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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -45.129354 0.0000000) to (31.911272 45.129354 4.9837035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4482660 6.0539378 4.9837035 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -45.129354 0.0000000) to (31.911272 45.129354 4.9837035) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4482660 6.0539378 4.9837035 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -45.129354 0.0000000) to (31.911272 45.129354 4.9837035) create_atoms CPU = 0.004 seconds 660 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 = 9 24 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1312 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_535504325462_003#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 = 9 24 2 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) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5831.723 0 -5831.723 13176.902 73 0 -5923.0275 0 -5923.0275 9190.928 Loop time of 3.54642 on 1 procs for 73 steps with 1312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5831.72300547673 -5923.02190130825 -5923.02748779015 Force two-norm initial, final = 59.838017 0.25395007 Force max component initial, final = 10.363959 0.043733554 Final line search alpha, max atom move = 1.0000000 0.043733554 Iterations, force evaluations = 73 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.4648 | 3.4648 | 3.4648 | 0.0 | 97.70 Neigh | 0.032287 | 0.032287 | 0.032287 | 0.0 | 0.91 Comm | 0.026896 | 0.026896 | 0.026896 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02242 | | | 0.63 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8310.00 ave 8310 max 8310 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: 228280.0 ave 228280 max 228280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228280 Ave neighs/atom = 173.99390 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 = 9 24 2 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 : 73 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press Volume 73 0 -5923.0275 0 -5923.0275 9190.928 14354.413 81 0 -5923.6302 0 -5923.6302 -79.860354 14428.235 Loop time of 0.284666 on 1 procs for 8 steps with 1312 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 = -5923.02748779014 -5923.63003749346 -5923.63021234204 Force two-norm initial, final = 193.40485 1.6461445 Force max component initial, final = 188.62293 1.1444102 Final line search alpha, max atom move = 0.00032497848 0.00037190870 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27586 | 0.27586 | 0.27586 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019165 | 0.0019165 | 0.0019165 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006891 | | | 2.42 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8318.00 ave 8318 max 8318 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: 228520.0 ave 228520 max 228520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228520 Ave neighs/atom = 174.17683 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 = 9 24 2 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) = 5.612 | 5.612 | 5.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5923.6302 0 -5923.6302 -79.860354 Loop time of 6.745e-06 on 1 procs for 0 steps with 1312 atoms 192.7% 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 | | 6.745e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8336.00 ave 8336 max 8336 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: 228272.0 ave 228272 max 228272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228272 Ave neighs/atom = 173.98780 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 = 9 24 2 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) = 5.612 | 5.612 | 5.612 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 -5923.6302 -5923.6302 31.861855 90.856916 4.9840702 -79.860354 -79.860354 -126.8837 -120.13557 7.4382005 2.2773615 589.4338 Loop time of 7.127e-06 on 1 procs for 0 steps with 1312 atoms 266.6% 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 | | 7.127e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8336.00 ave 8336 max 8336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114136.0 ave 114136 max 114136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 228272.0 ave 228272 max 228272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 228272 Ave neighs/atom = 173.98780 Neighbor list builds = 0 Dangerous builds = 0 1312 -5923.63021234204 eV 2.2773615041261 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04