|
|
| (10 intermediate revisions by 3 users not shown) |
| Line 2: |
Line 2: |
|
| |
|
|
| |
|
| == F77 General Programs == | | === Fortran77 === |
|
| |
|
| +------------------------------+
| | * [[Radial Distribution Function]] |
| | RADIAL DISTRIBUTION FUNCTION | ''(by Luca)''
| |
| +------------------------------+
| |
| | |
| You can find the definition of the Radial Distribution Function (RDF) in the following:
| |
|
| |
| http://rings-code.sourceforge.net/index.php?option=com_content&view=article&id=50:rdf&catid=36:phy-chi&Itemid=58
| |
| | |
| | |
| | |
| '''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: [[Image: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:
| |
| [[Image: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:
| |
| | |
| [[Image: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
| |