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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -35.897097 0.0000000) to (31.087798 35.897097 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5798612 5.5226303 6.0968188 Created 621 atoms using lattice units in orthogonal box = (0.0000000 -35.897097 0.0000000) to (31.087798 35.897097 6.0968188) create_atoms CPU = 0.004 seconds 621 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5798612 5.5226303 6.0968188 Created 628 atoms using lattice units in orthogonal box = (0.0000000 -35.897097 0.0000000) to (31.087798 35.897097 6.0968188) create_atoms CPU = 0.004 seconds 628 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 21 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 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 1244 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_800536961967_003#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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5404.0521 0 -5404.0521 14479.619 133 0 -5506.8888 0 -5506.8888 12170.879 Loop time of 4.0546 on 1 procs for 133 steps with 1244 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 = -5404.05214154802 -5506.88419326351 -5506.88878344917 Force two-norm initial, final = 63.194680 0.24040096 Force max component initial, final = 11.216300 0.062922461 Final line search alpha, max atom move = 0.77534197 0.048786425 Iterations, force evaluations = 133 243 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8628 | 3.8628 | 3.8628 | 0.0 | 95.27 Neigh | 0.1143 | 0.1143 | 0.1143 | 0.0 | 2.82 Comm | 0.039653 | 0.039653 | 0.039653 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0378 | | | 0.93 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5853.00 ave 5853 max 5853 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: 163792.0 ave 163792 max 163792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163792 Ave neighs/atom = 131.66559 Neighbor list builds = 5 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 133 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press Volume 133 0 -5506.8888 0 -5506.8888 12170.879 13607.633 141 0 -5507.5354 0 -5507.5354 -39.926329 13702.714 Loop time of 0.173224 on 1 procs for 8 steps with 1244 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 = -5506.88878344918 -5507.53523369763 -5507.53543761975 Force two-norm initial, final = 207.29915 1.2098937 Force max component initial, final = 180.77679 1.0314970 Final line search alpha, max atom move = 0.00031669457 0.00032666951 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16642 | 0.16642 | 0.16642 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001363 | 0.001363 | 0.001363 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005441 | | | 3.14 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5853.00 ave 5853 max 5853 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: 163812.0 ave 163812 max 163812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163812 Ave neighs/atom = 131.68167 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.185 | 5.185 | 5.185 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5507.5354 0 -5507.5354 -39.926329 Loop time of 6.314e-06 on 1 procs for 0 steps with 1244 atoms 174.2% 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 | | 6.314e-06 | | |100.00 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5850.00 ave 5850 max 5850 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: 163594.0 ave 163594 max 163594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163594 Ave neighs/atom = 131.50643 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 = 6.84 ghost atom cutoff = 6.84 binsize = 3.42, bins = 10 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.84 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) = 5.185 | 5.185 | 5.185 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 -5507.5354 -5507.5354 31.131774 72.276736 6.0898163 -39.926329 -39.926329 -120.77739 -35.850721 36.849124 2.2406726 844.28595 Loop time of 6.946e-06 on 1 procs for 0 steps with 1244 atoms 287.9% 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 | | 6.946e-06 | | |100.00 Nlocal: 1244.00 ave 1244 max 1244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5850.00 ave 5850 max 5850 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 81797.0 ave 81797 max 81797 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 163594.0 ave 163594 max 163594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 163594 Ave neighs/atom = 131.50643 Neighbor list builds = 0 Dangerous builds = 0 1244 -5507.53543761974 eV 2.24067259881941 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04