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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -45.961174 0.0000000) to (32.499458 45.961174 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0184182 6.2416410 5.1067972 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -45.961174 0.0000000) to (32.499458 45.961174 5.1067972) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0184182 6.2416410 5.1067972 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -45.961174 0.0000000) to (32.499458 45.961174 5.1067972) create_atoms CPU = 0.002 seconds 650 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 18 1 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1298 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_984358344196_004#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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.717 | 6.717 | 6.717 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5109.2753 0 -5109.2753 43613.803 87 0 -5383.5617 0 -5383.5617 5480.7451 Loop time of 3.4838 on 1 procs for 87 steps with 1298 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 = -5109.27531594965 -5383.55663341402 -5383.56172787575 Force two-norm initial, final = 363.67587 0.30725637 Force max component initial, final = 113.00595 0.030191278 Final line search alpha, max atom move = 1.0000000 0.030191278 Iterations, force evaluations = 87 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4225 | 3.4225 | 3.4225 | 0.0 | 98.24 Neigh | 0.027485 | 0.027485 | 0.027485 | 0.0 | 0.79 Comm | 0.020401 | 0.020401 | 0.020401 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0134 | | | 0.38 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11737.0 ave 11737 max 11737 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: 495844.0 ave 495844 max 495844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495844 Ave neighs/atom = 382.00616 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.717 | 6.717 | 6.717 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -5383.5617 0 -5383.5617 5480.7451 15256.181 92 0 -5383.9397 0 -5383.9397 9.9571921 15303.893 Loop time of 0.174901 on 1 procs for 5 steps with 1298 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 = -5383.56172787575 -5383.93962721502 -5383.93965406634 Force two-norm initial, final = 158.71712 0.49035674 Force max component initial, final = 127.25496 0.18906662 Final line search alpha, max atom move = 0.00091054755 0.00017215415 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17021 | 0.17021 | 0.17021 | 0.0 | 97.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00083155 | 0.00083155 | 0.00083155 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003859 | | | 2.21 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11769.0 ave 11769 max 11769 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: 495956.0 ave 495956 max 495956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495956 Ave neighs/atom = 382.09245 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.855 | 6.855 | 6.855 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5383.9397 0 -5383.9397 9.9571921 Loop time of 2.423e-06 on 1 procs for 0 steps with 1298 atoms 165.1% 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 | | 2.423e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11751.0 ave 11751 max 11751 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: 495644.0 ave 495644 max 495644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495644 Ave neighs/atom = 381.85208 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.855 | 6.855 | 6.855 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 -5383.9397 -5383.9397 32.619594 91.687684 5.1169642 9.9571921 9.9571921 19.866699 17.195789 -7.1909115 2.4088225 947.90254 Loop time of 3.985e-06 on 1 procs for 0 steps with 1298 atoms 0.0% 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 | | 3.985e-06 | | |100.00 Nlocal: 1298.00 ave 1298 max 1298 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11751.0 ave 11751 max 11751 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 247822.0 ave 247822 max 247822 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 495644.0 ave 495644 max 495644 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495644 Ave neighs/atom = 381.85208 Neighbor list builds = 0 Dangerous builds = 0 1298 -5383.93965406634 eV 2.40882252190385 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04