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 = 3.6150004 3.6150004 3.6150004 Created orthogonal box = (0.0000000 -53.129438 0.0000000) to (18.784093 53.129438 5.1123825) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8699500 5.9032709 5.1123825 Created 432 atoms using lattice units in orthogonal box = (0.0000000 -53.129438 0.0000000) to (18.784093 53.129438 5.1123825) create_atoms CPU = 0.002 seconds 432 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8699500 5.9032709 5.1123825 Created 434 atoms using lattice units in orthogonal box = (0.0000000 -53.129438 0.0000000) to (18.784093 53.129438 5.1123825) create_atoms CPU = 0.001 seconds 434 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 6 34 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 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 862 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_762798677854_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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2985.576 0 -2985.576 23427.463 78 0 -3020.431 0 -3020.431 6762.5691 Loop time of 0.643175 on 1 procs for 78 steps with 862 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2985.57598926078 -3020.42860741905 -3020.43101325724 Force two-norm initial, final = 222.86277 0.11839650 Force max component initial, final = 73.937370 0.027648358 Final line search alpha, max atom move = 1.0000000 0.027648358 Iterations, force evaluations = 78 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61669 | 0.61669 | 0.61669 | 0.0 | 95.88 Neigh | 0.012545 | 0.012545 | 0.012545 | 0.0 | 1.95 Comm | 0.0077267 | 0.0077267 | 0.0077267 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006211 | | | 0.97 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 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: 73940.0 ave 73940 max 73940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73940 Ave neighs/atom = 85.777262 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -3020.431 0 -3020.431 6762.5691 10204.196 84 0 -3020.6321 0 -3020.6321 -361.1778 10252.071 Loop time of 0.0296271 on 1 procs for 6 steps with 862 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 = -3020.43101325724 -3020.63102620119 -3020.6321376225 Force two-norm initial, final = 88.596587 4.4516716 Force max component initial, final = 81.438356 3.8765435 Final line search alpha, max atom move = 0.00032987459 0.0012787732 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027975 | 0.027975 | 0.027975 | 0.0 | 94.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030003 | 0.00030003 | 0.00030003 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001352 | | | 4.56 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 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: 73904.0 ave 73904 max 73904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73904 Ave neighs/atom = 85.735499 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3020.6321 0 -3020.6321 -361.1778 Loop time of 1.56e-06 on 1 procs for 0 steps with 862 atoms 192.3% 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 | | 1.56e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 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: 73844.0 ave 73844 max 73844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73844 Ave neighs/atom = 85.665893 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 = 6.4274532 ghost atom cutoff = 6.4274532 binsize = 3.2137266, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.427453175 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) = 4.724 | 4.724 | 4.724 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 -3020.6321 -3020.6321 18.77755 106.82593 5.1108839 -361.1778 -361.1778 -605.60869 -271.5016 -206.42312 2.2388885 388.70562 Loop time of 1.872e-06 on 1 procs for 0 steps with 862 atoms 213.7% 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 | | 1.872e-06 | | |100.00 Nlocal: 862.000 ave 862 max 862 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36922.0 ave 36922 max 36922 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73844.0 ave 73844 max 73844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73844 Ave neighs/atom = 85.665893 Neighbor list builds = 0 Dangerous builds = 0 862 -3020.6321376225 eV 2.23888852087669 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01