Add model for cubic sponge phase (Trac #289)

[ajj]

Student of Tommy Nylander, Maria Valldeperas, has asked to be able to add a model for her system which is a cubic sponge phase of lipids.

Might be doable with python, but I suspect that some polydispersity will be needed from previous fitting of these systems that Tommy is working on.

Paper attached.

Migrated from http://trac.sasview.org/ticket/289

{
    "status": "assigned",
    "changetime": "2019-03-25T17:46:30",
    "_ts": "2019-03-25 17:46:30.063239+00:00",
    "description": "Student of Tommy Nylander, Maria Valldeperas, has asked to be able to add a model for her system which is a cubic sponge phase of lipids.\n\nMight be doable with python, but I suspect that some polydispersity will be needed from previous fitting of these systems that Tommy is working on.\n\nPaper attached.",
    "reporter": "ajj",
    "cc": "",
    "resolution": "",
    "workpackage": "SasModels New Model",
    "time": "2015-01-12T08:00:37",
    "component": "SasView",
    "summary": "Add model for cubic sponge phase",
    "priority": "minor",
    "keywords": "",
    "milestone": "SasView Next Release +1",
    "owner": "none",
    "type": "enhancement"
}

[ajj]

Trac update at 2015/01/12 08:01:53: ajj changed attachment from "" to "SAXS_cubic_lipid.pdf"

[butlerpd]

Trac update at 2015/02/01 23:14:46: butler changed workpackage from "SasView Bug Fixing" to "SasModels New Model"

[butlerpd]

Trac update at 2019/03/03 01:55:26:

• butler commented:

actually Maria worked with me to get !SasView 4.2.x (developer versions) to work (is how we found the problems with double loading of math etc). I believe she eventually got this to work and I may have the code that enventually worked. We should ask her and/or Tommy about getting that added?

• butler changed owner from "ajj" to "none"
• butler changed status from "new" to "assigned"

[butlerpd]

Trac update at 2019/03/03 17:08:15:

• butler changed _comment0 from:

The reference she used for her model is:

L. Porcar, W.A. Hamilton, P.D. Butler, G.G. Warr; Langmuir 19, 10779-10794 (2003)

Equations 1 for S(Q) and 2 for P(Q).

to:

1551633265596227

• butler commented:

The reference she used for her model is:

L. Porcar, W.A. Hamilton, P.D. Butler, G.G. Warr; Langmuir 19, 10779-10794 (2003)

Equations 1 for S(Q) and 2 for P(Q).

[butlerpd]

Trac update at 2019/03/25 17:46:30: butler commented:

Maria Valldeperas implemented this model for her thesis. Attached are the various files she created in the process that can be used as a starting point. The first two are just equation 1 and 2 from the paper listed above (the disk "form factor" and the "structure factor" used to create the sponge). She then modified equation one to: since the first part of the equation was not changing much the fitting and I wanted to simplify the model

She also created two versions of this simplified model with a single and a double "broad peak" respectively. We need to figure out which of these we need to/want to implement.

[butlerpd]

Trac update at 2019/03/25 17:52:52:

• butler changed attachment from "" to "Eq.1 Porcar et al. L3_Sq.py"
• butler commented:

Original Equation 1

[butlerpd]

Trac update at 2019/03/25 17:53:33:

• butler changed attachment from "" to "Eq.2_Porcar_et_al. L3 Pq.py"
• butler commented:

Original Equation 2

[butlerpd]

Trac update at 2019/03/25 17:56:24:

• butler changed attachment from "" to "L3 Sq_1peak_Eq.1 modified.py"
• butler commented:

Modified Equation 1 with one peak

[butlerpd]

Trac update at 2019/03/25 17:57:49:

• butler changed attachment from "" to "L3 Sq_2peaks_Eq.1 modified.py"
• butler commented:

Modified Equation 2 with 2 peaks

[butlerpd]

I had to change the .py to .txt in order to be able to add these. they are available from the trac link above but if that ever ges away I thought it would be good to have them here.

Eq.2_Porcar_et_al. L3 Pq.txt Eq.1 Porcar et al. L3_Sq.txt L3 Sq_1peak_Eq.1 modified.txt L3 Sq_2peaks_Eq.1 modified.txt

[butlerpd]

Probably we should look at the 1 and 2 peak modifications to see if they make sense and/or they can be written in a way that the right parameter choices get you back to the original?