TOAST Online User Manual  1. Mesh generation and manipulation

1.1 femmesh

Introduction

Usage

General features

• Definition of circular, rectangular or irregular meshes.
• Variable, user-definable mesh resolution.
• Automatic mesh generation from imported outline data.
• Interactive local element subdivision.
• Node positioning and deletion.
• Tools for regional modification of element absorption, scattering and refractive index.
• Element group specification.

Manual

File menu

Meshes can be saved, loaded or printed to a PostScript file. Moreover it is possible to load a polygonal ``outline'' to which a mesh ``frontline'' can be fitted.

BBox menu

This menu provides options for the automatic or manual adjustment of the boundary box dimensions.

Refresh button

Redraws the mesh.

Check mesh button

Checks the consistency of the mesh. This is normally only necessary after manual changes have been made. The following problems are looked for:

• An element has a vertex outside the node list range.
• More than one vertex of a single element refers to the same node.
• The node list contains unused nodes.
• Two different nodes have the same coordinates.

New button - Creating a new mesh

When choosing this option the following window appears.

Select one of the following three mesh types:

Circular

• Define the mesh resolution by choosing the number of sectors and rings into which the circle is to be divided. This determines the element size and node density of the mesh.

A value of 6 for the number of sectors is usually optimal, as this produces the most regular triangular elements. The number of rings is typically between 16 and 50, depending on the physical size of the circle, the optical properties and the required accuracy of the solution. Less than 4 rings should never be used. A standard value is 32 for a circle of 25 mm radius and typical optical properties.
• The physical mesh radius is defined in mm.
• The thickness of the outer layer can be set separately to fine-tune the mesh to specific needs. If manual setting is not required then ``Bnd layer thickness'' should be set to ``Auto''.
• Note that the element structure for the outer two rings differs from that of the inner rings to provide a better numerical accuracy at the boundary.

Rectangular

• Select a mesh structure. It is highly recommended to choose the second type, splitting each rectangle into four triangles.
• Specify the number of element columns and rows into which the mesh is to be divided.
• Define the physical dimensions of the mesh by specifying the coordinates of the left, right, lower and upper boundaries.

Irregular

To generate an irregularly shaped mesh one needs to define its ``frontline'', that is an outer boundary defined by actual mesh nodes. A customized mesh frontline can be defined in two ways.

• Create manually:
• Select ``Create manually'' in the ``frontlines'' menu.
• Move the mouse pointer into the mesh display window. Click the left mouse button to drop the nodes making up the frontline.
• Note that the nodes making up the boundary have to be dropped by going clockwise around the boundary to distinguish between ``inside'' and ``outside''.
• Nodes should be dropped evenly, as this produces more regular and stable meshes. If you click on ``Force equidistant front nodes'' before dropping the first node, then equal spacing is ensured automatically.
• After dropping the last node, click the middle mouse button to close the boundary.
• The frontline can be saved to (and later loaded from) disk by choosing the appropriate option in the ``frontlines'' menu.
• Create from outline:
• Load an outline by choosing the ``Load outline'' option in the ``File'' menu of the control panel.
• Select ``Create from outline'' in the ``Frontlines'' menu.
• A suitable mesh can now be fitted automatically to the outline by clicking the ``Apply'' button.
• More than one frontline can be created for the same mesh. This is useful in there are internal structures along which the element structure should be aligned. The following restrictions apply:
• Frontlines must not intersect.
• The mesh must be compact, i.e. there must be one frontline enclosing all other frontlines.
• Internal frontlines need not be created clockwise.

Refine button - Refining a mesh locally

The node density of a mesh can be locally increased by subdividing elements manually.

• Click on the ``Refine'' button.
• Move the mouse pointer into the mesh display window and click on the element to be refined. The element is split into two elements.
• Note that at least one, possibly more of the element's neighbours are also refined automatically in order to maintain the integrity of the mesh structure.
• A mesh should be refined before optimisation, since the optimisation process removes the refinement information from the mesh file.

