Editing RDF (section)

== Examples of the most common inputs ==

Finally, I post some examples that contribute (I hope!) to make all the keywords clearer. Enjoy!



''Example 1''

Box of water; 3D-RDF for the oxygens; they are not connected between themselves. 
* [[Image: np1.png|640x480px]]

''Example 2''

Box of water; 3D-RDF for the oxygen 150 with all the other oxygens of H2O; again, the atoms are not connected.
* [[Image: np2.png|640x480px]]

''Example 3''

Box of water; 3D-RDF between 10 random oxygens and all the other oxygens (including this 10). Not connected.
* [[Image: np3.png|640x480px]]

''Example 4''

Box of water; 3D-RDF between 10 random oxygens and all the hydrogens. Please notice that, even if 20 hydrogens are connected to these 10 oxygens, the fact that I'm computing the RDF between 10 O 
and 128 H does not let me specify a ratio, and so YOU HAVE TO PUT CONNECTIVITY = F/f/N/n.
* [[Image: np4.png|640x480px]]

''Example 5''

Box of water; 3D-RDF between 10 random oxygens and their 20 CONNECTED hydrogens. Both groups are disordered and have to be specified separately. Nevertheless, they are connected (conn=T/t/F/f and ratio 1:2).
* [[Image: np5.png|640x480px]]

''Example 6''

Box of hydrogen molecules (100); 3D-RDF; the H atoms are connected to each other.
* [[Image: np6.png|640x480px]]

''Example 7''

Surface of Pt with 17 NH2 molecules and 64 H2O. Please, notice the value of the cut-off radius: it's TOO BIG. The program will complain because it is bigger than the smallest lattice vector of the cell, and in order to avoid the interaction of one atom with its image, it will suggest one value for the cut-off (the smallest lattice vector).
In this case, we are computing 3 BI-DIMENSIONAL RDF, one between O and H (line 13, connected), one between O and O (line 14, disconnected), and one between H and H (line 15, disconnected).
* [[Image: np7.png|640x480px]]

''Example 8''
Most complicated example I could think of.

Surface of Pt with 15 NH3 molecules and 64 H2O. 

Pt atoms: from 1 to 90; N atoms: from 91 to 105; their connected H atoms: from 106 to 150.
H atoms of water: from 151 to 278; O atoms: from 279 to 342.

Again, the cut-off is too big and the program will complain.

We are computing 7 BIDIMENSIONAL RDF (2D-RDF).

Line 13: Classical RDF (H(water) - O). Atoms are connected.

Line 14: RDF between the 15 N of NH3 (labelled Nh because the labels have to be done by 2 characters/numbers) and the 64 oxygens of H2O; atoms are not connected.

Line 15: RDF between the 15 N of NH3 and their corresponding hydrogens. Atoms are connected. Ratio: 1:3.

Line 16: RDF between 10 random Pt atoms and all the N atoms. The Pt atoms have to be specified below: line 17: blank/commented line; line 18: atoms; line 19: blank/commented line.

Line 20: RDF of all the H of the system (45 from NH3 and 128 from H2O).

Line 21: RDF between 5 random N atoms and their linked 15 H atoms. Both groups are made up by not consecutive labels, so you have to specify each of them (line 23 and 25). Line 26: blank line.

Line 27: RDF between 70 consecutive Pt atoms and all the hydrogens of the system.
* [[Image: np8.png|640x480px]]