XML syntax - contrast

The strength of this version of yanera is its ability to fit any number of data sets simultaneously. This might arise from data taken on samples that are very similar, and sharing model parameters would be a good idea. Cases might include; changing contrast through D₂O concentration, adding or removing layers in-situ, polarization, etc.

Contrast

Any number of additional models can be specified in the XML file with additional <model/> tags. These models represent changes in contrast or structure, and are built based on the first model. It is only required that changes to the base model are specified.

Some examples are given below. Each one is a <model/> of secondary contrast in its entirety; it was the first model which gives a complete model, with all layers. The <model/> examples shown here specify only the changes.

Example 1

    <model data_idref="data2">
      <polarized>POLARIZED_DOWN</polarized>
      <layer/>
    </model>

This is a simple polarized experiment, where the second data set, "data2", represents the polarized down case. The sample has not changed in structure at all. One <layer/> tag, even empty, must be included.

Example 2

    <model data_idref="data2">
      <layer layer_idref="id1">
        <rsld fix="NO">-1.000</rsld>
      </layer>
    </model>

Here we identify a layer in the first model section by its "layer_id" and change its SLD. The model is exactly the same, except one layer (or one repeating layer) has changed a single parameter. Any or all parameters can be changed in this way, e.g.. A multilayer ABABA is compared with another of ACACA, where A is identical in the two samples, but B and C differ in some regard.

This requires that in the first model, a layer with the same "layer_id" be given, such as:

    ...
        <layer layer_id="id1">
          <name>repeating layer type 1</name>
          <thik fix="NO">10.000</thik>
          <sigz fix="NO"> 0.500</sigz>
          <rsld fix="NO"> 0.000</rsld>
        </layer>
    ...

Example 3

    <model data_idref="data2">
      <layer layer_idref="id1">
        <include>no</include>
      </layer>
    </model>

In an extreme case, one layer may be missing entirely. Use the <include/> tag, and set it's value to "no" (default is always "yes"). An example might be a case when a top layer was added in-situ; multilayer ABAB became ABABA. Use the more complete, second sample condition as the first model and delete the layer from the second model.

Example 4

    <model data_idref="data2">
      <name>model 2 name</name>
      <layer layer_idref="l1a" component_idref="c2">
        <rsld fix="NO"> 0.230</rsld>
      </layer>
    </model>

Changing contrasts (and excluding layers) also works for component layers. In this example, The layer referenced by layer_id "l1a" (which happens to be also share a common component component_id "c2") the SLD parameter is different in this model. If this layer was not a common component originally, it is made one now.

Example 5

    <model data_idref="data2">
      <layer layer_idref="id1">
        <parm name="c" fix="NO"> 25.000</parm>
      </layer>
    </model>

Changing contrasts (and excluding layers) also works for functional layers. In this example, the parameter "c" is changed and is now an independent parameter from the "c" in the first model.