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 -41.275141 0.0000000) to (29.185932 41.275141 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4299408 5.2793785 4.4508129 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -41.275141 0.0000000) to (29.185932 41.275141 4.4508129) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4299408 5.2793785 4.4508129 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -41.275141 0.0000000) to (29.185932 41.275141 4.4508129) create_atoms CPU = 0.001 seconds 346 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 = 10 27 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 = 690 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 = 10 27 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) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4394.7597 0 -4394.7597 114503.29 66 0 -4679.2971 0 -4679.2971 12575.62 Loop time of 0.366376 on 1 procs for 66 steps with 690 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 = -4394.75968232605 -4679.29358395181 -4679.29713159716 Force two-norm initial, final = 352.62514 0.25889818 Force max component initial, final = 118.85420 0.042708265 Final line search alpha, max atom move = 0.67785298 0.028949925 Iterations, force evaluations = 66 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35919 | 0.35919 | 0.35919 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037502 | 0.0037502 | 0.0037502 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003434 | | | 0.94 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3862.00 ave 3862 max 3862 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: 40548.0 ave 40548 max 40548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40548 Ave neighs/atom = 58.765217 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 = 10 27 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 : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -4679.2971 0 -4679.2971 12575.62 10723.374 71 0 -4679.5817 0 -4679.5817 -7.1730742 10767.414 Loop time of 0.0244864 on 1 procs for 5 steps with 690 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 = -4679.29713159716 -4679.58013863129 -4679.58166786517 Force two-norm initial, final = 159.91517 0.89961786 Force max component initial, final = 134.99745 0.57658064 Final line search alpha, max atom move = 7.8969369e-05 4.5532209e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023171 | 0.023171 | 0.023171 | 0.0 | 94.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024298 | 0.00024298 | 0.00024298 | 0.0 | 0.99 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001073 | | | 4.38 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 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: 40696.0 ave 40696 max 40696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40696 Ave neighs/atom = 58.979710 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 = 10 27 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) = 4.644 | 4.644 | 4.644 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4679.5817 0 -4679.5817 -7.1730742 Loop time of 1.575e-06 on 1 procs for 0 steps with 690 atoms 127.0% 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 | | 1.575e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 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: 40576.0 ave 40576 max 40576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40576 Ave neighs/atom = 58.805797 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 = 10 27 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) = 4.644 | 4.644 | 4.644 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 -4679.5817 -4679.5817 29.161968 82.87923 4.4550121 -7.1730742 -7.1730742 -61.228174 -46.166402 85.875353 2.4378702 417.3613 Loop time of 1.797e-06 on 1 procs for 0 steps with 690 atoms 166.9% 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 | | 1.797e-06 | | |100.00 Nlocal: 690.000 ave 690 max 690 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3842.00 ave 3842 max 3842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20288.0 ave 20288 max 20288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40576.0 ave 40576 max 40576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40576 Ave neighs/atom = 58.805797 Neighbor list builds = 0 Dangerous builds = 0 690 -4679.58166786517 eV 2.43787018707732 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