Added examples for body rounded/polygon and rounded/polyhedron

examples/body/data.cubes

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+LAMMPS data file for polygons: cubes, moment of inertia I = m edge^2/ 6
+2 atoms
+2 bodies
+1 atom types
+0 6 xlo xhi
+0 6 ylo yhi
+0 6 zlo zhi
+
+Atoms
+
+1 1 1 1 1.5 1.5 1.5
+2 1 1 1 4.0 4.0 4.0
+
+Bodies
+
+1 3 79
+8 12 6
+0.667 0.667 0.667 0 0 0
+1 1 1
+1 -1 1
+-1 -1 1
+-1 1 1
+1 1 -1
+1 -1 -1
+-1 -1 -1
+-1 1 -1
+0 1
+1 2
+2 3
+3 0
+4 5
+5 6
+6 7
+7 4
+0 4
+1 5
+2 6
+3 7
+0 1 2 3
+4 5 6 7
+0 1 5 4
+1 2 6 5
+2 3 7 6
+3 0 4 7
+0.5
+2 3 79
+8 12 6
+0.667 0.667 0.667 0 0 0
+1 1 1
+1 -1 1
+-1 -1 1
+-1 1 1
+1 1 -1
+1 -1 -1
+-1 -1 -1
+-1 1 -1
+0 1
+1 2
+2 3
+3 0
+4 5
+5 6
+6 7
+7 4
+0 4
+1 5
+2 6
+3 7
+0 1 2 3
+4 5 6 7
+0 1 5 4
+1 2 6 5
+2 3 7 6
+3 0 4 7
+0.5
+

examples/body/in.cubes

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+# 3d rounded cubes
+
+variable    r     index 3
+variable    steps index 10000
+
+units       lj
+dimension   3
+
+atom_style  body rounded/polyhedron 1 10
+
+read_data   data.cubes
+
+replicate   $r $r $r
+
+velocity    all create 1.2 187287 dist gaussian mom yes rot yes
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 1
+variable c_n        equal 20
+variable c_t        equal 5
+variable mu         equal 0
+variable A_ua       equal 1
+
+pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_coeff * * ${k_n} ${k_na}
+
+comm_modify vel yes
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+#fix          1 all nve/body
+fix          1 all nvt/body temp 1.2 1.2 0.1
+#fix          1 all npt/body temp 1.2 1.2 0.1 iso 0.002 0.02 1.0
+
+compute      p2 all pressure 1_temp
+
+compute      1 all body/local id 1 2 3
+dump         1 all local 1000 dump.* index c_1[1] c_1[2] c_1[3] c_1[4]
+
+#dump         2 all image 1000 image.*.jpg type type &
+#             zoom 1.5 adiam 1.5 body yes 0 0 view 60 15
+#dump_modify  2 pad 6
+
+thermo_style custom step ke pe etotal c_p2 c_1_temp
+
+thermo       1000
+
+run          ${steps}
+

examples/body/in.pour3d

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+# pouring 3d rounded polyhedron bodies
+
+variable    steps index 6000
+
+units       lj
+boundary    p p fm
+comm_modify vel yes
+
+atom_style  body rounded/polyhedron 1 8
+atom_modify map array
+
+region		reg block 0 50 0 50 0 50 units box
+create_box	4 reg
+
+variable cut_inner  equal 0.5
+variable k_n        equal 100
+variable k_na       equal 5
+variable c_n        equal 20
+variable c_t        equal 5
+variable mu         equal 0
+variable A_ua       equal 1
+
+pair_style body/rounded/polyhedron ${c_n} ${c_t} ${mu} ${A_ua} ${cut_inner}
+pair_coeff * * ${k_n} ${k_na}
+
+neighbor     0.5 bin
+neigh_modify every 1 delay 0 check yes
+
+timestep     0.001
+
+fix          1 all nve/body
+fix          2 all gravity 1.0 spherical 0.0 -180.0
+
+molecule     object molecule.cube molecule.tetra toff 1 &
+             molecule.rod3d toff 2 molecule.point3d toff 3
+
+region       slab block 5 45 5 45 25 35 units box
+fix          ins all pour 500 0 4767548 vol 0.4 10 region slab mol object &
+             molfrac 0.25 0.25 0.25 0.25
+
+fix          4 all wall/body/polyhedron 2000 50 50 zplane 0.0 NULL
+
+#compute      1 all body/local type 1 2 3
+#dump         1 all local 1000 dump.polyhedron index c_1[1] c_1[2] c_1[3] c_1[4]
+#dump         10 all custom 1000 tmp.dump id type x y z radius
+
+thermo_style custom step atoms ke pe etotal press
+
+thermo       1000
+
+#dump	     2 all image 500 image.*.jpg type type &
+#	     zoom 1.5 adiam 1.5 body yes 0 0 view 75 15
+#dump_modify  2 pad 6
+
+run	     ${steps}
+
+

examples/body/molecule.cube

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+# 3d polygon body: cubes, moment of inertia I = m edge^2/ 6
+
+1 atoms
+3 79 body
+
+Coords
+
+1 0 0 0
+
+Types
+
+1 1
+
+Masses
+
+1 1.0
+
+Body Integers
+
+8 12 6
+
+Body Doubles
+
+0.667 0.667 0.667 0 0 0
+1 1 1
+1 -1 1
+-1 -1 1
+-1 1 1
+1 1 -1
+1 -1 -1
+-1 -1 -1
+-1 1 -1
+0 1
+1 2
+2 3
+3 0
+4 5
+5 6
+6 7
+7 4
+0 4
+1 5
+2 6
+3 7
+0 1 2 3
+4 5 6 7
+0 1 5 4
+1 2 6 5
+2 3 7 6
+3 0 4 7
+0.5
+

examples/body/molecule.point3d

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+# 2d polygon body: disks Izz = 1/2 m radius^2
+
+1 atoms
+3 10 body
+
+Coords
+
+1 0 0 0
+
+Types
+
+1 1
+
+Masses
+
+1 1.0
+
+Body Integers
+
+1 0 0
+
+Body Doubles
+
+1 1 1.125 0 0 0
+0 0 0 
+3.0

examples/body/molecule.rod3d

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+# 2d polygon body: rods Izz = 1/12 m length^2
+
+1 atoms
+3 13 body
+
+Coords
+
+1 0 0 0
+
+Types
+
+1 1
+
+Masses
+
+1 1.0
+
+Body Integers
+
+2 1 0
+
+Body Doubles
+
+1 1 1.333 0 0 0
+-2 0 0
+2 0 0
+0.5

examples/body/molecule.tetra

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+# 3d polygon body: regular tetrahedra, moment of inertia I = m edge^2/ 20
+
+1 atoms
+3 47 body
+
+Coords
+
+1 0 0 0
+
+Types
+
+1 1
+
+Masses
+
+1 1.0
+
+Body Integers
+
+4 6 4
+
+Body Doubles
+
+0.4 0.4 0.4 0 0 0
+1 1 1
+1 -1 -1
+-1 1 -1
+-1 -1 1
+0 1
+0 2
+0 3
+1 2
+2 3
+3 1
+0 1 2 -1
+0 1 3 -1
+0 2 3 -1
+1 2 3 -1
+0.5