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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -56.468106 0.0000000) to (28.234053 56.468106 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0913866 5.0913866 3.6150001 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -56.468106 0.0000000) to (28.234053 56.468106 3.6150001) create_atoms CPU = 0.002 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0913866 5.0913866 3.6150001 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -56.468106 0.0000000) to (28.234053 56.468106 3.6150001) create_atoms CPU = 0.002 seconds 490 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3262.2379 0 -3262.2379 60908.617 91 0 -3455.1649 0 -3455.1649 5614.6167 Loop time of 4.49042 on 1 procs for 91 steps with 978 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 = -3262.23790687034 -3455.16191737991 -3455.16488218695 Force two-norm initial, final = 323.57896 0.16367568 Force max component initial, final = 67.139443 0.033774436 Final line search alpha, max atom move = 1.0000000 0.033774436 Iterations, force evaluations = 91 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3691 | 4.3691 | 4.3691 | 0.0 | 97.30 Neigh | 0.059887 | 0.059887 | 0.059887 | 0.0 | 1.33 Comm | 0.037605 | 0.037605 | 0.037605 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02387 | | | 0.53 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9990.00 ave 9990 max 9990 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: 220296.0 ave 220296 max 220296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 220296 Ave neighs/atom = 225.25153 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.436 | 5.436 | 5.436 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -3455.1649 0 -3455.1649 5614.6167 11526.959 96 0 -3455.321 0 -3455.321 -70.134762 11573.682 Loop time of 0.191611 on 1 procs for 5 steps with 978 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 = -3455.16488218695 -3455.320657008 -3455.32099802472 Force two-norm initial, final = 80.921549 1.6277630 Force max component initial, final = 68.717342 1.6080491 Final line search alpha, max atom move = 0.00033800842 0.00054353415 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18578 | 0.18578 | 0.18578 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014558 | 0.0014558 | 0.0014558 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004379 | | | 2.29 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9996.00 ave 9996 max 9996 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: 220036.0 ave 220036 max 220036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 220036 Ave neighs/atom = 224.98569 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.574 | 5.574 | 5.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3455.321 0 -3455.321 -70.134762 Loop time of 6.395e-06 on 1 procs for 0 steps with 978 atoms 187.6% 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 | | 6.395e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10002.0 ave 10002 max 10002 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: 219740.0 ave 219740 max 219740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219740 Ave neighs/atom = 224.68303 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 5.574 | 5.574 | 5.574 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 -3455.321 -3455.321 28.197319 113.36859 3.6205202 -70.134762 -70.134762 -222.31703 -9.92167 21.834411 2.310735 156.53583 Loop time of 6.936e-06 on 1 procs for 0 steps with 978 atoms 245.1% 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 | | 6.936e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10002.0 ave 10002 max 10002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109870.0 ave 109870 max 109870 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219740.0 ave 219740 max 219740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219740 Ave neighs/atom = 224.68303 Neighbor list builds = 0 Dangerous builds = 0 978 -3455.32099802472 eV 2.31073501944009 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05