1 Brief introduction

2 Getting started

In this section you will get to know the alien simulator. A detailed reference is given in Section 4 whereas in Section 3 you find information about the model it is based on.

At first you should start a new simulation by clicking Simulation -> New in the menu. Some initial energy can be placed in the simulation. It is represented as particles that move in an empty space. For a universe of size 1200 x 600 one can choose, e.g., a value of 1e+7. The simulation parameters and symbol map have meaningful default values and can be keept as they are for the moment. Clicking OK generates a new universe which particles carrying the initial energy.

There are two modes for viewing the simulation: pixel view and item view. The pixel view is set as default and gives a overview about where the particles and cells are situated. Cells can have different colors. The default color is blue. The particles are shown in red. The item view however gives a much more detailed insign. One can not only inspect precise position, velocity, energy and internal states but also change them. To switch between these modes View -> Editor has to be toggled in the menu. It is recommended to zoom into the universe before switching to the item view. In that view one can select one or more particles or cells. If one selects just one entity by clicked on it all the internal informations on additional windows in the upper left corner are shown.

It is also possible to load some collection of cells and particles into the simulation. Some standard examples are provided with this software. One can load them in Collection -> Load into the current universe. For instance one may load a replicator collection. It is recommended to use the item view for loading collections. If one would like to load the collection more then one time at different positions please click on Collection -> Random multiplier to clone the collections as many times as desired.

To start the simulation please toggle Simulation -> Run. On the bottom status line one should see the current timestep and the timesteps per second (TPS). Also limiting TPS is possible there by clicking on the restrict TPS-button. Beside that button one can enter a TPS limit. Toggling again Simulation -> Run will pause the simulation. Loading and saving is also possible via the Simulation menu entries. Sometimes it is convenient to restore a universe via snapshots. In Simulation -> Snapshot and Simulation -> Restore one can save the universe in temporary memory and restore it at any time later.

3 alien model

The alien model combines a physical and a computation model and can be seen some realization of artificial programmable matter.

Throughout this section simulation parameters (such as mutation probability) are denoted by the bracket notation [...] -> ... -> [...]. A overview of the parameters is given in 4.4.2 Simulation parameters.

3.1 Physics framework

3.1.1 Rigid body motion

A motion of the cell clusters is calculated via rigid body dynamics. Thus every cluster performs a linear movement and a rotation with respect to its center position. Collision of two clusters result in one of the following scenario: cluster fusion or collision. The former case takes place if the relative velocities of the touching cells exceeds the fusion velocity and if each cell is able to establish new bonds. In the fusion process kinetic energy is transformed into internal energy whereas the linear and angular momentum is preserved. In the latter case a rigid collision is conducted, which preserves the overall kinetic energy (rotation and linear part) of the involving objects.

3.1.2 Thermodynamics

Each cell object looses internal energy through radiation. This process is realized by emitting energy particles to its environment. These particles have a velocity but no mass and they carry a specific amount of energy. Whenever the internal energy of a cell is below some value (see [cell properties]->[min value]) it becomes unstable and transforms itself into an energy particle. It may also lead to a destruction of the superordinate cell cluster into two or more separated parts. If two energy particles collide they form a single particle with the combined energy. When the amount of energy exceeds a given value needed to form a cell (see [cell properties]->[min value]) and its kinetic energy, the particle transforms with a fixed probability (see [cell properties]->[transformation probability]) into a cell. Therefore dynamic creation and destruction processes of cells are implemented.

3.1.3 Space

Every cell cluster and energy particle object is embedded in a common space where all the physical actions take place. Topologically the space is 2D torus, which means that the opposite boundaries are to be considered as the same.

3.1.4 Entities

3.1.4.2 Cell cluster

Cells are able to form bonds with other cells (see [cell properties]->[max bonds]). Cell clusters are simply set of cells connected together. Physically they rotate and move with respect to their center position.

3.1.4.3 Energy particle

This type of entity carries energy through space. It moves with a particular velocity but has no mass. Energy particle can fuse if they collide together and be absorbed if they collisde with cells. Furthermore every cell emits energy particle from time to time and thus looses internal energy.

3.1.4.4 Token

Token are used to coordinate the information processing capability of the cells. They carry a memory storage and have an internal energy.

