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PDOS String Reads labels #51

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PDOS String Reads labels #51

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ajm143
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@ajm143 ajm143 commented Mar 9, 2022

This is a first draft of pdos string reading labels as well as atom species. It is an attempt to solve Issue #31 . Expected behaviour:

  • PDOS: "Si:Exi" --> Match only the Si that is labelled Exi
  • PDOS: "Si" --> Match all the Si that are not labelled Exi
  • PDOS: Si --> Match all of the Si regardless of label or not.

I have made extensive use of the test-suite to catch as many different scenarios as I can. Fresh eyes are valuable now.

N.B. This includes PR #48 as I required a working test suite. I suggest we accept #48 first.

ajm143 and others added 18 commits February 17, 2022 09:35
@ajm143
projection_analyse_substring was a subroutine inside projection_get_s…
f7e7d40 
…tring which made it difficult to manage. I've made it a subroutine of the module -- it still passes the test suite, and I can't see a reason why it was so.
@ajm143
Made the seperators modul variables.
8263ce2
@ajm143
Tidied the pdos string functions ready to add labels
0d84699
@ajm143
First version that can read inverted commas. It doesn't yet understan…
28720fc 
…d what's inside them, i.e. Si:exi, and will get upset.
@ajm143
More debugging in electronic and parameters to help with PDOS string
c41bfbf
@ajm143
Further developments in OptaDOS's PDOS string
2390cf3
@ajm143
This looks like a version that works. In certain cases, it now needs …
0a3a595 
…to learn that C matches C:exi and C matches C only.
@ajm143
Now a first attempt at "C" matching only C and C matching C and C:exi
a3ab939
@ajm143
Some beautification of code and output, before the inevitable testing…
0f38a93 
… and debugging starts.
@ajm143
Added many more comment and have tested on a number of examples that …
4c17d69 
…all pass.
@ajm143
Merge branch 'example' into pdos_string
e514c93
@ajm143
Merge branch 'example' into pdos_string
c5bd60a
@ajm143
Added the tests for the new PDOS string
06736ce
@ajm143
Merge branch 'example' into pdos_String
954506c
@ajm143
Merge branch 'origin/PR48' into pdos_string
8ea1698
@ajm143
Updated User Guide
5374fc6 
- Added hyperlinks to aid navigation (why not)
- Listed the new compilers, and depricated the ones that TCM can no longer support.
- Updated the description ofthe PDOS string to include labels
Tweaked input file for compaitbility with NAG compiler
9b4db75
@ajm143
- Fprettified the commit that I made from TCM.
485e193 
- Added a new checkpoint. GaAs which has two labels
- Added the testopt_pdos_Ga_label to the test suite to test more pdos_string handling
- Solved some over-long lines in projection_utils
@ajm143 ajm143 requested a review from jryates March 9, 2022 11:32
@ajm143 ajm143 linked an issue Mar 9, 2022 that may be closed by this pull request
PDOS Output Gets muddled with Labelled Atoms i.e. C:exi #31
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@ajm143 ajm143 assigned ajm143 and jryates and unassigned ajm143 Nov 23, 2022
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jryates commented Mar 22, 2023

@ajm143 we are getting three tests failing.

All done. ERROR: only 30 out of 33 tests passed.
Failed tests in:
	/Users/yates/Documents/CODE/optados/optados/test-suite/tests/testopt_pdos_match_inc_label
	/Users/yates/Documents/CODE/optados/optados/test-suite/tests/testopt_pdos_match_label
	/Users/yates/Documents/CODE/optados/optados/test-suite/tests/testopt_pdos_match_not_label

These all use:
Si2.pdos_fmt.bz2 -> ../../checkpoints/Si2_core/Si2.pdos_fmt.bz2

I have reproduced this with gfortran on osx and ifort in TCM. The pdos spectra are a bit different. I suspect something has got mixed up in your benchmarks - however, it would be best if you can repeat and confirm.

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PDOS Output Gets muddled with Labelled Atoms i.e. C:exi
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