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Replace PD_AMORPHOUS with PD_AMORPHOUS_PEAK #158

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will close #129

PD_AMORPHOUS was insufficient to describe the same amorphous phase being present in more that one diffractogram; it could only link to peaks and diffractograms. The new category gives amorphous peak positions and intensities, and links them to actual instansiations by PD_PEAK in diffractograms.

Essentially, an amorphous phase has peak positions and intensities, widths are an implementation detail, which is the same as how crystalline phases work.

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rowlesmr commented Feb 5, 2024

Is it possible to add a method to give point-wise contributions of an amorphous phase to a diffractogram?

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rowlesmr commented Feb 5, 2024

Is it possible to add a method to give point-wise contributions of an amorphous phase to a diffractogram?

Ah! Forgot... already possible through PD_CALC_COMPONENT.


To maintain complete generality, amorphous peak positions are given only in
terms of d spacing, and peak intensities as relative intensities. These are
then instansiated in a specific diffractogram by related data items in
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Suggested change
then instansiated in a specific diffractogram by related data items in
then instantiated in a specific diffractogram by related data items in

_description.text
;
Relative integrated area for the peak. This value must be obeyed by any
peaks used in an diffractogram which are assigned to peaks in this phase.
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peaks used in an diffractogram which are assigned to peaks in this phase.
peaks used in a diffractogram which are assigned to peaks in this phase.

_type.source Assigned
_type.container Single
_type.contents Word
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All other peak ids in this dictionary seem to be of the Code content type so maybe it would make sense to change this to Code as well?

I also prefer to have case-sensitive identifiers (as would be mandated by the Word type), but it might be worthwhile to sacrifice that for consistency. Alternatively, we could have a separate PR that changes all of these identifiers to Word to make them case sensitive if that seems reasonable.

_type.source Assigned
_type.container List
_type.dimension '[]'
_type.contents Text
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_type.contents Text
_type.contents ByReference
_type.contents_referenced_id '_pd_peak_overall.id'

_type.purpose Encode
_type.source Assigned
_type.container List
_type.dimension '[]'
_type.contents Code
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_type.contents Code
_type.contents ByReference
_type.contents_referenced_id '_pd_peak.id'

_type.contents Code
_type.container List
_type.dimension '[]'
_type.contents Text
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Suggested change
_type.contents Text
_type.contents ByReference
_type.contents_referenced_id '_pd_diffractogram.id'

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This constructs simply means "Take the content type from _pd_diffractogram.id". Helps to keep the content types in sync.

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PD_PEAK needs diffractogram_id? and some musings on it's use in PD_AMORPHOUS
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