3.2 Information processing model

3.2.2.1 Computer

The computer cell function provides a little executable program consisting of instructions in machine code. The machine code is stored in the cell. Their instructions can access the memory storage of the cell as well as of the token. Both memory storages can have a maximum size of 256 bytes and all variables and addresses are one byte long. In calculations all values are interpreted as 8 bit signed integers. The number of instructions a computer cell function can have is indicated in [cell properties]->[computer]->[max instructions], the size of the cell memory in [cell properties]->[computer]->[cell memory size] and the size of the token memory in [cell properties]->[computer]->[token memory size].
Each instruction consists of three bytes (3x8=24 bits) with the following assigment:

3.2.2.2 Propulsion

A controlled acceleration can be performed by the propulsion cell function. It uses three input bytes and produces one output byte. Both are read and stored in the token memory. Their addresses depend on the implementation. In the following we introduce symbolic names for them.

3.2.2.3 Scanner

The task of the scanner cell function is to determine the cells of its own cluster. It provides the relative position and the precise internal data of the cells in an iterative procedure. The iteration depth is controlled by an index. The algorithm works as follows (the cell on which the scanner points to at index i is denoted by C(i)).

This lookup algorithm is illustrated in the following picture. There, the cell that contains the token (red circle) invokes the scanner cell function. The token comes from the cell C(1). The curved arrows indicate the clockwise search for the next cell. We see that the cells are indexed (counterclockwise) in a spiral manner.


The scanner cell function uses the subsequent bytes for communication.

The aim of the 'constructor cell function' (the corresponding cell will be denoted as `constructor') is not only to create a new cell but also to bond and create new cell structures. To this end, a part of the surrounding of the cell is be taken as a construction site. When the constructor creates a new cell the whole construction site will be moved and rotated if necessary (the remaining part as well) in order to obtain free space for the new cell. This may take several processing steps. When this is completed the new desired cell is placed and bonded to the construction site. The constructor can be seen as an artificial equivalent to a biological ribosome, which creates and folds proteins from amino acides.
A typical situation is illustrated in the subsequent picture.

In the next picture a typical construction process is shown.

After this introductory example we are going to explain the programming of the constructor. For convenience, most arguments coincide with output bytes of the scanner and thus share the same addresses in the token memory. This allows us to use certain output bytes of the scanner directly as input bytes for the constructor in order to easily replicate the cluster's own structure. The constructor uses the following bytes.

3.2.2.7 Communicator

The communicator cell function allows to transmit and receive messages form other communicator cells in the vicinity. The message can be sent in one of the 256 channels. Furthermore relative position information given in angle and distance can be transmitted. As always, all angles are measured clockwise with respect to the axis given by the invoked cell and the cell where the token came from. The receivers obtains the transformed position (in angle and distance) with respect to their position and orientation. The following bytes are used to program the communicator.

3.3 Energy guidance system

Tokens carry an amount of energy. They dissipate energy via radiation as cells do. Furthermore each time they pass to a cell energy can be transferred to or from the cell. This process can be controlled via memory entries in the token.

3.4 Simulation Parameters

4 Program documentation

4.1 Main Program

After starting the program one will find a menu bar and a tool bar on the top, a view of the artificial universe (initially empty) in the center and a status bar on the buttom. A alien simulation consists of the universe with its entities, simulation parameters and some information for convenience such as metadata and a symbol map. Entire simulations can be created, loaded, saved, run and paused via the menu entries in Simulation.

If a new simulation should be created a dialog appears which allows one to specify the grid (see 4.4.1 Grid), the initial amount of energy, simulation parameters (see 4.4.2 Simulation parameters) and a symbol map (see 4.4.3 Symbol map).

Assume a new simulation has been created. By toggling Simulation -> Run the simulation starts. That means new timesteps are calculated on separate threads consecutively. By toggling Simulation -> Run again the simulation is paused.

In order to facilitate experimenting with simulations one can take snapshots via Simulation -> Snapshot. The simulation will then be saved in some temporary internal memory. After clicking on Simulation -> Restore it will be loaded. It is also possible to compute only one timestep and showing the result by invoking Simulation -> Step forward. In that case one can step back via Simulation -> Step backward. These functionalities are also accessible through the toolbar.

4.2 Views

The main programm provides two different views designed for different purposes: pixel and item view. To toggle between these views please click on View -> Editor. The item view is also referred to as editor because it offers editor tabs that allow to change physical states and internals of cells, tokens and particles.

4.2.1 Pixel view

The pixel view is the default view when creating or loading a universe. In that view each cell and particle is visually presented as a pixel. The color of a cell depends on the information specified in its metadata and its amount of energy. Tokens are visualized as white glowing dots. One can zoom in and zoom out by clicking on View -> Zoom in and View -> Zoom out, respectively. A fullscreen mode can be toggled via View -> Fullscreen.

