Introduction and Getting Started

The AHA Model

This is a large scale simulation model (under development) that implements a general decision-making architecture in evolutionary agents. Each agent is programmed as a whole virtual organism including the genome, rudimentary physiology, the hormonal system, a cognitive architecture and behavioural repertoire. They "live" in a stochastic spatially explicit virtual environment with physical gradients, predators and prey. The primary aim of the whole modelling machinery is to understand the evolution of decision making mechanisms, personality, emotion and behavioural plasticity within a realistic ecological framework. An object-oriented approach coupled with a highly modular design not only allows to cope with increasing layers of complexity inherent in such a model system but also provides a framework for the system generalizability to a wide variety of systems. We also use a "physical-machine-like" implementation philosophy and a coding standard integrating the source code with parallel detailed documentation that increases understandability, replicability and reusability of this model system.

The cognitive architecture of the organism is based on a set of motivational (emotional) systems that serves as a common currency for decision making. Then, the decision making is based on predictive assessment of external and internal stimuli as well as the agent's own motivational (emotional) state. The agent makes a subjective assessment and selects, from the available repertoire, the behaviour that would reduce the expected motivational (emotional) arousal. Thus, decision making is based on predicting one's own internal state. As such, the decision-making architecture integrates motivation, emotion, and a very simplistic model of consciousness.

The purpose of the AHA model is to investigate a general framework for modelling proximate decision-making and behavior. From this we will investigate adaptive goal-directed behaviour that is both guided by the external environment and still is endogeneously generated.

Other research topics include individual differences, personality as well as consequences of emotion and personality to population ecology.

We think that understanding and modelling complex adaptive behaviour requires both extraneous (environmental) factors and stimuli as well as endogeneous mechanisms that produce the behaviour. Explicit proximate representation of the motivation and emotion systems, self-prediction can be an important component in linking environment, genes, physiology, behavior, personality and consciousness.

Fortran is used due to its simplicity and efficiency. For example, check out this paper.

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Subdirectories of the AHA Model code

• \dox -- contains pictures, plots and other resources for the full Doxygen documentation that is extracted from the source code.
• \pfunit -- unit tests using pFUnit, so far rather rudimentary.
• \tools -- various accessory tools, post-processing of the data generated by the model etc. .

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Getting started

Building and running the mode is based on the GNU Make. Both the AHA Model code and the HEDTOOLS (code or static library) are needed to build the model. These two components of the AHA Model framework are described in the Overview of the AHA Fortran modules.

Normally, the AHA Model code and the HEDTOOLS code are placed in two subdirectories of the working directory using two separate commands to get the code of the AHA Model and HEDTOOLS from the repositories (svn co https://... or hg clone ssh://... if Mercurial is used -- check out Subversion).

With the current main Subversion repository, getting the code requires these commands:

svn co https://subversion.uib.no/repos/aha-fortran/tags/AHA_R/R1 AHA-R1
svn co https://subversion.uib.no/repos/aha-fortran/tags/HEDTOOLS/1.1 HEDTOOLS

or these, if Mercurial is used (here local folders are capital):

hg clone https://bitbucket.org/teg_uib/aha-r1 AHA-R1
hg clone ssh://[email protected]/teg_uib/hedtools HEDTOOLS

or still these, if GitHub git-based repo is used:

git clone [email protected]:sbudaev/AHA-R1.git
git clone [email protected]:sbudaev/HEDTOOLS.git

Thus, the layout of the working directory after HEDG2_01 and HEDTOOLS are downloaded is like this:

workdir
 |
 |-- AHA-R1
 |    |-- dox
 |    |-- pfunit
 |    `-- tools
 |
 `-- HEDTOOLS

Building the AHA Model is done in the model directory (here HEDG2_01). If you use the terminal, go there with

cd AHA-R1

Here are the main commands to build and run the AHA Model:

• Build the model from the source code: make;
• Build and run the model:make run;
• Delete all build-related, data and temporary files make distclean;
• Get a quick help from the make system: make help.

See Makefile for build configuration. To get more information on the GNU Make see AHA Modelling Tools Manual, Using Microsoft Visual Studio and Using Code::Blocks IDE.

Environment variables

The model makes use of several environment variables to control certain global aspects of the execution. These variables have the AHA_ prefix and are listed below.

• AHA_DEBUG=TRUE sets the "debug mode";
• AHA_SCREEN=NO sets logger to write to the standard output as well as in the log file;
• AHA_DEBUG_PLOTS=YES enables generation of debug plots;
• AHA_ZIP_FILES=YES enables background compression of big output data files;
• AHA_CHECK_EXTERNALS=NO disables checking for external executable modules (this is a workaround against Intel Fortran compiler bug).

Makefile: GNU Make build configuration

Makefile to build the model executable from the source code.

This is a standard GNU Make Makefile to build the model from the sources. It also automatically generates some platform and compiler specific include files for the BASE_RANDOM and the IEEE math modules. See Working with the model section for details.

In addition to the GNU Make, this Makefile also depends on the grep, cut, sed and awk utilities that are installed on any Unix/Linux system, but usually absent on Windows. For Windows they can be obtained from several locations on the web, e.g. Cygwin or GnuWin32. See AHA Modelling Tools Manual for more information.

Main adjustable parameters

• FC sets the default compiler type. Normally GNU gfortran or Intel ifort.
• HOST_HPC_ROOT is the hostname to run the model executable in the HPC batch mode. If the hostname the Makefile is called in is this system, make run starts a new batch task. Otherwise, the model executable is just started normally.
• SRC is the name of the main source code (can be several files).
• DRV is the source code of the model "driver", that is the main Fortran program that produces the executable. It should be very very small. The "driver" is a separate file from the AHA Model modules.
• OUT is the executable file name that is actually run, on the Windows platform must have the .exe suffix. By default, the executable name is set to MODEL.exe for maximum portability.
• DOXYCFG the Doxygen documentation system configuration file name.
• DOXYPATH defines the Doxygen output directory where the documentation is generated. This could be set manually or parsed automatically using the grep command. Note that the output directory is set in the Doxyfile as: OUTPUT_DIRECTORY = ./model_docs.
• HEDTOOLS is the list of HEDTOOLS Fortran source files that are used in the AHA Model. Note that BASE_STRINGS in the list must go before BASE_CSV_IO because BASE_CSV_IO depends on procedures from BASE_STRINGS.
• HEDTOOLSDIR defines the path to the HEDTOOLS source code.
• IEEEPATH defines the path to the IEEE non-intrinsic math modules (part of HEDTOOLS).
• WINRM defines the command that is used to delete files and directories on the Windows platform. The native file delete command on the Windows platform is del or erase. However, if Cygwin is used, this native file removal command may not call with a "command not found" error. In such a case, use the Unix rm tool provided by Cygwin. .

The source code of the Makefile contains many other parameters and is well documented throughout.