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 -40.057316 0.0000000) to (9.4415999 40.057316 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2453333 4.4508129 4.4508129 Created 108 atoms using lattice units in orthogonal box = (0.0000000 -40.057316 0.0000000) to (9.4415999 40.057316 4.4508129) create_atoms CPU = 0.001 seconds 108 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2453333 4.4508129 4.4508129 Created 110 atoms using lattice units in orthogonal box = (0.0000000 -40.057316 0.0000000) to (9.4415999 40.057316 4.4508129) create_atoms CPU = 0.000 seconds 110 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 = 4 26 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 = 218 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 = 4 26 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) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1276.5025 0 -1276.5025 170244.68 52 0 -1474.5081 0 -1474.5081 43228.121 Loop time of 0.11078 on 1 procs for 52 steps with 218 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1276.50253226819 -1474.50679583408 -1474.50813941093 Force two-norm initial, final = 308.76942 0.14424376 Force max component initial, final = 124.11949 0.017591678 Final line search alpha, max atom move = 1.0000000 0.017591678 Iterations, force evaluations = 52 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10674 | 0.10674 | 0.10674 | 0.0 | 96.36 Neigh | 0.0011731 | 0.0011731 | 0.0011731 | 0.0 | 1.06 Comm | 0.0015688 | 0.0015688 | 0.0015688 | 0.0 | 1.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001296 | | | 1.17 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1836.00 ave 1836 max 1836 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: 12888.0 ave 12888 max 12888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12888 Ave neighs/atom = 59.119266 Neighbor list builds = 1 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 = 4 26 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 : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -1474.5081 0 -1474.5081 43228.121 3366.6407 67 0 -1475.5268 0 -1475.5268 1320.7536 3412.705 Loop time of 0.0248039 on 1 procs for 15 steps with 218 atoms 94.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1474.50813941093 -1475.52599573954 -1475.52682778415 Force two-norm initial, final = 175.44309 5.0559419 Force max component initial, final = 154.22426 3.5611757 Final line search alpha, max atom move = 0.0041079091 0.014628986 Iterations, force evaluations = 15 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021987 | 0.021987 | 0.021987 | 0.0 | 88.64 Neigh | 0.0011011 | 0.0011011 | 0.0011011 | 0.0 | 4.44 Comm | 0.00033263 | 0.00033263 | 0.00033263 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001384 | | | 5.58 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1830.00 ave 1830 max 1830 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: 12716.0 ave 12716 max 12716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12716 Ave neighs/atom = 58.330275 Neighbor list builds = 1 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 = 4 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) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1475.5268 0 -1475.5268 1320.7536 Loop time of 1.799e-06 on 1 procs for 0 steps with 218 atoms 166.8% 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 | | 1.799e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1830.00 ave 1830 max 1830 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: 12716.0 ave 12716 max 12716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12716 Ave neighs/atom = 58.330275 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 = 4 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) = 4.540 | 4.540 | 4.540 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 -1475.5268 -1475.5268 9.4363214 81.208191 4.453446 1320.7536 1320.7536 1670.9449 1195.4513 1095.8646 2.5810467 169.70649 Loop time of 1.634e-06 on 1 procs for 0 steps with 218 atoms 183.6% 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 | | 1.634e-06 | | |100.00 Nlocal: 218.000 ave 218 max 218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1830.00 ave 1830 max 1830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6358.00 ave 6358 max 6358 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 12716.0 ave 12716 max 12716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12716 Ave neighs/atom = 58.330275 Neighbor list builds = 0 Dangerous builds = 0 218 -1475.52682778415 eV 2.5810466712767 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