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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -57.193236 0.0000000) to (11.674520 57.193236 8.6222048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3066002 5.1993851 5.7481365 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.193236 0.0000000) to (11.674520 57.193236 8.6222048) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3066002 5.1993851 5.7481365 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.193236 0.0000000) to (11.674520 57.193236 8.6222048) create_atoms CPU = 0.001 seconds 530 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 30 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.093 | 5.093 | 5.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4596.8594 0 -4596.8594 9729.764 71 0 -4685.0302 0 -4685.0302 10316.84 Loop time of 1.2118 on 1 procs for 71 steps with 1056 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 = -4596.85939821631 -4685.02593012501 -4685.03018172329 Force two-norm initial, final = 47.051017 0.24285478 Force max component initial, final = 8.1727887 0.053555325 Final line search alpha, max atom move = 1.0000000 0.053555325 Iterations, force evaluations = 71 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.187 | 1.187 | 1.187 | 0.0 | 97.96 Neigh | 0.011288 | 0.011288 | 0.011288 | 0.0 | 0.93 Comm | 0.0068764 | 0.0068764 | 0.0068764 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006601 | | | 0.54 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6435.00 ave 6435 max 6435 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: 184396.0 ave 184396 max 184396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184396 Ave neighs/atom = 174.61742 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 30 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 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 71 0 -4685.0302 0 -4685.0302 10316.84 11514.155 79 0 -4685.4648 0 -4685.4648 -14.008178 11580.914 Loop time of 0.103952 on 1 procs for 8 steps with 1056 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 = -4685.03018172328 -4685.46475566391 -4685.46481267797 Force two-norm initial, final = 149.45409 0.42351367 Force max component initial, final = 136.55219 0.18134710 Final line search alpha, max atom move = 0.0010341568 0.00018754134 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10064 | 0.10064 | 0.10064 | 0.0 | 96.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00056538 | 0.00056538 | 0.00056538 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002744 | | | 2.64 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6708.00 ave 6708 max 6708 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: 184524.0 ave 184524 max 184524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184524 Ave neighs/atom = 174.73864 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.238 | 5.238 | 5.238 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4685.4648 0 -4685.4648 -14.008178 Loop time of 1.905e-06 on 1 procs for 0 steps with 1056 atoms 210.0% 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 | | 1.905e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6708.00 ave 6708 max 6708 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: 184308.0 ave 184308 max 184308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184308 Ave neighs/atom = 174.53409 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 4 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.238 | 5.238 | 5.238 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 -4685.4648 -4685.4648 11.663675 115.15814 8.6220947 -14.008178 -14.008178 -4.3246615 -12.611494 -25.088378 2.2129931 415.32605 Loop time of 2.139e-06 on 1 procs for 0 steps with 1056 atoms 280.5% 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 | | 2.139e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6708.00 ave 6708 max 6708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92154.0 ave 92154 max 92154 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184308.0 ave 184308 max 184308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184308 Ave neighs/atom = 174.53409 Neighbor list builds = 0 Dangerous builds = 0 1056 -4685.46481267797 eV 2.21299310499237 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01