add an example for RDF and ADF computation with water molecules

examples/rdf-adf/in.spce

@@ -0,0 +1,43 @@
+units		real	
+atom_style	full
+
+read_data	data.spce
+
+pair_style      lj/cut/coul/long 12.0 12.0
+pair_coeff      * * 0.0     1.0
+pair_coeff      1 1 0.15535 3.166
+kspace_style	pppm 1.0e-6
+
+bond_style	harmonic
+angle_style	harmonic
+dihedral_style	none
+improper_style	none
+
+bond_coeff	1 1000.00 1.000
+angle_coeff	1 100.0 109.47
+
+# need to set bond/angle inclusion to > 0.0
+# so that intramolecular pairs are included in neighbor lists (required for second ADF)
+special_bonds   lj/coul 1.0e-100 1.0e-100 1.0
+
+neighbor        2.0 bin
+timestep        2.0
+neigh_modify    every 1 delay 2 check yes
+
+fix		1 all shake 0.0001 20 0 b 1 a 1
+fix		2 all nvt temp 300.0 300.0 100.0
+
+velocity all create 300.0 6244325
+
+thermo 100
+run 500
+
+reset_timestep 0
+
+compute gofr all rdf 100  1 1  2 2  1 2  # O-O, H-H, O-H
+compute gofa all adf  45  1 1 1  2.0 3.5  2.0 3.5 &
+                          1 2 1  0.0 1.2  1.5 2.5
+fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
+fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
+
+run 1000