Unable to Add Phase to the GSAS project

[rsvoguri123]

I have written the below script

import sys, os
sys.path.insert(0,'c:/gsas/gsas-ii/gsasii/')
import GSASIIscriptable as g2sc
datadir = 'C:/users/rajvog/documents/Python/GSASSDPD/'
pathwrap=lambda fil: os.path.join(datadir,fil)
gpx=g2sc.G2Project(newgpx = pathwrap('FB.gpx'))
phase0=gpx.add_phase(pathwrap('sample.cif'))

But I am getting the below error. please help

G2ImportException Traceback (most recent call last)
Cell In[97], line 8
6 pathwrap=lambda fil: os.path.join(datadir,fil)
7 gpx=g2sc.G2Project(newgpx = pathwrap('FB.gpx'))
----> 8 phase0=gpx.add_phase(pathwrap('sample.cif'))

File C:\GSAS/GSAS-II/GSASII\GSASIIscriptable.py:1287, in G2Project.add_phase(self, phasefile, phasename, histograms, fmthint, mag, spacegroup, cell)
1285 raise G2ImportException(f'File {phasefile} does not exist')
1286 # TODO: handle multiple phases in a file
-> 1287 phasereaders = import_generic(phasefile, Readers['Phase'], fmthint=fmthint)
1288 phasereader = phasereaders[0]
1290 if phasereader.MPhase and mag:

File C:\GSAS/GSAS-II/GSASII\GSASIIscriptable.py:407, in import_generic(filename, readerlist, fmthint, bank)
405 primaryReaders.append(reader)
406 if not secondaryReaders and not primaryReaders:
--> 407 raise G2ImportException("Could not read file: ", filename)
409 with open(filename, 'r'):
410 rd_list = []

G2ImportException: ('Could not read file: ', 'C:\users\rajvog\documents\Python\GSASSDPD\sample.cif')

[briantoby]

Have you run your CIF through a syntax checker? The PyCIFRW package that GSAS-II uses is very particular in requiring valid CIF syntax.

[briantoby]

anything new here?

[GKNB]

Hello, dev team. I have the same issue.

I am running legacy code, which we last used about 14 months ago. This time, the only difference is that we installed the latest gsas-II, since the old python environment on Polaris machine (at ALCF) is not supported anymore.

We get the following error:

Traceback (most recent call last):
File "/lus/eagle/projects/RECUP/twang/exalearn_stage2/executable/simulation_sample.py", line 293, in
main()
File "/lus/eagle/projects/RECUP/twang/exalearn_stage2/executable/simulation_sample.py", line 287, in main
_sim_impl(rank, size, "cubic", conf_name_cubic, sample_cubic)
File "/lus/eagle/projects/RECUP/twang/exalearn_stage2/executable/simulation_sample.py", line 206, in _sim_impl
phase = gpx.add_phase(cif,phasename=name,fmthint='CIF')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lus/eagle/projects/RECUP/twang/g2full_04282025/GSAS-II/GSASII/GSASIIscriptable.py", line 1350, in add_phase
phasereaders = import_generic(phasefile, Readers['Phase'],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/lus/eagle/projects/RECUP/twang/g2full_04282025/GSAS-II/GSASII/GSASIIscriptable.py", line 446, in import_generic
raise G2ImportException(f"Could not read file: {filename}")
GSASII.GSASIIscriptable.G2ImportException: Could not read file: /lus/eagle/projects/RECUP/twang/exalearn_stage2/cif_file_in/1001460.cif

Since the student who gave us the cif file has graduated, does anyone know how to convert an old cif file to one that is consistent with the latest GSAS-II package? Thanks! The old cif file is attached (I rename it to 1001460.txt to support uploading), and we actually have two more of such kind of cif files.

1001460.txt

======================================
Updates:

I notice that you mentioned PyCIFRW package. I just used pip to install that, and did the following:

python -c "from CifFile import ReadCif; cf = ReadCif('/lus/eagle/projects/RECUP/twang/exalearn_stage2/cif_file_in/1001460.cif'); print(cf)"

I did not get any error, and got quite reasonable results, saved in output.txt.

output.txt

[rsvoguri123]

Hi All,
This issue got solved. The above mentioned was successfully ran.
The root cause was IDE. when I am using Jupyter, then only I got above mentioned error. If I run above code in python termimnal of GSAS, then it works.

Still if you want to use Jupyter, the above code works by using 'subprocess'

[briantoby]

I really don't understand why this code would not work in Jupyter. I don't use that much. If you want to reopen and supply more info, I'll debug. If you are good with your work-around, that is fine too.

[briantoby]

Hello, dev team. I have the same issue.

