 Neighbor list builds = 3 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 96 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.423 | 5.423 | 5.423 Mbytes Step Temp E_pair E_mol TotEng Press Volume 96 0 -3549.5674 0 -3549.5674 7646.5752 15044.498 107 0 -3550.214 0 -3550.214 -29.861411 15181.948 Loop time of 0.169098 on 1 procs for 11 steps with 912 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 = -3549.56738014967 -3550.21081572133 -3550.21402122139 Force two-norm initial, final = 143.06483 0.67119687 Force max component initial, final = 129.27101 0.51160285 Final line search alpha, max atom move = 0.00018010021 9.2139782e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16538 | 0.16538 | 0.16538 | 0.0 | 97.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068977 | 0.00068977 | 0.00068977 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003025 | | | 1.79 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7188.00 ave 7188 max 7188 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: 224544.0 ave 224544 max 224544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224544 Ave neighs/atom = 246.21053 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3550.214 0 -3550.214 -29.861411 Loop time of 1.762e-06 on 1 procs for 0 steps with 912 atoms 113.5% 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 | | 1.762e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7156.00 ave 7156 max 7156 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: 223956.0 ave 223956 max 223956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223956 Ave neighs/atom = 245.56579 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 5.560 | 5.560 | 5.560 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 -3550.214 -3550.214 24.89639 87.223894 6.9912633 -29.861411 -29.861411 -53.960931 -32.082557 -3.5407469 2.6232452 705.20784 Loop time of 2.726e-06 on 1 procs for 0 steps with 912 atoms 220.1% 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 | | 2.726e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7156.00 ave 7156 max 7156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111978.0 ave 111978 max 111978 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223956.0 ave 223956 max 223956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223956 Ave neighs/atom = 245.56579 Neighbor list builds = 0 Dangerous builds = 0 912 -3550.21402122139 eV 2.62324519170117 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02