LAMMPS (13 Feb 2017) # Demonstrate SNAP Ta potential # Initialize simulation variable nsteps index 100 variable nrep equal 4 variable a equal 3.1803 units metal # generate the box and atom positions using a BCC lattice variable nx equal ${nrep} variable nx equal 4 variable ny equal ${nrep} variable ny equal 4 variable nz equal ${nrep} variable nz equal 4 boundary p p p lattice bcc $a lattice bcc 3.1803 Lattice spacing in x,y,z = 3.1803 3.1803 3.1803 region box block 0 ${nx} 0 ${ny} 0 ${nz} region box block 0 4 0 ${ny} 0 ${nz} region box block 0 4 0 4 0 ${nz} region box block 0 4 0 4 0 4 create_box 2 box Created orthogonal box = (0 0 0) to (12.7212 12.7212 12.7212) 1 by 2 by 2 MPI processor grid create_atoms 1 box Created 128 atoms mass 1 183.84 mass 2 4.0026 set group all type/fraction 2 0.05 3590153 # Change 5% of W to He 5 settings made for type/fraction group tungsten type 1 123 atoms in group tungsten group helium type 2 5 atoms in group helium # choose potential include W.SNAP_HePair.pot # DATE: 2017-02-20 CONTRIBUTOR: Mitchell Wood mitwood@sandia.gov CITATION: Wood, M. A. and Thompson, A. P. to appear in arxiv Feb2017, W-He and He-He from Juslin, N. and Wirth, B. D. Journal of Nuclear Materials, 423, (2013) p61-63 # # Definition of SNAP+ZBL+Tabulated potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 # Specify hybrid with SNAP, ZBL, and long-range Coulomb pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 ${zblcutouter} snap table spline 10000 table spline 10000 pair_style hybrid/overlay zbl 4 4.8 snap table spline 10000 table spline 10000 pair_coeff 1 1 zbl ${zblz} ${zblz} pair_coeff 1 1 zbl 74 ${zblz} pair_coeff 1 1 zbl 74 74 pair_coeff * * snap W_2940_2017_2.snapcoeff W W_2940_2017_2.snapparam W NULL Reading potential file W_2940_2017_2.snapcoeff with DATE: 2017-02-20 SNAP Element = W, Radius 0.5, Weight 1 Reading potential file W_2940_2017_2.snapparam with DATE: 2017-02-20 SNAP keyword rcutfac 4.73442 SNAP keyword twojmax 8 SNAP keyword gamma 1 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword diagonalstyle 3 pair_coeff 2 2 table 1 He_He_JW2013.table HeHe Reading potential file He_He_JW2013.table with DATE: 2017-02-20 WARNING: 1 of 4999 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:476) pair_coeff 1 2 table 2 W_He_JW2013.table WHe Reading potential file W_He_JW2013.table with DATE: 2017-02-20 WARNING: 3 of 325 force values in table are inconsistent with -dE/dr. Should only be flagged at inflection points (../pair_table.cpp:476) #Hybrid/overlay will take all pair styles and add their contributions equally, order of pair_coeff doesnt matter here #This is not the case for pair_style hybrid ... where only one pair_coeff is read for each type combination, order matters here. # Setup output thermo 10 thermo_modify norm yes # Set up NVE run timestep 0.5e-3 neighbor 1.0 bin neigh_modify once no every 1 delay 0 check yes # Run MD velocity all create 300.0 4928459 fix 1 all nve run ${nsteps} run 100 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 5 5 6 neighbor lists, perpetual/occasional/extra = 6 0 0 (1) pair zbl, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton/skip stencil: none bin: none (2) pair snap, perpetual, skip from (6) attributes: full, newton on pair build: skip stencil: none bin: none (3) pair table, perpetual, skip from (5) attributes: half, newton on pair build: skip stencil: none bin: none (4) pair table, perpetual, skip from (5) attributes: half, newton on pair build: skip stencil: none bin: none (5) neighbor class addition, perpetual, half/full from (6) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (6) neighbor class addition, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Memory usage per processor = 7.65426 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -10.438105 0 -10.39963 -5445.2808 10 292.13979 -10.437097 0 -10.39963 -5516.3963 20 272.55728 -10.434585 0 -10.399629 -5460.4268 30 245.06559 -10.431059 0 -10.399629 -5016.6351 40 212.79459 -10.42692 0 -10.399629 -3924.2175 50 178.03903 -10.422462 0 -10.399629 -2354.5485 60 141.62155 -10.417791 0 -10.399628 -595.41345 70 107.24843 -10.413383 0 -10.399628 1138.4107 80 79.985938 -10.409886 0 -10.399628 2392.1106 90 62.568933 -10.407652 0 -10.399628 3141.7027 100 56.697933 -10.406899 0 -10.399628 3583.9538 Loop time of 2.8757 on 4 procs for 100 steps with 128 atoms Performance: 1.502 ns/day, 15.976 hours/ns, 34.774 timesteps/s 99.9% CPU use with 4 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7363 | 2.8122 | 2.8636 | 2.9 | 97.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011014 | 0.062439 | 0.13842 | 19.3 | 2.17 Output | 0.00023842 | 0.00025076 | 0.0002861 | 0.0 | 0.01 Modify | 9.2506e-05 | 9.9301e-05 | 0.00010395 | 0.0 | 0.00 Other | | 0.0006654 | | | 0.02 Nlocal: 32 ave 32 max 32 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 431 ave 431 max 431 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 856.25 ave 885 max 818 min Histogram: 1 0 0 0 1 0 0 0 1 1 FullNghs: 1712.5 ave 1738 max 1658 min Histogram: 1 0 0 0 0 0 0 0 2 1 Total # of neighbors = 6850 Ave neighs/atom = 53.5156 Neighbor list builds = 0 Dangerous builds = 0 Total wall time: 0:00:02