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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -36.158575 0.0000000) to (25.567973 36.158575 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8739354 4.9307147 4.4508129 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -36.158575 0.0000000) to (25.567973 36.158575 4.4508129) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8739354 4.9307147 4.4508129 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -36.158575 0.0000000) to (25.567973 36.158575 4.4508129) create_atoms CPU = 0.000 seconds 266 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 24 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 530 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3334.3897 0 -3334.3897 123328.44 103 0 -3584.3785 0 -3584.3785 12734.965 Loop time of 0.453817 on 1 procs for 103 steps with 530 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 = -3334.38974945153 -3584.37522770818 -3584.37853275045 Force two-norm initial, final = 382.16149 0.21282310 Force max component initial, final = 102.41664 0.043549328 Final line search alpha, max atom move = 1.0000000 0.043549328 Iterations, force evaluations = 103 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.44441 | 0.44441 | 0.44441 | 0.0 | 97.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0049789 | 0.0049789 | 0.0049789 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004427 | | | 0.98 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3190.00 ave 3190 max 3190 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: 31216.0 ave 31216 max 31216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31216 Ave neighs/atom = 58.898113 Neighbor list builds = 0 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 103 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 103 0 -3584.3785 0 -3584.3785 12734.965 8229.5662 109 0 -3584.6937 0 -3584.6937 -532.159 8263.3177 Loop time of 0.0193317 on 1 procs for 6 steps with 530 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 = -3584.37853275045 -3584.69185745712 -3584.69368627146 Force two-norm initial, final = 135.35550 5.0714202 Force max component initial, final = 125.86795 3.7235195 Final line search alpha, max atom move = 0.00013095907 0.00048762863 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.018281 | 0.018281 | 0.018281 | 0.0 | 94.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019519 | 0.00019519 | 0.00019519 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008555 | | | 4.43 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3158.00 ave 3158 max 3158 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: 31336.0 ave 31336 max 31336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31336 Ave neighs/atom = 59.124528 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3584.6937 0 -3584.6937 -532.159 Loop time of 1.791e-06 on 1 procs for 0 steps with 530 atoms 167.5% 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 | | 1.791e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3146.00 ave 3146 max 3146 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: 31248.0 ave 31248 max 31248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31248 Ave neighs/atom = 58.958491 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.603 | 4.603 | 4.603 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 -3584.6937 -3584.6937 25.554302 72.709464 4.4473312 -532.159 -532.159 -585.56526 -289.52246 -721.38926 2.4457424 507.35268 Loop time of 1.419e-06 on 1 procs for 0 steps with 530 atoms 140.9% 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 | | 1.419e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3146.00 ave 3146 max 3146 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15624.0 ave 15624 max 15624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31248.0 ave 31248 max 31248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31248 Ave neighs/atom = 58.958491 Neighbor list builds = 0 Dangerous builds = 0 530 -3584.69368627146 eV 2.44574237569485 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42