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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -53.658356 0.0000000) to (32.858898 53.658356 9.9073306) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9743451 6.0975404 6.6048870 Created 1041 atoms using lattice units in orthogonal box = (0.0000000 -53.658356 0.0000000) to (32.858898 53.658356 9.9073306) create_atoms CPU = 0.002 seconds 1041 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9743451 6.0975404 6.6048870 Created 1065 atoms using lattice units in orthogonal box = (0.0000000 -53.658356 0.0000000) to (32.858898 53.658356 9.9073306) create_atoms CPU = 0.001 seconds 1065 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2106 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_099716416216_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6959.0634 0 -6959.0634 7525.9951 57 0 -7062.2656 0 -7062.2656 1052.5542 Loop time of 6.09842 on 1 procs for 57 steps with 2106 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 = -6959.06342602137 -7062.25877687489 -7062.26560136576 Force two-norm initial, final = 200.68278 0.21084211 Force max component initial, final = 75.344983 0.012406791 Final line search alpha, max atom move = 1.0000000 0.012406791 Iterations, force evaluations = 57 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0584 | 6.0584 | 6.0584 | 0.0 | 99.34 Neigh | 0.023914 | 0.023914 | 0.023914 | 0.0 | 0.39 Comm | 0.0058763 | 0.0058763 | 0.0058763 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01028 | | | 0.17 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5624.00 ave 5624 max 5624 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: 161844.0 ave 161844 max 161844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 161844 Ave neighs/atom = 76.849003 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -7062.2656 0 -7062.2656 1052.5542 34936.308 62 0 -7062.4668 0 -7062.4668 -31.326052 34982.499 Loop time of 0.425314 on 1 procs for 5 steps with 2106 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 = -7062.26560136576 -7062.46070491197 -7062.46681965873 Force two-norm initial, final = 79.752984 1.2155904 Force max component initial, final = 78.739515 0.73938121 Final line search alpha, max atom move = 9.7530610e-05 7.2112300e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42281 | 0.42281 | 0.42281 | 0.0 | 99.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003108 | 0.0003108 | 0.0003108 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002195 | | | 0.52 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5618.00 ave 5618 max 5618 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: 162320.0 ave 162320 max 162320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162320 Ave neighs/atom = 77.075024 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7062.4668 0 -7062.4668 -31.326052 Loop time of 2.042e-06 on 1 procs for 0 steps with 2106 atoms 195.9% 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 | | 2.042e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5618.00 ave 5618 max 5618 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: 162070.0 ave 162070 max 162070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162070 Ave neighs/atom = 76.956315 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 11 34 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.203 | 5.203 | 5.203 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 -7062.4668 -7062.4668 32.78194 107.83301 9.8961085 -31.326052 -31.326052 -30.111511 -30.041807 -33.824838 2.6585161 1058.4765 Loop time of 2.034e-06 on 1 procs for 0 steps with 2106 atoms 245.8% 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 | | 2.034e-06 | | |100.00 Nlocal: 2106.00 ave 2106 max 2106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5618.00 ave 5618 max 5618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81035.0 ave 81035 max 81035 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 162070.0 ave 162070 max 162070 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 162070 Ave neighs/atom = 76.956315 Neighbor list builds = 0 Dangerous builds = 0 2106 -7062.46681965873 eV 2.65851612047319 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07