pdCIFplotter error

masanao

Dear all,

I have started using pdCIFplotter (windows stand-alone version).
However, the software notified the following error and cannot open the .cif file.

"Star Format error: Attempt to insert duplicate item name _geom_bond_atom_site_label_1"
Traceback (most recent call last):
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 936, in gui
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 329, in read_cif
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\parse_cif.py", line 472, in init
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\CifFile_module.py", line 3108, in ReadCif
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 2251, in ReadStar
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 162, in input
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 182, in dblock
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 194, in dataseq
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 203, in data
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 77, in makeloop
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 601, in AddItem
CifFile.StarFile.StarError:
Star Format error: Attempt to insert duplicate item name _geom_bond_atom_site_label_1

The following link is the .cif file I created but cannot open.
https://www.dropbox.com/s/oujuigx6j8fnp2l/Y2O3_trial.cif?dl=0

Could you please give me advice how to solve this problem?

Thank you.

Kind regards,

rowlesmr

Hi masanao

The error is "Star Format error: Attempt to insert duplicate item name "geom_bond_atom_site_label_1". This means that you have defined the data item "geom_bond_atom_site_label_1" more than once in a data block.

From a quick inspection, "_geom_bond_atom_site_label_1" appears on lines 85 and 186, which are both in the first data block.

Are you able to post your input file so I can see how this came about?

Thanks

Matthew

masanao

Dear Matthew,

Thank you so much for your reply.

The following is a link to my .inp file.
https://www.dropbox.com/s/6p8tp9ah9q8aty5/Y2O3_Rietveld_template_Rigaku_v3.inp?dl=0
Please check.

Thank you so much for your help.

Kind regards,

Masanao

rowlesmr

I've had a little fiddle, and all I can think of is that the cif.inc file has somehow been altered.

Try using my current version: https://pastebin.com/fGgZfETm

masanao

Dear Matthew,

Thank you so much for your info.

I've downloaded the text file.
Sorry, I'm rather a beginner.
How should I use this .txt file?

Should I replace the content of cif.inc file to the provided text file?

Kind regards,

Masanao

masanao

Dear Matthew,

I've replaced my cif.inc file to the file you provided.

However, I've got the same errors.

There has been an error in reading the CIF file. Please check that it is of a valid format before continuing. Some information may be apparant from the text below:

Star Format error: Attempt to insert duplicate item name _geom_bond_atom_site_label_1

Traceback (most recent call last):
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 936, in gui
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 329, in read_cif
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\parse_cif.py", line 472, in init
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\CifFile_module.py", line 3108, in ReadCif
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 2251, in ReadStar
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 162, in input
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 182, in dblock
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 194, in dataseq
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 203, in data
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 77, in makeloop
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 601, in AddItem
CifFile.StarFile.StarError:

Star Format error: Attempt to insert duplicate item name _geom_bond_atom_site_label_1

The created .cif file and .inp file as well as .xy file are as follows.

https://www.dropbox.com/s/l3666kibve3tnw4/Y2O3_trial_2.cif?dl=0
https://www.dropbox.com/s/fjq1z2bl9hqadvt/Y2O3_Rietveld_template_Rigaku_v4.inp?dl=0
https://www.dropbox.com/s/qzuqlva6yxxydcn/Y2O3_1.xy?dl=0

Thank you for your help.

Kind regards,

Masanao

rowlesmr

Got it.

I think the line Out_CIF_Bonds_Angles(aac.cif) is also writing to to your Y2O3_trial.cif file.

If I comment out that line, it works.

Which version of TOPAS are you using? It may be a bug.

masanao

Hi Matthew,

I'm using TOPAS Academic V7.
In my environment, it still does not work even if I delete the line...
Apparently, there is a lot of duplication in the files.
when I delete all the duplications, pdCIFplotter can read .cif files.

By the way, when specimens have several crystal structures, I've got the following file.
But I cannot read it.
What is wrong with the .cif file?

https://www.dropbox.com/s/m1rqafbvv4z1w2c/control_1%20%282%29.cif?dl=0

Thank you for your support.