To some extend it is possible to manipulate velocities and angular velocities of entities within this view. By pressing the left mouse button and moving the mouse cursor nearby entities are accelerated in the direction where the cursor moves. By pressing both mouse buttons simultaneously entities close to the moving cursor get an angular acceleration.

4.2.2 Item view

In the item view entities are rendered with vector graphic in order to exhibit more details and enable precise manipulation capabilities. When the item view is active an extended toolbar appears on the upper left corner. It is recommended to zoom in before toggling to this view. More precise position information, connections between cells, token branch numbers and cell functions are visualized. The latter on can be toggled by clicking View -> Cell info. If an arrow between two cells is shown it means that a token can pass in this direction, i.e., the token branch number to the cell where the arrow goes is by +1 higher modulo the value of branch number. If, however, only a line is rendered between two cells it stands for a cell connection.

One particularity is that entities can be selected and manipulated. There are two methods available:
1) Selecting a single entity (cell or particle) by clicking on it with the left mouse button.
2) Defining a rectangle in order to select all entities inside. To do this click on some empty space and hold the left mouse button while moving the cursor.

To center a selection on the view please click on View -> Center selection or on the corresponding button in the extended toolbar.

Once entities are selected one can move them by drag and drop quite easily:

In the case when only one cell or particle is selected subwindows with editor tabs appear on the upper left corner of the center view. If a cell is selected one finds tabs for cluster, cell and metadata properties (cluster editor). If, additionally, one or more token exist on that cell further tabs for each token appear (token editor). When the selected cell has a computer cell function two more tabs showing the symbol map and a cell computer editor. Note that the symbol map can also be edited via Settings -> Symbol map -> Edit (see 4.4.3 Symbol map). However for convenvience in this context it is also shown in a tab.
For a selected particle only one tab that allows to edit its physical properties is shown.

4.2.2.1 Cluster editor

The cluster editor consists of three tabs: one tab for the properties of the entire cluster (tab named cluster), one for the selected cell (tab named cell) and one for the metadata (tab named metadata).

4.2.2.2 Cell Computer editor

For a cell having a computer functions a cell computer editor tab is shown. There on can edit the cell memory as well as a source code which will be executed when a token passes that cell. When the source code is changed one should click on the compiler button in order to inject the executable program to the cell. An immediate feedback if there are compilation errors or not. Each line in the source code field should correspond to one instruction.

4.2.2.3 Token editor

In the token editor one can edit the energy value and each memory byte of a token. The memory is partitioned into blocks. There are two type of blocks. If a symbol name from the symbol map refers to a token memory byte, e.g. [13], a block with size 1 corresponding to the memory byte, e.g. 13, is created and carries the symbol's name. Memory bytes where no symbols refer to are named as pure data block. If more than one symbols refer to the same byte the block carries all their names.

4.2.2.4 Symbol map editor

The symbol editor is simultaneously shown with the cell computer editor. One reason why the symbol editor is shown here in a tab (it can also be edited in Settings -> Symbol map -> Edit) is that it is very convenient to look up or introduce new symbols when using them in the source code for the cell computer. For more information about symbol map see 4.4.3 Symbol map.

4.3 Manipulation tools

Besides creating and manipulating single entites alien also tools for mass creation. Both functionalities are explained in this subsection.

4.3.1 Single entities

One can create, copy, paste and delete cells, token on cells as well as particles as follows.

4.3.2 Collections

A collection is a set of entities in the alien universe: particles, cells and tokens on them. Is is usually an rectangle section from the universe. Collections can be created, saved, loaded, deleted, moved and multiplied. For some of these operations a collection has to be selected. This can be performed in the item view. In Section 4.2.2 Item view we have already learned how to move collections. It is convenient to distinguish between two sets:

4.4 Settings

Simulation parameters can be setted up in the new simulation dialog or by invoking Settings -> Simulation parameters -> Edit at any later time. After clicking on OK-button the new simulation parameters are active in the current possibly runngin simulation.

4.4.2 Symbol map

Symbol map allows to defined aliases for constant or variables. For instance, a symbol SOME_CONSTANT could be 4 whereas SOME_VARIABLE could be [4]. Brackets [...] as well as (...) indicate a memory access. See 3.2.2.1 Computer for more details.

There are two possibilities for editing the symbol map: via dialog Settings -> Symbol map -> Edit or in a tab in item view, cf. 4.2.2.4 Symbol map editor.

4.5 Monitoring

It is possible the monitor some characteristic values such as total energy, number of cells or number of clusters etc. To this end, one can open a monitor by toggling View -> Monitor (or in the toolbar). The monitor is a partially transparent sub-window showing such informations.