genXrnPattern binary location/installation?

fmentink · November 5, 2025, 2:19pm

Hi there,
I wanted to use the PXrd function generation under Crystal/Plot Theoretical …
As I attempted to use it, the binary was missing. I tried to look for the information as to where to place it, but so far I am unsuccessful.
Since I am using Linux I assumed it may need to be located in .local/share/OpenChemistry/Avogadro but that did not seem to work.
Would you mind explaining in the documentation how we could use it?
Thanks.

(System Ubuntu 24.04, version 1.102.1).

ghutchis · November 5, 2025, 3:15pm

It’s looking in the same directory as the main binary. It will also check the GENXRDPATTERN_EXECUTABLE environment variable too.

It should check the whole PATH though:

github.com/OpenChemistry/avogadrolibs

avogadro/qtplugins/plotxrd/plotxrd.cpp

4b5eea466


      
            return true;
          }
          
          bool PlotXrd::executeGenXrdPattern(const QStringList& args,
                                             const QByteArray& input, QByteArray& output,
                                             QString& err)
          {
            QString program;
            // If the GENXRDPATTERN_EXECUTABLE environment variable is set, then
            // use that
            QByteArray xrdExec = qgetenv("GENXRDPATTERN_EXECUTABLE");
            if (!xrdExec.isEmpty()) {
              program = xrdExec;
            } else {
          // Otherwise, search in the current directory, and then ../bin
          #ifdef _WIN32
              QString executable = "genXrdPattern.exe";
          #else
              QString executable = "genXrdPattern";
          #endif
              QString path = QCoreApplication::applicationDirPath();

On the roadmap is to clean this up a bit so other programs can supply an XRD pattern (e.g., a Python plugin using pymatgen)

ghutchis · November 5, 2025, 4:45pm

This pull request should also check PATH for the genXrdPattern binary.

github.com/OpenChemistry/avogadrolibs

Enable the XRD display from other programs (just return a spectra)

master ← ghutchis:fix-xrd-plot

opened 04:13PM - 05 Nov 25 UTC

ghutchis

+65 -32

Also enable genXrd binary download on Mac and Windows Developer Certificate o…f Origin Version 1.1 Copyright (C) 2004, 2006 The Linux Foundation and its contributors. 1 Letterman Drive Suite D4700 San Francisco, CA, 94129 Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Developer's Certificate of Origin 1.1 By making a contribution to this project, I certify that: (a) The contribution was created in whole or in part by me and I have the right to submit it under the open source license indicated in the file; or (b) The contribution is based upon previous work that, to the best of my knowledge, is covered under an appropriate open source license and I have the right under that license to submit that work with modifications, whether created in whole or in part by me, under the same open source license (unless I am permitted to submit under a different license), as indicated in the file; or (c) The contribution was provided directly to me by some other person who certified (a), (b) or (c) and I have not modified it. (d) I understand and agree that this project and the contribution are public and that a record of the contribution (including all personal information I submit with it, including my sign-off) is maintained indefinitely and may be redistributed consistent with this project or the open source license(s) involved.

fmentink · November 5, 2025, 8:32pm

Thank you for all the update.
Just for the sake of completeness, I tried having it in the same folder but this not working (executable name is correct and I can run it from a terminal)

ghutchis · November 5, 2025, 9:01pm

What’s the error message when you try to use it in Avogadro?

It hasn’t been extensively tested, so it’s possible that it’s failing.

fmentink · November 5, 2025, 9:23pm

same error, the executable (located in /usr/bin/ next to the avogadro one) could not be found. (even of course after restarting the avogadro, and even running it in a terminal for which the last lines are
Open Babel formats ready: 145
Setting default format to cjson.
current version is newer than latest release
“Error: could not find genXrdPattern executable!”
Error in generateXrdPattern : “Error: could not find genXrdPattern executable!”)

ghutchis · November 5, 2025, 9:28pm

Try the continual build, which should check PATH for the program:

Looks like it should be pretty easy to build a Python script with pyobjcryst as an alternative to the binary. (In other words, I’ll see if I can port this to a Python script.)

Alternatively, I’ll see if I can fork Patrick’s repo and add in some options (e.g., XRD vs. neutron diffraction)