Kind regards,

Masanao

rowlesmr

In TOPAS, you've got spaces in your phase names.

eg "ZrO2 tetragonal" should be entered as "ZrO2_tetragonal"

Lots of things in the CIF file are constructed using the phase name. Line four of the CIF is "data_ZrO2 cubic_0": this is the start of a data block called "ZrO2" followed by a string ("cubic_0") that shouldn't be there, as per the CIF standard.

I also note that none of the strctures in that CIF file have a doubling of the bond/angle information.
.

You should also give your sites meaningful names. Instead of "s1" and "s2", use something like "Zr1" and "O1"

masanao

Dear Matthew,

After revising the .cif file, pdCIFplotter could open the file!
Thank you so much for your advice.

Kind regards,

Masanao

Navindra

Hi all,

I tried to open my cif using the pdCIFplotter and I get the following errors. I tried updating the cif.inc file but the errors are still coming up. I have attached my .inp and .cif files. Could you please give me a suggestion.

Thanks.
Best regards,
Navi

lw1114a-rietveld2-01.txt

15kB

rbcovf2.txt

924kB

mpl.version='3.4.3'
1
Now reading C:/Users/user/Desktop/Topas jEdit ex/HTB1114/RbCoVF2.cif. This may take a while.
Incorrect number of loop values for loop containing ['pd_phase_id', 'pd_phase_block_id', 'pd_phase_mass%']
Unexpected error:
Traceback (most recent call last):
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 80, in makeloop
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 771, in CreateLoop
ValueError: Request to loop datanames ['pd_phase_id', 'pd_phase_block_id', 'pd_phase_mass%'] with different lengths: {0, 1}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 2251, in ReadStar
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 165, in input
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 182, in dblock
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 194, in dataseq
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 203, in data
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\YappsStarParser_1_1.py", line 84, in makeloop
ValueError: Incorrect number of loop values for loop containing ['pd_phase_id', 'pd_phase_block_id', 'pd_phase_mass%']

Star Format error: Syntax error in input file: last value parsed was '1'
Parser status:
(_line 744) data_name = 'pd_proc_ls_prof_wR_factor'
(_line 744) data_value_1 = '0.01205'
(_line 745) data_name = 'pd_proc_ls_prof_wR_expected'
(_line 745) data_value_1 = '0.00399'
(_line 746) LBLOCK = 'loop'
(_line 747) data_name = 'pd_phase_id'
(_line 748) data_name = 'pd_phase_block_id'
(_line 749) data_name = 'pd_phase_mass%'
(_line 750) data_value_1 = '1'
(_line 750) data_name = '0'

Traceback (most recent call last):
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 936, in gui
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\gui.py", line 329, in read_cif
File "C:\Users\184277j\Documents\GitHub\pdCIFplotter\src\pdCIFplotter\parse_cif.py", line 472, in init
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\CifFile_module.py", line 3108, in ReadCif
File "c:\users\184277j\appdata\local\programs\python\python39\lib\site-packages\CifFile\StarFile.py", line 2268, in ReadStar
CifFile.StarFile.StarError:
Star Format error: Syntax error in input file: last value parsed was '1'
Parser status:
(_line 744) data_name = 'pd_proc_ls_prof_wR_factor'
(_line 744) data_value_1 = '0.01205'
(_line 745) data_name = 'pd_proc_ls_prof_wR_expected'
(_line 745) data_value_1 = '0.00399'
(_line 746) LBLOCK = 'loop'
(_line 747) data_name = 'pd_phase_id'
(_line 748) data_name = 'pd_phase_block_id'
(_line 749) data_name = 'pd_phase_mass%'
(_line 750) data_value_1 = '1'
(_line 750) data_name = '0'

rowlesmr

Navindra

Hi Navindra

I think the issue is that you don't have a phase name for your structures.

Try putting "phase_name SOMETHING_MEANINGFUL" in each str block.

The issue is that I use the phase name appended with an underscore and a numeral. Without the phase name, you get an underscore and a numeral which is parsed as a dataname, not a datavalue. This causes issues.

Matthew

rowlesmr

Hi Navindra

I can't download your files for some reason.

Can you email them through to rowlesmr at gmail dot com so I can have a look?

Thanks

Matthew

johnsoevans

Sorry, the download issue was a consequence of the upgrade we did on Monday. It should now be fixed.