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Spatial distribution functions: sdf.f

This utility computes spatial distribution functions and creates a file which can be visualized using gOpenMol package (http://.www.csc.fi/gopenmol/).

Compilation:

f77 -O3 -o sdf sdf.f tranal_base.f

The input into sdf utility consists of a NAMELIST section SDFIN and subsequent lines defining sites which will be displayed for visualization of the molecule around which SDF is calculated

The NAMELIST section

 $SDFIN
 parameter=value(s),
 ...
 $END

contains the following parameters

After the NAMELIST section, there is a section in the input file which describes which atoms are displayed in the center of SDF as a structure defining the local basis. The first line of this section may be either an integer number or the word ``ALL''.

If an integer number is specified, it defines the number of atoms displayed in the central structure. Then this number of lines follows, each line per atom, each consisting of NOI + 1 values.

The first position in each line is one of numbers 1,2,3. Positions from 2 to NOI + 1 define sites which are to be displayed, for each of NOI equivalent local coordinate system.

The number in the first position of each line means the following:

1 - coordinates of this atom are averaged independently of the next atom

2 - average coordinates of this atom are calculated taking into account the next atom also (for example, if these are two hydrogens of water)

3 - average coordinates of this atom are calculated taking into account the next two atoms (for instance, treating hydrogens in CH3 group)

Example of these lines for water:

1 1
2 2 
1 3

and for methanol (see the order of atoms in CH3OH.mmol file)

1  1
1  2
1  3
3  4
2  5
1  6

If parameter ALL is specified in the first (and the only) line of this section, then all the atoms of the molecule defining the local basis are displayed, without any special treatment of averaging coordinates of equivalent atoms.

Note about Gopenmol From 2011, there is no longer support for gOpenMol package, though the source and binary executable are still available from the developers.


next up previous contents
Next: Distribution of torsion angles: Up: Tranal utility Previous: Radial distribution functions: rdf.f   Contents
Alexander Lyubartsev 2015-02-06