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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -41.845783 0.0000000) to (29.589437 41.845783 5.1122761) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7412341 6.2456393 5.1122761 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -41.845783 0.0000000) to (29.589437 41.845783 5.1122761) create_atoms CPU = 0.004 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7412341 6.2456393 5.1122761 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -41.845783 0.0000000) to (29.589437 41.845783 5.1122761) create_atoms CPU = 0.004 seconds 538 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1070 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3475.9771 0 -3475.9771 74622.625 79 0 -3780.3069 0 -3780.3069 -82.430372 Loop time of 2.46701 on 1 procs for 79 steps with 1070 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 = -3475.97713476968 -3780.30331842758 -3780.30693497855 Force two-norm initial, final = 773.09214 0.18672190 Force max component initial, final = 256.86236 0.032117045 Final line search alpha, max atom move = 1.0000000 0.032117045 Iterations, force evaluations = 79 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4013 | 2.4013 | 2.4013 | 0.0 | 97.33 Neigh | 0.022896 | 0.022896 | 0.022896 | 0.0 | 0.93 Comm | 0.022765 | 0.022765 | 0.022765 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0201 | | | 0.81 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6574.00 ave 6574 max 6574 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: 155408.0 ave 155408 max 155408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155408 Ave neighs/atom = 145.24112 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.020 | 5.020 | 5.020 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3780.3069 0 -3780.3069 -82.430372 12659.971 83 0 -3780.4219 0 -3780.4219 0.50845622 12658.981 Loop time of 0.11737 on 1 procs for 4 steps with 1070 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3780.30693497855 -3780.41985196646 -3780.42186556562 Force two-norm initial, final = 49.207516 0.84468060 Force max component initial, final = 35.745004 0.60482569 Final line search alpha, max atom move = 0.00020146919 0.00012185374 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11161 | 0.11161 | 0.11161 | 0.0 | 95.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012268 | 0.0012268 | 0.0012268 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004538 | | | 3.87 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6594.00 ave 6594 max 6594 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: 153900.0 ave 153900 max 153900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153900 Ave neighs/atom = 143.83178 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.158 | 5.158 | 5.158 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3780.4219 0 -3780.4219 0.50845622 Loop time of 6.685e-06 on 1 procs for 0 steps with 1070 atoms 179.5% 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 | | 6.685e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6586.00 ave 6586 max 6586 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: 153784.0 ave 153784 max 153784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153784 Ave neighs/atom = 143.72336 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.158 | 5.158 | 5.158 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 -3780.4219 -3780.4219 29.487352 83.962168 5.1130417 0.50845622 0.50845622 -7.3272844 -67.708218 76.560871 2.3658804 538.22841 Loop time of 7.007e-06 on 1 procs for 0 steps with 1070 atoms 299.7% 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 | | 7.007e-06 | | |100.00 Nlocal: 1070.00 ave 1070 max 1070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6586.00 ave 6586 max 6586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76892.0 ave 76892 max 76892 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 153784.0 ave 153784 max 153784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153784 Ave neighs/atom = 143.72336 Neighbor list builds = 0 Dangerous builds = 0 1070 -3780.42721556562 eV 2.36588040438039 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03