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Update simple_model.md - spelling
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andyfaff authored Sep 23, 2024
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Expand Up @@ -33,10 +33,10 @@ All previous suggestions and variants are removed in order to avoid confusion.
The reflectivity file can be related to a sample model without the *external* connection
manufactorers lab journal....).
- **data analysis**
The standadisation allows the analysis software to automatically create a starting model which is
The standardisation allows the analysis software to automatically create a starting model which is
not too far from the real one.
- **indexing of data and analysis**
A standadised model might be used for indexing and filing of the data - within the lab or on a more general
A standardised model might be used for indexing and filing of the data - within the lab or on a more general
scale. This might be used to train AI algorithms.


Expand All @@ -49,8 +49,8 @@ This langage allows to provide a **very simple** model description on only 2 lin
stack: air | Ni 100 | SiO2 0.5 | Si
```
The key words used in the *stack* (here `air`, `Ni`, `SiO2` and `Si`) either refere to an
external data base (`https://slddb.esss.dk/slddb/`), a local dictionary or a declaration within the *model* entry.
The key words used in the *stack* (here `air`, `Ni`, `SiO2` and `Si`) either refer to an
external data base (`https://slddb.esss.dk/slddb/`), a local dictionary, or a declaration within the *model* entry.

More complexity (e.g. magnetic induction, roughness, reduced density, ...) can be provided by adding a few more lines.

Expand All @@ -62,7 +62,7 @@ More complexity (e.g. magnetic induction, roughness, reduced density, ...) can b

Detailed models for complex samples might reach several tens of lines, thus they are no longer
that *simple*.
The idea then is, that recuring fragments (sub-stacks, layers, materials) are defined in detail and stored in a
The idea then is, that recurring fragments (sub-stacks, layers, materials) are defined in detail and stored in a
local dictionary or even in the orso data base.
The model description in the header then stays simple and easy to use.

Expand Down Expand Up @@ -166,15 +166,15 @@ Each substack is made up of one or several layers. It has a unique name which is
repetitions:
int
optional (default: 1)
defines how often the substack is repeated. A negaive value means an inversion of the order.
defines how often the substack is repeated. A negative value means an inversion of the order.
stack:
str
optional
Same rules as for the top-level stack apply.
sequence:
list
optional
Instead of an other stack, the layers and their sequence are defined.
Instead of another stack, the layers and their sequence are defined.
```

> Examples:
Expand Down Expand Up @@ -240,7 +240,7 @@ If information about a layer besides its chemical composition (and thus the dens
> material: Fe
> ```
>
> - a bit more detailed, therefor no internal reference
> - a bit more detailed, therefore no internal reference
>
> ``` YAML
> layers:
Expand All @@ -264,7 +264,7 @@ A composit behaves like a material, but is made up from (on or) several material
It enables an easy way to define mixtures (solvents, interdiffusion, absorption).

``` YAML
compositis:
composits:
<name>:
<material 1>: <rel. density 1>
<material 2>: <rel. density 2>
Expand Down Expand Up @@ -388,10 +388,10 @@ This is a list of places where to look for information about materials or pre-de
> sequence:
> - SLD: 1.23
> thickness: 0.5
> - matrial: CH2
> - material: CH2
> thickness: 2.2
> mass_density: 0.83
> - matrial: CH2
> - material: CH2
> thickness: 2.2
> mass_density: 0.83
> - SLD: 1.23
Expand All @@ -408,7 +408,7 @@ A string to declare where the model parameters come from.

> Example:
> ``` YAML
> origin: thicknesses based on XR mesurements, nominal compositions
> origin: thicknesses based on XR measurements, nominal compositions
> ```


Expand All @@ -423,12 +423,12 @@ accept an *absurd* choice at some point.

- `sample` already defined
- `model`
- `origin` provides some informaton about how trustworthy the model is (*guess* vs. *based on XRD*)
- `origin` provides some information about how trustworthy the model is (*guess* vs. *based on XRD*)
- `stack`
- `layer`
- `material`
- `composit` material mixture
- `roghness` sigma of the errorfunction describing the density variation at an 'interface'
- `roughness` sigma of the error function describing the density variation at an 'interface'
- `composition`
- `density` (which one?)
- `mass_density`
Expand Down Expand Up @@ -494,7 +494,7 @@ sample:
tail
material: tailstuff
thickness: 22.
compoisits:
composits:
water:
H2O: 0.3
D2O: 0.7
Expand All @@ -516,10 +516,10 @@ sample:
reference: ORSO model language | 1.0 | https://www.reflectometry.org/projects/simple_model
```

Here `film` referes to a stack with 5 repetitions of some organic bilayer, which in turn consists of 4 sublayers. These are defined either again as layer (here for the tails) or directly with a thickness and a material. The `materials` section allows to define the materials used above. When missing, the name is taken as the chemical formula (e.g. Si or SiO2) or as a pre-defined material (water, air) and the corresponding values are taken from a data base.
Here `film` refers to a stack with 5 repetitions of some organic bilayer, which in turn consists of 4 sublayers. These are defined either again as layer (here for the tails) or directly with a thickness and a material. The `materials` section allows to define the materials used above. When missing, the name is taken as the chemical formula (e.g. Si or SiO2) or as a pre-defined material (water, air) and the corresponding values are taken from a data base.

These examples show how a model might be declared. There are various ways to do so for exactly the same model, and the choice depends mainly on the human readability and on *logical units* (like POPC). For automated writing (e.g. as an output from the data analysis software), we will have to find a reasonable and programmable approach....

### Implementation and examples
The model desciption has been implemented as a .ort header item in a Pull Request to the orsopy package with options to resolve layers for software to easily build a model system from the specification. Header examples and some automatic plotting scripts are included, too.
The model description has been implemented as a .ort header item in a Pull Request to the orsopy package with options to resolve layers for software to easily build a model system from the specification. Header examples and some automatic plotting scripts are included, too.
See the [Pull Request](https://github.com/reflectivity/orsopy/pull/83) for more details.

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