General programs
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F77 General Programs
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| RADIAL DISTRIBUTION FUNCTION | (by Luca)
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You can find the definition of the Radial Distribution Function (RDF) in the following:
Name: x.RDF
Launching: x.RDF > output (in output some details of the calculation are reported)
Input file: geom.dat, param.dat
Output file: Global.dat, fort.X (X = 1, 2, ..., N; see below)
Used subprograms: none
- General Description
x.RDF takes a system described in geom.dat and creates other 26 replica of the system adding or subtracting the lattice vectors.
The initial system is at the centre of this 3x3x3 supersystem.
It then computes the distances between the atoms in the initial system and the atoms in all the 26 outer cells, and inside the initial cell as well.
It then computes the RDF and write it in fort.X (X = 1, N).
- Description of the Input files
In geom.dat there are the coordinates and label of all the atoms of my system in XYZ. Moreover, all atoms have to be written "in the VASP way", i.e. first all the atoms of type A, then all the atoms of type B and so on. An example of geom.dat for a box of 96 water molecules: File:Ex geomRDF.tgz
In param.dat, many different parameters, specifying the cell size and what kind of RDF you want, are specified. Here I attach an example: File:Ex paramRDF.tgz and in the page you can find all the explanation you need. It refers to 96 molecules of water.
Atoms Categ Types LP Increment 288 3 2 14.2058 0.05 Lattice Vectors: 1 0 0 0 1 0 0 0 1 Species and number of atoms in each of them: O H 96, 192 1, 96, 1, 96 1, 96, 97, 288 97, 288, 97, 288
In the case above, we have 288 atoms (96 water molecules). Types is the number of different atoms in my system (2: oxygen and hydrogen). Categ is the number of different RDF I want to compute; in the case of H2O, the maximum number of categories I can compute is 3: RDF(Oxygen-Oxygen), or RDF(Oxygen-Hydrogen) or RDF(Hydrogen-Hydrogen). You can specify a smaller number (for example, 1) and define which RDF you want (see below). LP: lattice parameter; Increment: incremental step of search In line 11, it's reported how many atoms of each species there are in the initial system (96 O and 192 H, in this case).
Finally, from line 13, the categories for the RDF are specified through the first and the last atom of the category. For example, line 13 refers to the atoms that specify the RDF(Oxygen-Oxygen): the first group (1,96) are all the oxygens, and the second group (1,96) are all oxygens, again. In line 14, the category for RDF(Oxygen-Hydrogen) is specified, and in line 15 the RDF(Hydrogen-Hydrogen).
INSTALLATION STEPS
1) First of all, download the program:
uncompress it and compile it: f77 Cell.f -o x.Cell. Place it in a directory of your choice (for simplicity, named directory A).
2) Download the script:
File:Ngeom.tgz
and uncompress it.
3) CHANGE IN LINE 14 OF ngeom.sh path=/home/lbellarosa/src/complex/Cell with the path of where you put your directory A.
4) Now you can run the script typing:
ngeom.sh OUTCAR