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 = 2.8502431 2.8502431 2.8502431 Created orthogonal box = (0.0000000 -34.442468 0.0000000) to (42.179746 34.442468 6.9816412) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0446331 4.2459803 4.6544275 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -34.442468 0.0000000) to (42.179746 34.442468 6.9816412) create_atoms CPU = 0.001 seconds 877 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0446331 4.2459803 4.6544275 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -34.442468 0.0000000) to (42.179746 34.442468 6.9816412) create_atoms CPU = 0.001 seconds 877 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1740 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7280.8606 0 -7280.8606 22522.297 60 0 -7424.9297 0 -7424.9297 -2988.6683 Loop time of 9.92124 on 1 procs for 60 steps with 1740 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7280.86056665826 -7424.92335239344 -7424.92970594751 Force two-norm initial, final = 138.86317 0.23568825 Force max component initial, final = 17.935050 0.022142025 Final line search alpha, max atom move = 1.0000000 0.022142025 Iterations, force evaluations = 60 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.882 | 9.882 | 9.882 | 0.0 | 99.60 Neigh | 0.022418 | 0.022418 | 0.022418 | 0.0 | 0.23 Comm | 0.0065129 | 0.0065129 | 0.0065129 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0103 | | | 0.10 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5725.00 ave 5725 max 5725 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: 114224.0 ave 114224 max 114224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114224 Ave neighs/atom = 65.645977 Neighbor list builds = 2 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.099 | 5.099 | 5.099 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -7424.9297 0 -7424.9297 -2988.6683 20285.501 63 0 -7424.9928 0 -7424.9928 246.37271 20245.608 Loop time of 0.573208 on 1 procs for 3 steps with 1740 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 = -7424.9297059475 -7424.99151521075 -7424.99280534087 Force two-norm initial, final = 73.234115 0.26159619 Force max component initial, final = 67.348707 0.036674378 Final line search alpha, max atom move = 0.00011963017 4.3873621e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.57139 | 0.57139 | 0.57139 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027484 | 0.00027484 | 0.00027484 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001539 | | | 0.27 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5722.00 ave 5722 max 5722 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: 114080.0 ave 114080 max 114080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114080 Ave neighs/atom = 65.563218 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.237 | 5.237 | 5.237 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7424.9928 0 -7424.9928 246.37271 Loop time of 1.802e-06 on 1 procs for 0 steps with 1740 atoms 222.0% 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 | | 1.802e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5722.00 ave 5722 max 5722 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: 114164.0 ave 114164 max 114164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114164 Ave neighs/atom = 65.611494 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.237 | 5.237 | 5.237 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 -7424.9928 -7424.9928 42.17252 68.884937 6.9691049 246.37271 246.37271 -2.9018028 743.91936 -1.8994197 2.2509513 1731.7672 Loop time of 1.925e-06 on 1 procs for 0 steps with 1740 atoms 207.8% 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 | | 1.925e-06 | | |100.00 Nlocal: 1740.00 ave 1740 max 1740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5722.00 ave 5722 max 5722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57082.0 ave 57082 max 57082 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114164.0 ave 114164 max 114164 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114164 Ave neighs/atom = 65.611494 Neighbor list builds = 0 Dangerous builds = 0 1740 -7424.99280534087 eV 2.2509512549844 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11