Editing RDF (section)

== param.dat: detailed examination ==

I will examine this file, row by row (excluding the blank lines, important only for the program ''x.RDF'').

 ''1st row'': commented. This is not read by ''x.RDF'', but it is important for the user because specifies which parameters we want to use for the RDF calculation.

 ''2nd row'' 
             '''nCat''': number of categories I want to compute. This is basically the number of different RDF I want to calculate. For example, if I have a dynamics with water, I can be interested in
                   the calculation of RDF between the oxygens, and between oxygens and hydrogens: in this case, nCat = 2.
             '''nTyp''': number of different species of atoms. For example, if I have specified ''Pt H O C H O'' in row 9 (see below), nTyp = 6.
             '''dR''': step of the grid (in angstrom) on which I compute the RDF. If, by definition, RDF is the normalized number of atoms between ''R'' and ''R+dR'', this dR is the theoretical ''dR''.
             '''dZ''': only used for 2D-RDF. Specified as an initial guess for the distribution of layers. It tells roughly the height of each layer on which compute the 2D-RDF.
             '''ncyc''': number of geometries in the file ''Movie.xyz''. If you have just one snapshot, put 1.
             '''DN''': it tells ''x.RDF'' after how many snapshot you want to compute a new RDF. The initial RDF is always computed. For example, if you have a dynamics with 150 fs, you could ask the 
                 program to print the RDF every 30 fs (DN = 30). In this case, you would have 6 output files: (1) for the initial RDF, (2) at 30 fs, (3) at 60 fs, (4) at 90 fs, (5) at 120 fs, 
                 and (6) at 150 fs.
             '''rcut''': cut-off radius (in angstrom) for the RDF. Basically, I will not compute the RDF of one atom with any other more than rcut angstrom away.
             '''dimensionality''': if specifies if I want a BI-dimensional (dimensionality=2) or TRI-dimensional (dimensionality=3) RDF.
             '''Fifth?''': logical flag (Y/y/T/t for "yes", any other label for "no")for the computation of the 5th closest member of the second group to the elements of the first group. Sometimes, this 
                      weird kind of RDF are required to double check the state of the solvent.

 ''4th row'': commented. This is not read by ''x.RDF'', but it is important for the user because specifies which parameters we want to use for the RDF calculation.

 ''5th-10th rows'': classical POSCAR/CONTCAR lines. Lattice constant (5th), lattice vectors (6th-8th), species (9th) and how many atoms per species (10th).

 ''12th row'': commented. This is not read by ''x.RDF'', but it is important for the user because specifies which parameters we want to use for the RDF calculation.

 ''13th-xxth row'': in this line, I specify the two groups between which I want to compute the RDF. Please, notice that the number of lines depends on the variable '''nCat''' (line 2). For example, 
                in the case of water, if I want to compute RDF between oxygens (RDF(OO)), between oxygens and hydrogens (RDF(OH)), and between hydrogens (RDF(HH)), I have to specify '''nCat''' = 3 in
                the 2nd line, and you will have a line 13 where you specify the two groups of oxygen, a line 14 where you specify the group of oxygen and the group of hydrogen, and a line 15 
                where you specify a group of hydrogens and the group of hydrogens.
                The first 5 columns belong to the first group of atoms. It specifies their label (used in the name of the output!!! It has to be 2 letters, only "H" is not accepted), the number of atoms '''N''' 
                that belong to that group, if they are '''consecutive''', and the first ('''i10''') and the last ('''i1f''') atom of the group. If the atoms are consecutive (Y/y/T/t), the program automatically 
                puts in this group each atom from '''i10''' and '''i1f'''. This is done for practical reasons: in the example of the figure above, I should have put all the integer number for the atoms from 1 to 128, creating
                a long boring unreadable input!
                Columns from 6 to 10 do the same, but for group 2. 
                The last two columns (11 and 12)  specify if Group 1 and 2 '''are connected'''. If they are (conn=Y/y/T/t), the '''ratio''' of atoms is read in column 12. 
                The program itself will compute the connectivity between the two groups, and it will print it in an output file called '''connectivity.dat'''.
                In the case of methane, you could have 100 H atoms and 25 C atoms; in this case, the ratio is 4:1.