`gOpenMol` — the gOpenMol plt format

The module provides a simple implementation of a reader for gOpenMol plt files. Plt files are binary files. The Plt reader tries to guess the endianess of the file, but this can fail (with a TypeError); you are on your own in this case.

Only the reader is implemented. If you want to write gridded data use a format that is more standard, such as OpenDX (see OpenDX).

Background

gOpenMol http://www.csc.fi/english/pages/g0penMol plt format.

Used to be documented at http://www.csc.fi/gopenmol/developers/plt_format.phtml but currently this is only accessible through the internet archive at http://web.archive.org/web/20061011125817/http://www.csc.fi/gopenmol/developers/plt_format.phtml

Grid data plt file format

Copyright CSC, 2005. Last modified: September 23, 2003 09:18:50

Plot file (plt) format The plot files are regular 3D grid files for plotting of molecular orbitals, electron densities or other molecular properties. The plot files are produced by several programs. It is also possible to format/unformat plot files using the pltfile program in the utility directory. It is also possible to produce plot files with external (own) programs. Produce first a formatted text file and use then the pltfile program to unformat the file for gOpenMol. The format for the plot files are very simple and a description of the format can be found elsewhere in this manual. gOpenMol can read binary plot files from different hardware platforms independent of the system type (little or big endian machines).

Format of the binary `*.plt` file

The *.plt file binary and formatted file formats are very simple but please observe that unformatted files written with a FORTRAN program are not pure binary files because there are file records between the values while pure binary files do not have any records between the values. gOpenMol should be able to figure out if the file is pure binary or FORTRAN unformatted but it is not very well tested.

Binary `*.plt` (grid) file format

Record number and meaning:

#1: Integer, rank value must always be = 3
#2: Integer, possible values are 1 ... 50. This value is not used but
it can be used to define the type of surface!
Values used (you can use your own value between 1... 50):

1:   VSS surface
2:   Orbital/density surface
3:   Probe surface
200: Gaussian 94/98
201: Jaguar
202: Gamess
203: AutoDock
204: Delphi/Insight
205: Grid

Value 100 is reserved for grid data coming from OpenMol!

#3: Integer, number of points in z direction
#4: Integer, number of points in y direction
#5: Integer, number of points in x direction
#6: Float, zmin value
#7: Float, zmax value
#8: Float, ymin value
#9: Float, ymax value
#10: Float, xmin value
#11: Float, xmax value
#12 ... Float, grid data values running (x is inner loop, then y and last z):

Loop in the z direction
Loop in the y direction
Loop in the x direction

Example:

nx=2  ny=1  nz=3

0,0,0   1,0,0     y=0, z=0
0,0,1   1,0,0     y=0, z=1
0,0,2   1,0,2     y=0, z=2

The formatted (the first few lines) file can look like:

3 2
65 65 65
-3.300000e+001 3.200000e+001 -3.300000e+001 3.200000e+001 -3.300000e+001 3.200000e+001
-1.625609e+001 -1.644741e+001 -1.663923e+001 -1.683115e+001 -1.702274e+001 -1.721340e+001
-1.740280e+001 -1.759018e+001 -1.777478e+001 -1.795639e+001 -1.813387e+001 -1.830635e+001
...

Formatted `*.plt` (grid) file format

Line numbers and variables on the line:

line #1: Integer, Integer. Rank and type of surface (rank is always = 3)
line #2: Integer, Integer, Integer. Zdim, Ydim, Xdim (number of points in the z,y,x directions)
line #3: Float, Float, Float, Float, Float, Float. Zmin, Zmax, Ymin, Ymax, Xmin,Xmax (min and max values)
line #4: ... Float. Grid data values running (x is inner loop, then y and last z) with one or several values per line:

 1. Loop in the z direction
 2. Loop in the y direction
 3. Loop in the x direction

Classes

class gridData.gOpenMol.Plt(filename=None)[source]

A class to represent a gOpenMol plt file.

Only reading is implemented; either supply a filename to the constructor

>>> G = Plt(filename)

or load the file with the read method

>>> G = Plt()
>>> G.read(filename)

The data is held in GOpenMol.array and all header information is in the dict GOpenMol.header.

Plt.shape: D-tuplet describing size in each dimension
Plt.origin: coordinates of the centre of the grid cell with index 0,0,…,0
Plt.delta: DxD array describing the deltas

property edges

Edges of the grid cells, origin at centre of 0,0,..,0 grid cell.

Only works for regular, orthonormal grids.

histogramdd()[source]: Return array data as (edges,grid), i.e. a numpy nD histogram.

read(filename)[source]: Populate the instance from the plt file filename.

gOpenMol — the gOpenMol plt format