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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -36.207487 0.0000000) to (18.101933 36.207487 3.6203867) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0685414 5.0685414 3.6203867 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.207487 0.0000000) to (18.101933 36.207487 3.6203867) create_atoms CPU = 0.001 seconds 201 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0685414 5.0685414 3.6203867 Created 201 atoms using lattice units in orthogonal box = (0.0000000 -36.207487 0.0000000) to (18.101933 36.207487 3.6203867) create_atoms CPU = 0.000 seconds 201 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 ghost atom cutoff = 6 binsize = 3, bins = 7 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 396 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_390178379548_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 ghost atom cutoff = 6 binsize = 3, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1380.1469 0 -1380.1469 10812.204 60 0 -1396.5572 0 -1396.5572 -7492.356 Loop time of 0.86876 on 1 procs for 60 steps with 396 atoms 96.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1380.14689297268 -1396.55585205763 -1396.55716125266 Force two-norm initial, final = 23.128599 0.091347135 Force max component initial, final = 7.2210240 0.022600164 Final line search alpha, max atom move = 1.0000000 0.022600164 Iterations, force evaluations = 60 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86316 | 0.86316 | 0.86316 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029079 | 0.0029079 | 0.0029079 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002687 | | | 0.31 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704.00 ave 2704 max 2704 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: 30488.0 ave 30488 max 30488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30488 Ave neighs/atom = 76.989899 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1396.5572 0 -1396.5572 -7492.356 4745.7877 64 0 -1396.6065 0 -1396.6065 -1061.224 4724.0711 Loop time of 0.0563099 on 1 procs for 4 steps with 396 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 = -1396.55716125266 -1396.60534137754 -1396.6064533548 Force two-norm initial, final = 29.962266 0.12427279 Force max component initial, final = 21.784146 0.036770325 Final line search alpha, max atom move = 0.00048354986 1.7780285e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.055096 | 0.055096 | 0.055096 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018445 | 0.00018445 | 0.00018445 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00103 | | | 1.83 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2672.00 ave 2672 max 2672 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: 30510.0 ave 30510 max 30510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30510 Ave neighs/atom = 77.045455 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 ghost atom cutoff = 6 binsize = 3, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1396.6065 0 -1396.6065 -1061.224 Loop time of 2.098e-06 on 1 procs for 0 steps with 396 atoms 143.0% 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 | | 2.098e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2672.00 ave 2672 max 2672 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: 30516.0 ave 30516 max 30516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30516 Ave neighs/atom = 77.060606 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 ghost atom cutoff = 6 binsize = 3, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.578 | 4.578 | 4.578 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 -1396.6065 -1396.6065 18.079569 72.414975 3.6082778 -1061.224 -1061.224 -3.989237 -3181.0564 1.3735714 2.3174147 161.66478 Loop time of 2.087e-06 on 1 procs for 0 steps with 396 atoms 239.6% 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 | | 2.087e-06 | | |100.00 Nlocal: 396.000 ave 396 max 396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2672.00 ave 2672 max 2672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15258.0 ave 15258 max 15258 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30516.0 ave 30516 max 30516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30516 Ave neighs/atom = 77.060606 Neighbor list builds = 0 Dangerous builds = 0 396 -1396.6064533548 eV 2.31741474579287 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01