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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -80.600680 0.0000000) to (49.357635 80.600680 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7080258 5.7571914 6.6478321 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -80.600680 0.0000000) to (49.357635 80.600680 9.9717481) create_atoms CPU = 0.004 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7080258 5.7571914 6.6478321 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -80.600680 0.0000000) to (49.357635 80.600680 9.9717481) create_atoms CPU = 0.003 seconds 2357 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 = 17 53 4 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 16 atoms, new total = 4692 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 = 17 53 4 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) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15167.988 0 -15167.988 20477.317 94 0 -15768.948 0 -15768.948 876.81534 Loop time of 25.694 on 1 procs for 94 steps with 4692 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15167.9884042399 -15768.9467326139 -15768.9482941155 Force two-norm initial, final = 781.24906 0.58954000 Force max component initial, final = 108.08009 0.13795443 Final line search alpha, max atom move = 0.99848795 0.13774583 Iterations, force evaluations = 94 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.577 | 25.577 | 25.577 | 0.0 | 99.54 Neigh | 0.049906 | 0.049906 | 0.049906 | 0.0 | 0.19 Comm | 0.024372 | 0.024372 | 0.024372 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04277 | | | 0.17 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9133.00 ave 9133 max 9133 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: 252680.0 ave 252680 max 252680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252680 Ave neighs/atom = 53.853367 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 = 17 53 4 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 : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.781 | 5.781 | 5.781 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -15768.948 0 -15768.948 876.81534 79340.392 97 0 -15769.143 0 -15769.143 145.93592 79400.132 Loop time of 0.687712 on 1 procs for 3 steps with 4692 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 = -15768.9482941155 -15769.1360655955 -15769.1426412319 Force two-norm initial, final = 160.93956 13.869604 Force max component initial, final = 159.52607 11.224664 Final line search alpha, max atom move = 4.3148244e-05 0.00048432452 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.68416 | 0.68416 | 0.68416 | 0.0 | 99.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039135 | 0.00039135 | 0.00039135 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003157 | | | 0.46 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9469.00 ave 9469 max 9469 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: 252432.0 ave 252432 max 252432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252432 Ave neighs/atom = 53.800512 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 = 17 53 4 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) = 5.919 | 5.919 | 5.919 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15769.143 0 -15769.143 145.93592 Loop time of 2.255e-06 on 1 procs for 0 steps with 4692 atoms 221.7% 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 | | 2.255e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9469.00 ave 9469 max 9469 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: 252400.0 ave 252400 max 252400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252400 Ave neighs/atom = 53.793691 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 = 17 53 4 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) = 5.919 | 5.919 | 5.919 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 -15769.143 -15769.143 49.331529 161.56227 9.9622331 145.93592 145.93592 226.37721 153.66534 57.765217 2.4814775 2195.9475 Loop time of 2.813e-06 on 1 procs for 0 steps with 4692 atoms 319.9% 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 | | 2.813e-06 | | |100.00 Nlocal: 4692.00 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9469.00 ave 9469 max 9469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 126200.0 ave 126200 max 126200 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 252400.0 ave 252400 max 252400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 252400 Ave neighs/atom = 53.793691 Neighbor list builds = 0 Dangerous builds = 0 4692 -15769.1426412319 eV 2.48147751208309 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27