LAMMPS (7 Aug 2019) # Demonstrate SNAP W-Be 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 1 by 1 MPI processor grid create_atoms 1 box Created 128 atoms create_atoms CPU = 0.000234842 secs mass 1 183.84 mass 2 9.012182 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 beryllium type 2 5 atoms in group beryllium # choose potential include WBe_Wood_PRB2019.snap # Definition of SNAP+ZBL potential. variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz1 equal 74 variable zblz2 equal 4 # Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap pair_style hybrid/overlay zbl 4 ${zblcutouter} snap pair_style hybrid/overlay zbl 4 4.8 snap pair_coeff 1 1 zbl ${zblz1} ${zblz1} pair_coeff 1 1 zbl 74 ${zblz1} pair_coeff 1 1 zbl 74 74 pair_coeff 1 2 zbl ${zblz1} ${zblz2} pair_coeff 1 2 zbl 74 ${zblz2} pair_coeff 1 2 zbl 74 4 pair_coeff 2 2 zbl ${zblz2} ${zblz2} pair_coeff 2 2 zbl 4 ${zblz2} pair_coeff 2 2 zbl 4 4 pair_coeff * * snap WBe_Wood_PRB2019.snapcoeff WBe_Wood_PRB2019.snapparam W Be SNAP Element = W, Radius 0.5, Weight 1 SNAP Element = Be, Radius 0.417932, Weight 0.959049 SNAP keyword rcutfac 4.8123 SNAP keyword twojmax 8 SNAP keyword rfac0 0.99363 SNAP keyword rmin0 0 SNAP keyword bzeroflag 1 SNAP keyword quadraticflag 0 # 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 = 5.8123 ghost atom cutoff = 5.8123 binsize = 2.90615, bins = 5 5 5 2 neighbor lists, perpetual/occasional/extra = 2 0 0 (1) pair zbl, perpetual, half/full from (2) attributes: half, newton on pair build: halffull/newton stencil: none bin: none (2) pair snap, perpetual attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Per MPI rank memory allocation (min/avg/max) = 4.268 | 4.268 | 4.268 Mbytes Step Temp E_pair E_mol TotEng Press 0 300 -8.5980876 0 -8.5596125 -35284.855 10 299.29029 -8.5979965 0 -8.5596125 -35299.259 20 288.99334 -8.5966759 0 -8.5596124 -35004.093 30 269.91027 -8.5942284 0 -8.5596123 -34447.077 40 243.57361 -8.5908505 0 -8.5596121 -33687.105 50 212.21385 -8.5868284 0 -8.5596119 -32821.864 60 178.77144 -8.5825391 0 -8.5596116 -31971.17 70 146.71854 -8.578428 0 -8.5596113 -31245.51 80 119.50956 -8.5749383 0 -8.5596111 -30724.137 90 99.872785 -8.5724197 0 -8.559611 -30440.244 100 89.604584 -8.5711027 0 -8.5596109 -30392.805 Loop time of 3.16831 on 1 procs for 100 steps with 128 atoms Performance: 1.364 ns/day, 17.602 hours/ns, 31.563 timesteps/s 199.5% CPU use with 1 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1672 | 3.1672 | 3.1672 | 0.0 | 99.97 Neigh | 0.00030208 | 0.00030208 | 0.00030208 | 0.0 | 0.01 Comm | 0.00029612 | 0.00029612 | 0.00029612 | 0.0 | 0.01 Output | 0.00019813 | 0.00019813 | 0.00019813 | 0.0 | 0.01 Modify | 0.00014448 | 0.00014448 | 0.00014448 | 0.0 | 0.00 Other | | 0.0001433 | | | 0.00 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 727 ave 727 max 727 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 3710 ave 3710 max 3710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 7420 ave 7420 max 7420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 7420 Ave neighs/atom = 57.9688 Neighbor list builds = 1 Dangerous builds = 0 Total wall time: 0:00:03