plt files from nwchem


Just Got Here
Hi,

I'm trying to calculate an ESP surface using NWChem. I am having a hard time reading the plt file written by task esp. I had assumed that this is a gOpenMol format file, however neither gOpenMol, VMD, or molekel will read this file.

The file is human readable, with this format:

     3      3
22 20 25
-0.42697E+01 0.62303E+01-0.38831E+01 0.56169E+01-0.51360E+01 0.68640E+01
 0.340044852884E-02  0.381225316441E-02
0.426078263990E-02 0.473955239880E-02
0.523648838835E-02 0.573289391650E-02
0.620373486530E-02 0.661995450468E-02
0.695262211765E-02 0.717749921059E-02
0.727827952570E-02 0.724789075773E-02
0.708865782040E-02 0.681220609970E-02
0.643882110382E-02 0.599525668875E-02
0.551078472812E-02 0.501272467896E-02
0.452314555797E-02 0.405757155766E-02
0.362538731672E-02 0.323111953778E-02
0.287588273479E-02 0.255861269983E-02
0.227698113735E-02
0.368739857524E-02 0.416211549822E-02
0.468598380889E-02 0.525313417182E-02
0.585042979465E-02 0.645540081392E-02
0.703595979636E-02 0.755342356919E-02
0.796884563512E-02 0.825011533849E-02

gOpenMol plt files are machine readable, so I have to assume that this is actually a different file format. Is there a program that is able to read NWChem plt files?

Thanks,
Chris

Forum Vet
Need to use Pltfile to convert to plt binary format
One step is needed to convert the human readable to machine readable,
that is to use the gOpenMol Pltfile converter.
In practice, you would need to follow the following steps

  1. rename filename.plt to filename.plt.txt
  2. start gOpenMol
  3. open the Run menu
  4. select the Pltfile (conversion) utility
  5. choose filename.plt.txt as input file name and filename.plt as the output file name
  6. select Formatted ==> Unformatted
  7. read the filename.xyz file by going to: File -> Import -> Coord -> Browse -> Apply; you should see your system in the main graphical window as connections between atoms
  8. plot the density by going to Plot -> Contour
  9. first click Browse and read the gOpenMol filename.plt file:
  10. then click Import
  11. define desired Contour level
  12. click Apply

More details at: http://www.cmmp.ucl.ac.uk/~lev/codes/lev00/node71.html

Clicked A Few Times
gOpenmol Does not work here
Hello,

When I follow these instructions, gOpenmol gives an error saying that it can't read the contour:

"can't read "contour": no such variable
    while executing
"show contour mapping $contour"
    (procedure "Apply" line 12)
    invoked from within
"Apply .gomcontour"
    (in namespace inscope "::gom::gui::Contour" script line 1)
    invoked from within
"::namespace inscope ::gom::gui::Contour {Apply .gomcontour}"
    ("uplevel" body line 1)
    invoked from within
"uplevel \#0 $cmd"
    (procedure "Button::_release" line 19)
    invoked from within
"Button::_release .gomcontour.buttons.f.apply"
    (command bound to event)"



Is there another program that can read NWChem plt files? I have tried ECCE, Avogadro, Molekel, Molden, gOpenmol, and Jmol and all have failed.

Forum Vet
gOpenmol is the only option for ESP files
Could you please post the output of the pltfile utility?

Thanks, Edo

PS I have made the gOpenmol instructions a bit more clear, please let me know if it helps

Clicked A Few Times
Quote:username
gOpenmol is the only option for ESP files
Could you please post the output of the pltfile utility?

Thanks, Edo

PS I have made the gOpenmol instructions a bit more clear, please let me know if it helps


Thanks very much Edoapra! The extra clarification made all of the difference.

Is there any way I could load pre-selected color schemes? It would greatly simplify what I have to do.

Thanks so much for your quick reply! I really appreciate it.

-Dave

Clicked A Few Times
Loading ESP Maps
Hello,

unfortunately it looks like mapping the electrostatic potential is not possible with the current version of gOpenmol.

I am attempting to follow instructions from http://www.lct.jussieu.fr/manuels/Gaussian98/show/epotgombeg001.htm

and http://faculty.ycp.edu/~jforesma/educ/visual/ESP/html/ESPgOpen.htm

but both of these reference a mapping function which is not possible in the gOpenmol which I downloaded a few days ago. The current "Contour Control" menu no longer has the mapping function, which makes mapping the electrostatic potential extremely difficult.

Is there another way I could get the version of gOpenmol that these tutorials used?

What exactly was gOpenmol superseded by? If it is the only application that can read NWChem electrostatic potential, is it really obsolete?

much appreciated!


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