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 = 3.4524642 3.4524642 3.4524642 Created orthogonal box = (0.0000000 -36.700198 0.0000000) to (36.700198 36.700198 3.4524642) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8717077 4.8717077 3.4524642 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -36.700198 0.0000000) to (36.700198 36.700198 3.4524642) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8717077 4.8717077 3.4524642 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -36.700198 0.0000000) to (36.700198 36.700198 3.4524642) create_atoms CPU = 0.002 seconds 454 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 19 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3947.4133 0 -3947.4133 62438.378 49 0 -4066.0409 0 -4066.0409 27813.259 Loop time of 1.91742 on 1 procs for 49 steps with 906 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3947.41330210346 -4066.03804836309 -4066.04093975732 Force two-norm initial, final = 160.95558 0.19200997 Force max component initial, final = 54.273568 0.057963321 Final line search alpha, max atom move = 1.0000000 0.057963321 Iterations, force evaluations = 49 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8668 | 1.8668 | 1.8668 | 0.0 | 97.36 Neigh | 0.022411 | 0.022411 | 0.022411 | 0.0 | 1.17 Comm | 0.01649 | 0.01649 | 0.01649 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01174 | | | 0.61 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7777.00 ave 7777 max 7777 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: 181236.0 ave 181236 max 181236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181236 Ave neighs/atom = 200.03974 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.003 | 5.003 | 5.003 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -4066.0409 0 -4066.0409 27813.259 9300.2792 58 0 -4067.0514 0 -4067.0514 325.69573 9366.6323 Loop time of 0.236646 on 1 procs for 9 steps with 906 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 = -4066.04093975723 -4067.05108242734 -4067.0514265804 Force two-norm initial, final = 303.29354 3.7182975 Force max component initial, final = 248.57267 3.1909014 Final line search alpha, max atom move = 0.00031951799 0.0010195504 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22891 | 0.22891 | 0.22891 | 0.0 | 96.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018376 | 0.0018376 | 0.0018376 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005894 | | | 2.49 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7784.00 ave 7784 max 7784 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: 181228.0 ave 181228 max 181228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181228 Ave neighs/atom = 200.03091 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.141 | 5.141 | 5.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4067.0514 0 -4067.0514 325.69573 Loop time of 6.745e-06 on 1 procs for 0 steps with 906 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: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7761.00 ave 7761 max 7761 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: 180640.0 ave 180640 max 180640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180640 Ave neighs/atom = 199.38190 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 10 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.141 | 5.141 | 5.141 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 -4067.0514 -4067.0514 36.755199 73.992814 3.4440952 325.69573 325.69573 146.92075 550.21372 279.95273 2.2043852 124.39083 Loop time of 6.726e-06 on 1 procs for 0 steps with 906 atoms 267.6% 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 | | 6.726e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7761.00 ave 7761 max 7761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90320.0 ave 90320 max 90320 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180640.0 ave 180640 max 180640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180640 Ave neighs/atom = 199.38190 Neighbor list builds = 0 Dangerous builds = 0 906 -4067.05142658264 eV 2.20438523852914 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02