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 = 5.4235095 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 = 5.4235095 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 = 0.001 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3285.3934 0 -3285.3934 121015.3 37 0 -3588.2853 0 -3588.2853 12432.361 Loop time of 0.169155 on 1 procs for 37 steps with 530 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3285.39342661604 -3588.28204841291 -3588.28529496123 Force two-norm initial, final = 454.56152 0.22726486 Force max component initial, final = 131.41017 0.052495600 Final line search alpha, max atom move = 0.45888755 0.024089578 Iterations, force evaluations = 37 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16578 | 0.16578 | 0.16578 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016157 | 0.0016157 | 0.0016157 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001763 | | | 1.04 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2691.00 ave 2691 max 2691 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: 31180.0 ave 31180 max 31180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31180 Ave neighs/atom = 58.830189 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -3588.2853 0 -3588.2853 12432.361 8229.5662 47 0 -3589.0286 0 -3589.0286 234.32312 8261.1229 Loop time of 0.0325943 on 1 procs for 10 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 = -3588.28529496123 -3589.02852396177 -3589.02860554061 Force two-norm initial, final = 178.49069 2.3562254 Force max component initial, final = 178.22434 1.3816717 Final line search alpha, max atom move = 0.0018795417 0.0025969096 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.030835 | 0.030835 | 0.030835 | 0.0 | 94.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030112 | 0.00030112 | 0.00030112 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001458 | | | 4.47 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2683.00 ave 2683 max 2683 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: 31316.0 ave 31316 max 31316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31316 Ave neighs/atom = 59.086792 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3589.0286 0 -3589.0286 234.32312 Loop time of 1.596e-06 on 1 procs for 0 steps with 530 atoms 125.3% 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 | | 1.596e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2699.00 ave 2699 max 2699 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: 31188.0 ave 31188 max 31188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31188 Ave neighs/atom = 58.845283 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) = 4.598 | 4.598 | 4.598 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 -3589.0286 -3589.0286 25.497483 72.941226 4.4418993 234.32312 234.32312 267.22504 214.09161 221.65272 2.3759503 414.73612 Loop time of 1.558e-06 on 1 procs for 0 steps with 530 atoms 128.4% 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 | | 1.558e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2699.00 ave 2699 max 2699 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15594.0 ave 15594 max 15594 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 31188.0 ave 31188 max 31188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 31188 Ave neighs/atom = 58.845283 Neighbor list builds = 0 Dangerous builds = 0 530 -3589.02860554061 eV 2.37595027304473 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