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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -40.197985 0.0000000) to (28.424267 40.197985 4.4664427) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2637532 5.4589856 4.4664427 Created 324 atoms using lattice units in orthogonal box = (0.0000000 -40.197985 0.0000000) to (28.424267 40.197985 4.4664427) create_atoms CPU = 0.001 seconds 324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2637532 5.4589856 4.4664427 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -40.197985 0.0000000) to (28.424267 40.197985 4.4664427) create_atoms CPU = 0.001 seconds 326 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 19 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 648 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2096.429 0 -2096.429 360912.43 194 0 -4122.2904 0 -4122.2904 5409.5982 Loop time of 1.21337 on 1 procs for 194 steps with 648 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2096.4290452521 -4122.28639640074 -4122.29042676197 Force two-norm initial, final = 3285.4812 0.36535585 Force max component initial, final = 928.16585 0.053545044 Final line search alpha, max atom move = 0.72171447 0.038644233 Iterations, force evaluations = 194 328 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.144 | 1.144 | 1.144 | 0.0 | 94.28 Neigh | 0.044724 | 0.044724 | 0.044724 | 0.0 | 3.69 Comm | 0.013375 | 0.013375 | 0.013375 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01131 | | | 0.93 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4983.00 ave 4983 max 4983 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: 108156.0 ave 108156 max 108156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108156 Ave neighs/atom = 166.90741 Neighbor list builds = 7 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 194 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.909 | 4.909 | 4.909 Mbytes Step Temp E_pair E_mol TotEng Press Volume 194 0 -4122.2904 0 -4122.2904 5409.5982 10206.699 197 0 -4122.3528 0 -4122.3528 30.965272 10225.996 Loop time of 0.0214596 on 1 procs for 3 steps with 648 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4122.29042676197 -4122.35219373464 -4122.35278018834 Force two-norm initial, final = 73.275862 1.2867577 Force max component initial, final = 65.915806 1.1358231 Final line search alpha, max atom move = 0.00013597114 0.00015443917 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020395 | 0.020395 | 0.020395 | 0.0 | 95.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021104 | 0.00021104 | 0.00021104 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008531 | | | 3.98 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4994.00 ave 4994 max 4994 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: 108240.0 ave 108240 max 108240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108240 Ave neighs/atom = 167.03704 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4122.3528 0 -4122.3528 30.965272 Loop time of 1.693e-06 on 1 procs for 0 steps with 648 atoms 118.1% 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 | | 1.693e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4981.00 ave 4981 max 4981 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: 108228.0 ave 108228 max 108228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108228 Ave neighs/atom = 167.01852 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 5.047 | 5.047 | 5.047 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 -4122.3528 -4122.3528 28.442498 80.526553 4.4647669 30.965272 30.965272 178.07128 -69.69095 -15.484518 2.6043042 436.71556 Loop time of 1.753e-06 on 1 procs for 0 steps with 648 atoms 171.1% 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 | | 1.753e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4981.00 ave 4981 max 4981 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54114.0 ave 54114 max 54114 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108228.0 ave 108228 max 108228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108228 Ave neighs/atom = 167.01852 Neighbor list builds = 0 Dangerous builds = 0 648 -4122.35278018834 eV 2.60430418680653 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01