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 = 3.6073527 3.6073527 3.6073527 Created orthogonal box = (0.0000000 -44.474431 0.0000000) to (15.724086 44.474431 5.1015671) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7930843 4.6815191 5.1015671 Created 304 atoms using lattice units in orthogonal box = (0.0000000 -44.474431 0.0000000) to (15.724086 44.474431 5.1015671) create_atoms CPU = 0.001 seconds 304 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7930843 4.6815191 5.1015671 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -44.474431 0.0000000) to (15.724086 44.474431 5.1015671) create_atoms CPU = 0.001 seconds 306 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 608 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_151002396060_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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2053.4266 0 -2053.4266 29258.231 103 0 -2137.8839 0 -2137.8839 4941.7279 Loop time of 4.56398 on 1 procs for 103 steps with 608 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2053.42659696109 -2137.88187767234 -2137.88391603076 Force two-norm initial, final = 148.84394 0.18528754 Force max component initial, final = 43.541794 0.030806916 Final line search alpha, max atom move = 1.0000000 0.030806916 Iterations, force evaluations = 103 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.4911 | 4.4911 | 4.4911 | 0.0 | 98.40 Neigh | 0.031576 | 0.031576 | 0.031576 | 0.0 | 0.69 Comm | 0.028718 | 0.028718 | 0.028718 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01257 | | | 0.28 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 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: 383744.0 ave 383744 max 383744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383744 Ave neighs/atom = 631.15789 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -2137.8839 0 -2137.8839 4941.7279 7135.2535 107 0 -2137.9413 0 -2137.9413 -205.77299 7161.6261 Loop time of 0.112383 on 1 procs for 4 steps with 608 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 = -2137.88391603078 -2137.94051807837 -2137.94125309565 Force two-norm initial, final = 40.323711 2.1775760 Force max component initial, final = 31.447805 1.6905974 Final line search alpha, max atom move = 0.00025303468 0.00042777977 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1099 | 0.1099 | 0.1099 | 0.0 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054566 | 0.00054566 | 0.00054566 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001935 | | | 1.72 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 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: 383268.0 ave 383268 max 383268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 383268 Ave neighs/atom = 630.37500 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.970 | 5.970 | 5.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2137.9413 0 -2137.9413 -205.77299 Loop time of 1.991e-06 on 1 procs for 0 steps with 608 atoms 200.9% 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 | | 1.991e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 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: 382240.0 ave 382240 max 382240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 382240 Ave neighs/atom = 628.68421 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 5.970 | 5.970 | 5.970 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 -2137.9413 -2137.9413 15.720405 89.245937 5.1045734 -205.77299 -205.77299 -297.46481 58.583859 -378.43801 2.3621242 564.53195 Loop time of 2.679e-06 on 1 procs for 0 steps with 608 atoms 224.0% 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 | | 2.679e-06 | | |100.00 Nlocal: 608.000 ave 608 max 608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10642.0 ave 10642 max 10642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 191120.0 ave 191120 max 191120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 382240.0 ave 382240 max 382240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 382240 Ave neighs/atom = 628.68421 Neighbor list builds = 0 Dangerous builds = 0 608 -2137.94125309565 eV 2.36212419499235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05