I am running legacy code, which we last used about 14 months ago. This time, the only difference is that we installed the latest gsas-II, since the old python environment on Polaris machine (at ALCF) is not supported anymore.

The problem here is that in the older software the PyCifRW package was included with our source code ("vendored" as I have learned this is called) because it was not easily available back when we adopted it. We switched to using it as a package in the most recent major update, as the docs do point out. If you don't have the package installed with the GUI you don't get the CIF reader as an option in the menu but scripting bypasses the menu. I have now added an error message for scripting if anyone else tries this.

Thanks also for letting us know that GSAS-II is used on the ALCF, BTW. Might help with some brownie points somewhere, someday...

[GKNB]

Hello, dev team. I have the same issue.
I am running legacy code, which we last used about 14 months ago. This time, the only difference is that we installed the latest gsas-II, since the old python environment on Polaris machine (at ALCF) is not supported anymore.

The problem here is that in the older software the PyCifRW package was included with our source code ("vendored" as I have learned this is called) because it was not easily available back when we adopted it. We switched to using it as a package in the most recent major update, as the docs do point out. If you don't have the package installed with the GUI you don't get the CIF reader as an option in the menu but scripting bypasses the menu. I have now added an error message for scripting if anyone else tries this.

Thanks also for letting us know that GSAS-II is used on the ALCF, BTW. Might help with some brownie points somewhere, someday...

Thanks for letting me know. We are currently not using GUI but only work with terminal. We still get similar issue and I just submit a new issue https://github.com/AdvancedPhotonSource/GSAS-II/issues/172 to explain what we have been going through. Thanks!

[rsvoguri123]

I really don't understand why this code would not work in Jupyter. I don't use that much. If you want to reopen and supply more info, I'll debug. If you are good with your work-around, that is fine too.

Thanks for interesting discussion and support. I would like to go ahead with this solution for the time being. I will update if I find anymore info.

[briantoby]

@rsvoguri123 I am wondering if your issue is as follows: when you run code in a Jupyter notebook, you are using the Python interpreter that was used to start the Jupyter server. That Python interpreter must have all the packages that GSAS-II needs and must match a set of binary files w/r to Python & numpy versions. Previously PyCifRW was not needed because the code for that was "vendored" (provided inside GSAS-II, but now that is expected to be installed. But when you run as a subprocess, you are likely using a different Python interpreter that does match the GSAS-II installation and that does provide PyCifRW.

[rsvoguri123]

@rsvoguri123 I am wondering if your issue is as follows: when you run code in a Jupyter notebook, you are using the Python interpreter that was used to start the Jupyter server. That Python interpreter must have all the packages that GSAS-II needs and must match a set of binary files w/r to Python & numpy versions. Previously PyCifRW was not needed because the code for that was "vendored" (provided inside GSAS-II, but now that is expected to be installed. But when you run as a subprocess, you are likely using a different Python interpreter that does match the GSAS-II installation and that does provide PyCifRW.

Absolutely yes!

[briantoby]

I can see that a better error message would be helpful. This is now what happens with scripting when PyCifRW is not available:

(py311) conda311 main % python -c "import G2script as G2sc; gpx=G2sc.G2Project(newgpx='/tmp/x.gpx'); gpx.add_phase('/Users/toby/shared/BC_corrected.cif',fmthint='cif')"
setting up GSASIIscriptable from /Users/toby/G2/main/GSASII
6 values read from /Users/toby/.GSASII/config.ini
GSAS-II binary directory: /Users/toby/.GSASII/GSASII-bin/mac_arm_p3.11_n1.26

Reading of file '/Users/toby/shared/BC_corrected.cif' failed.

No readers matched hint 'cif'

Not all importers are available due to uninstalled Python packages.
The following importer(s) are not available:
	CIF powder importer, CIF Phase importer, CIF HKLF importer
because the following optional Python package(s) are not installed:
	pycifrw

Available importers:
	GSAS Experiment (.EXP file) import
	JANA2006 phase import
	Original Protein Data Bank (.pdb file) import
	ICDD PDF Card (.str file) import
	GSAS-II project (.gpx file) import
	SHELX input (*.ins, *.res) file import
	RMCProfile structure (*.rmc6f) file import
	XYZ Cartesian coordinate file import
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/toby/G2/main/GSASII/GSASIIscriptable.py", line 1373, in add_phase
    phasereaders = import_generic(phasefile, Readers['Phase'],
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/toby/G2/main/GSASII/GSASIIscriptable.py", line 469, in import_generic
    raise G2ImportException(f"Could not read file: {filename}")
GSASII.GSASIIscriptable.G2ImportException: Could not read file: /Users/toby/shared/BC_corrected.cif