Grid data plt file format
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 grid data files are the main enginees for ploting isocontour surfaces. The *.plt files can either be generated directly by various programs inside the gOpenMol package or be imported from other programs.
Programs inside gOpenMol generating *.plt grid data files:
- The probsurf program generates the grid data for plotting Connolly type of surfaces.
- The vss program generates the grid data for plotting electrostatic potentials.
To assist in moving the binary *.plt files between different hardware platforms the pltfile program is included. Using the program it is possible to format a binary grid file and move it to an other platform and unformat the file again. The program can of course also be used interface the grid data from other programs with gOpenMol.
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):
1. Loop in the z direction 2. Loop in the y direction 3. Loop in the x direction
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:
#1: Integer, Integer. Rank and type of surface (rank is always = 3)
#2: Integer, Integer, Integer. Zdim, Ydim, Xdim (number of points in the z,y,x directions)
#3: Float, Float, Float, Float, Float, Float. Zmin, Zmax, Ymin, Ymax, Xmin,Xmax (min and max values)
#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
A file in this format can then be converted into binary with the pltfile program.
For an example of what a formatted *.plt file can look like please look above. If you are a programmer please look at the included utility programs for the code for doing the reading and writing of *.plt files