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 -41.752326 0.0000000) to (25.567973 41.752326 7.7090341) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6487224 4.7445825 5.1393560 Created 527 atoms using lattice units in orthogonal box = (0.0000000 -41.752326 0.0000000) to (25.567973 41.752326 7.7090341) create_atoms CPU = 0.003 seconds 527 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6487224 4.7445825 5.1393560 Created 533 atoms using lattice units in orthogonal box = (0.0000000 -41.752326 0.0000000) to (25.567973 41.752326 7.7090341) create_atoms CPU = 0.002 seconds 533 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 27 3 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 4 atoms, new total = 1056 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 27 3 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6202.5019 0 -6202.5019 116949.42 86 0 -7147.4133 0 -7147.4133 2779.8895 Loop time of 1.59868 on 1 procs for 86 steps with 1056 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 = -6202.50193448343 -7147.40674562496 -7147.41326977707 Force two-norm initial, final = 903.63584 0.26961282 Force max component initial, final = 153.09359 0.076642201 Final line search alpha, max atom move = 0.77927480 0.059725336 Iterations, force evaluations = 86 155 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5416 | 1.5416 | 1.5416 | 0.0 | 96.43 Neigh | 0.024467 | 0.024467 | 0.024467 | 0.0 | 1.53 Comm | 0.01334 | 0.01334 | 0.01334 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01929 | | | 1.21 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3518.00 ave 3518 max 3518 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: 62118.0 ave 62118 max 62118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62118 Ave neighs/atom = 58.823864 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 9 27 3 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 : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.549 | 4.549 | 4.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -7147.4133 0 -7147.4133 2779.8895 16459.132 91 0 -7147.7608 0 -7147.7608 -143.20618 16475.33 Loop time of 0.0709189 on 1 procs for 5 steps with 1056 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7147.41326977707 -7147.75994740241 -7147.76080188384 Force two-norm initial, final = 149.96913 2.6789604 Force max component initial, final = 144.12253 1.8205716 Final line search alpha, max atom move = 0.00015287305 0.00027831633 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067971 | 0.067971 | 0.067971 | 0.0 | 95.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00050037 | 0.00050037 | 0.00050037 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002448 | | | 3.45 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3477.00 ave 3477 max 3477 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: 61872.0 ave 61872 max 61872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61872 Ave neighs/atom = 58.590909 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 27 3 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7147.7608 0 -7147.7608 -143.20618 Loop time of 6.776e-06 on 1 procs for 0 steps with 1056 atoms 162.3% 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 | | 6.776e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3469.00 ave 3469 max 3469 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: 61842.0 ave 61842 max 61842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61842 Ave neighs/atom = 58.562500 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 27 3 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) = 4.686 | 4.686 | 4.686 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 -7147.7608 -7147.7608 25.531226 83.856383 7.6953135 -143.20618 -143.20618 -143.2995 -109.589 -176.73003 2.3965261 816.93098 Loop time of 6.916e-06 on 1 procs for 0 steps with 1056 atoms 260.3% 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 | | 6.916e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3469.00 ave 3469 max 3469 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30921.0 ave 30921 max 30921 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61842.0 ave 61842 max 61842 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61842 Ave neighs/atom = 58.562500 Neighbor list builds = 0 Dangerous builds = 0 1056 -7147.76080188384 eV 2.39652610771166 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42