Move button - Moving nodes

Nodes of an existing mesh can be moved to a new position.

• Click on the ``Move'' button.
• Select the node to be moved by clicking on it with the left mouse button.
• Click the left mouse button again at the new node position. The operation can be cancelled by clicking the middle mouse button.
• Note that a node can only be moved into one of the adjacent elements.

Join button - Joining nodes

Two nodes of an existing mesh can be merged into one node.

• Click on the ``Join'' button.
• Select the node to be joined by clicking on it with the left mouse button.
• Click the left mouse button again at the node it should be joined with. The operation can be cancelled by clicking the middle mouse button.
• Note that a node can only be merged with one of its neighbours.

Outline button - Viewing the outline

If an outline has been loaded, use this button to view or hide it.

Coeff button - Modifying optical parameters and element regions

The optical coefficients for each element can be set individually with the ``Modify Coefficients'' tool. Note that forward solvers always use the optical parameters defined in the mesh, while for the inverse solver there is a range of additional ways to specify the initial parameter distribution.

• Click on the ``Coeff'' button.
• Enter the new values for the coefficients.
• To apply the new values to all elements of the mesh, to elements with lower values than the specified, or to elements with higher values than the specified, click on the appropriate button.
• To apply the new values only to a certain region within the mesh, click one of the ``Paint mode'' buttons: Freehand, flood fill, rectangle, ellipse.
• For freehand: Left-click on any element in the display window you want to assign the new values to.
• For flood-fill: Left-click on one of the elements in the region you want to assign the new values to. The whole region is then filled with the new values.
• For rectangle: Left-click on the upper right corner of the rectangular region, and drag the cross-hair to the lower right corner.
• For ellipse: Left-click on the upper right corner of the bounding box of the ellipse, and drag the cross-hair to the lower right corner.
• Note that you must choose the appropriate ``Display'' option to actually view the distribution of coefficients.

Info button - Viewing mesh information

Information on the node positions, optical properties, etc. can be viewed with the ``Information'' tool.

• Select whether you want an information update upon clicking on the element, or moving across it.
• The optical properties and corresponding node numbers/positions of the element can now be seen.

Time button - Defining parameters for time-dependent simulations

In case you want to perform a time-dependent forward calculation, the required parameters can be entered using the ``Time resolution'' tool. Note that this option is not used at all by the inverse solver toast, and also not by the multi-source forward solver femdata since they generate their transforms of the temporal profile directly. In effect, this option can savely be ignored except where full time profiles are required, and presently it is only supported by a limited number of forward solvers.

• Select ``time-dependent'' simulation type.
• Enter the parameters.
• ``timestep length'' is the temporal interval of a single time step in picoseconds.
• ``Coupling parameter'' specifies how subsequent time steps are linked in the finite-difference scheme. 0.5 corresponds to a Crank-Nicholson scheme.
• ``no. of timesteps'' specifies the total number of steps.
• ``internal subdivision factor'' specifies how many time steps to skip for output. ``1'' outputs ever time step, ``2'' every second, etc.
• This information will be stored as part of the mesh file.

Source button - Defining source parameters

If you want to define a source position for a single-source forward calculation not femdata, the relevant parameters can be entered via the ``Source Specification'' tool. Note that this information is ignored by femdata and toast since they obtain source positions from a separate QM file.

• Check the ``Include source information'' box.
• Enter the relative source strength (usually ``1'') and its physical coordinates.
• This information will be stored as part of the mesh file.

Display options

• Select which of the optical parameters (absorption, scattering, refractive index or none) you want to displayed in the mesh view window.
• Use the sliders to adjust the brightness and contrast as desired.
• Use the zoom slider to zoom into a mesh.
• Note: Large zoom factors increase the program's memory requirements considerably and may fail on low-performance machines.