GENESIS Reference ManualMay 5, 2001: Elements

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## 8. Elements

Elements are the basic computing and organizational entities available to the user. Elements are organized in a hierarchical structure similar to a UNIX directory tree. Each element embodies a specific computation in the simulation. This computation may implement part of the model being simulated or may be part of the graphical interface or file I/O.

The state of an element is contained in the element's fields. Fields may be of any C defined type. A field protection facility provides for both the visibility and accessability of the element fields. Fields have default values which define the state of an element's fields when the element is created. The default values may be changed, changing the initial values of elements created subsequently.

Elements may need information from other elements to perform their calculations. This information is gathered from the other elements' fields via Messages.

A set of default element types (called ``objects'') is distributed with GENESIS. These are used as templates for the creation of the particular elements that are used in a GENESIS simulation. One example of an element type is the ``compartment'' object, which is used to create sections of neural membrane in a cell model. Another example is an ``xform'' object used to create graphical form widgets which might appear on the screen. The GENESIS distribution currently contains about 120 predefined objects. These are summarized in Objects.

## 8.1 Related Commands

The following GENESIS routines are used for creating and working with specific elements:

Routine | Description
addfield | Adds a new (extended) field to an element.
call | Allows an element to execute the function associated with
| the named action.
copy | Copies an element (and its children, if any) from one
| portion of the element tree to another.
create | Creates new element of specified element type.
createmap | Makes multiple copies of an element to form a 2-D array
delete | Deletes an element and all of its children.
deleteall | Deletes all existing elements. [not recommended]
deletefield | Deletes an extended field of an element.
egg | Generates coordinates for points on the surface of an ovoid.
exists | Tests for existence of specified element or field.
getfield | Returns value of field in data structure of specified element.
getfieldnames | Returns names of all existing fields in specified element.
isa | Tests to see if an element is derived from a specified object.
move | Moves an element and its children from one portion of the
| tree to another.
plane | Generates 3-d coordinates for a plane with specified
| dimensions and characteristics.
position | Sets xyz coordinates of an element and all of its children.
reclaim | Reclaims memory from deleted elements.
restore | Restores element state stored in file with save routine.
rotcoord | Rotates coordinates of elements in 3-d space.
save | Saves current field values for specified element in a file.
setfield | Sets value of field in data structure of specified element.
showfield | Displays value of field in data structure of specified element.

Other commands related to GENESIS elements are described in the sections on Hierarchical Structure, Objects, and Extended Objects.

## 8.2 Actions

Each element in a simulation is capable of performing one or more actions. An action can be described as an operation that an element performs on its data. The predefined actions of an element are inherited from the object that was used to create the element. Actions are defined within compiled functions that are attached to each object. Other actions may be added with the addaction command.

GENESIS calls many actions implicitly as part of the process of running a simulation, or as a side effect of certain commands. This allows particular object-specific behaviors to executed at particular points in simulation. For example, the PROCESS action is called at each step of the simulation. Other actions are not performed regularly in the simulation schedule, but are performed globally on all objects; these include the CHECK action and the RESET action, which are invoked using the check and reset commands, respectively. If a particular action is not defined for an element, a default behavior is performed on the element (SET sets the field, SHOW returns the field, CREATE leaves fields initialized from defaults, etc.).

The following predefined actions are common to many GENESIS objects.

PROCESS | Called on each simulation step as described by the simulation
| schedule to perform the element's update processing.
INIT | Called on each simulation step as described by the simulation
| schedule to initialize the element for this simulation step.
RESET | Called when the simulation is reset (reset command) to allow
| an element to reset itself to its default state.
CHECK | Called from the check command to allow an element to verify
| that it has all the information and the correct information
| needed to proceed with the simulation.
SET | Called when an element field is set (or once for a setfield
| command if SPECIAL_SET exists as an element field). The SET
| action must return 1 if it sets the field in question and 0
| if it doesn't.
SHOW | Called in order to perform special formating for field display
| or retrieval (getfield or showfield commands).
CREATE | Called when an element is created to initialize the element.
| Must return non zero if the initialization is successful.
COPY | Called when an element is copied.
DELETE | Called when an element is destroyed.
SAVE2 | Called by save command to save state of the element to a file.
RESTORE2 | Called by restore to restore previous state from a file.
DUMP | Called by the simdump command.
UNDUMP | Called by the simundump command.

There are also a number of actions that have to be explicitly invoked on an element-by-element basis, such as the TABCREATE action. You invoke these with the call command, e.g.

        call Na_tabchannel TABCREATE X 49 -0.1 0.05

This use of actions corresponds to the use of ``method calls'' in object-oriented languages such as Java.

There are also situations where you may want to explictly call an action (like RESET) for a particular element, without performing it on all elements (e.g. by issuing a reset command). This is because the the reset routine gives no control over the order in which the elements are RESET, and you may need to call the RESET action for specific elements in the proper order if the initial state of one element depends on the initial state of another element. For example:

        call Ca RESET     // Reset the Ca channel
        call conc RESET   // Reset the Ca_concen element next
        reset             // reset everything

Other predefined actions that are specific to the way the object is used are described in the documentation for the particular object. For a description of actions that are specific to XODUS elements (widgets), see XODUS Mouse Clicks. A list of actions that an object can perform can also be displayed using the showobject command.

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