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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -47.230710 0.0000000) to (23.615355 47.230710 4.0500000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5565542 5.5565542 4.0500000 Created 271 atoms using lattice units in orthogonal box = (0.0000000 -47.230710 0.0000000) to (23.615355 47.230710 4.0500000) create_atoms CPU = 0.002 seconds 271 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5565542 5.5565542 4.0500000 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -47.230710 0.0000000) to (23.615355 47.230710 4.0500000) create_atoms CPU = 0.001 seconds 273 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 = 6 22 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 544 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_664470114311_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1798.1424 0 -1798.1424 6386.6616 49 0 -1822.3005 0 -1822.3005 5047.8646 Loop time of 1.08839 on 1 procs for 49 steps with 544 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 = -1798.14242745303 -1822.2988541778 -1822.30045780283 Force two-norm initial, final = 24.051449 0.091473830 Force max component initial, final = 5.5112146 0.0090955858 Final line search alpha, max atom move = 1.0000000 0.0090955858 Iterations, force evaluations = 49 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0556 | 1.0556 | 1.0556 | 0.0 | 96.98 Neigh | 0.012889 | 0.012889 | 0.012889 | 0.0 | 1.18 Comm | 0.011831 | 0.011831 | 0.011831 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008115 | | | 0.75 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5486.00 ave 5486 max 5486 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: 94456.0 ave 94456 max 94456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94456 Ave neighs/atom = 173.63235 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1822.3005 0 -1822.3005 5047.8646 9034.4971 60 0 -1822.5679 0 -1822.5679 11.873068 9091.0501 Loop time of 0.178354 on 1 procs for 11 steps with 544 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1822.30045780283 -1822.56713644785 -1822.56786901872 Force two-norm initial, final = 60.696546 0.26004768 Force max component initial, final = 57.359428 0.15298911 Final line search alpha, max atom move = 0.00057538391 8.8027474e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15978 | 0.15978 | 0.15978 | 0.0 | 89.58 Neigh | 0.012171 | 0.012171 | 0.012171 | 0.0 | 6.82 Comm | 0.0016852 | 0.0016852 | 0.0016852 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00472 | | | 2.65 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 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: 94410.0 ave 94410 max 94410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94410 Ave neighs/atom = 173.54779 Neighbor list builds = 1 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 = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1822.5679 0 -1822.5679 11.873068 Loop time of 6.334e-06 on 1 procs for 0 steps with 544 atoms 173.7% 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 | | 6.334e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 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: 94412.0 ave 94412 max 94412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94412 Ave neighs/atom = 173.55147 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 = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 4.661 | 4.661 | 4.661 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 -1822.5679 -1822.5679 23.568293 95.457413 4.0408829 11.873068 11.873068 26.908561 6.4310665 2.2795774 2.5829981 398.74484 Loop time of 6.906e-06 on 1 procs for 0 steps with 544 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5066.00 ave 5066 max 5066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47206.0 ave 47206 max 47206 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94412.0 ave 94412 max 94412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94412 Ave neighs/atom = 173.55147 Neighbor list builds = 0 Dangerous builds = 0 544 -1819.26066747895 eV 2.5829981320343 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01