Tag: Object Oriented Programming

Python Tutorial: Child Classes

In the previous tutorial of the wordle-mania-series, we had a quick overview of how to construct a basic class in Python. Here we take our class adventure a step further and implement a child class. As before, the full source of this project can be found in our GitHub repo.

1. Building a child class.

The construction of a child class is near identical to the construction of a non-child class. The only difference being we need to somehow indicate the class is derived from another class. During our previous tutorial, we created the WordleAssistant class, so let’s use it as a parent for the WordleAssistant2 child class.

from .WordleAssistant import WordleAssistant

class WordleAssistant2(WordleAssistant):
    pass

First, note that we need to import the WordleAssistant class, which is stored in a file WordleAssistant.py, contained in the same folder as the file containing our child class (hence the “.” in front of WordleAssistant). At this point, most python developers will hate me for using the same name for what is considered a module and a class, as you could put multiple classes in a single file. Then again, once you start writing object oriented code, it is good practice to put only one class in a single file, which makes it rather strange to use different names.

Second, we put parent class between the brackets of the child class. Through this simple action, and the magic of inheritance, we just created an entirely new class containing all functions and functionality of the parent class. The keyword pass is used to indicate no further methods and attributes will be added.

2. Child class individuality.

Of course, we want our child class to not be just a wrapper of the parent class. The choice to use a child class can be twofold:

    1.  Extension of an existing class. This can either be because you are not the developer of the parent class, or (in case you are the developer) because you don’t want to accidentally destroy a working piece of software (c.q. parent class) while trying out some new features, or …
    2. Modification/implementation of specific class behavior. The standard (trivial) examples involve drawing classes, which in one child class draw circles, while in another it draws squares.
    3. Both of the above.

In our case, we are going to ‘upgrade‘ our WordleAssistant class by considering the prevalence of every letter at the specific position in the 5-letter word. This in contrast to our original implementation which only considered the prevalence of a letter anywhere in the word. Adding new functionality with “new” methods and attributes, happens as for the parent class. You just define the new methods and attributes, which should have names that differ from the names for methods and attributes already used by the parent class.

However, sometimes, you may want or have to modify existing methods. You can either replace the entire functionality overwriting that of the parent method, or you may extend that functionality.

2.1. Extending methods.

When you still want to make use of the functionality of the method of the parent class you could just copy that code, and add your own code to extend it. This however makes your code hard to maintain, as each time the parent class code is modified, you would need to modify your child class as well. This increases the risk of breaking the code. Luckily, similar as programming languages like C++ and Object Pascal,  there is a useful trick which allows you to wrap the parent class code in your overwritten child class method. A location where this trick is most often used is the initialization method. Below you can see the __init__ function of the  WordleAssistant2 child class.

def __init__(self, size: int = 5, dictionary : str = None ):
    super().__init__(size, dictionary)
    self.FullLettPrevSite = self._letterDistSite(self.FullWorddict)
    self.CurLettPrevSite = copy.deepcopy(self.FullLettPrevSite)

The super() function indicates we are going to access the methods of the parent of the class we are working in at the moment. The super().__init__() method therefor refers to the __init__ method of the WordleAssistant class. This means the __init__ method of the WordleAssistant2 child class will first perform the __init__ method of the WordleAssistant class and then execute the following two statements which initialize our new attributes. Pretty simple, and very efficient.

2.2. Overwriting methods.

In some cases, you don’t want to retain anything of the parent method. By overwriting a method, your child class will now use a totally new code which does not retain any functionality of the parent method. Note that in the previous section we were also overwriting the __init__ method, but we retained some functionality via the call using super(). An example case of a full overwrite is found in the _calcScore method:

def _calcScore(self, WD: dict, LP: list):
    for key in WD:
        WD[key]['score'] = 0
        for i in range(self.WordleSize):
            WD[key]['score'] += self.CurLettPrevSite[i][WD[key]['letters'][i]]

Although this method can still make use of attributes (self.WordleSize) and methods of the parent class, the implementation is very different and unrelated to that of the parent class. This is especially true in case of the python scripting language. Where a programming language like C++ or Object Pascal will require you to return the same type of result (e.g. the parent class returns an integer, then the child class can not return a string, or even a float.), python does not care.  It places the burden of checking this downstream: i.e. with the user. As a developer, it is therefore good practice to be better than standard python and take away as much of this burden from the future users of your code (which could be your future self.)

Finally, a small word of caution with regard to name mangling. Methods with two leading underscores can not be overwritten in the child class in the sense that these methods are not accessible outside the parent class. This means also inside a child class these methods are out of scope. If we had a __calcScore method instead, creating an additional __calcScore in our child class would give rise to a lot of confusion (for python and yourself) and unexpected behavior.

3. Additional sources:

Permanent link to this article: https://dannyvanpoucke.be/python-tutorial-child-classes/

Python Tutorial: Classes

Python, as any other scripting language allows you to define variables and functions. These are very basic entities when it comes to programming. However, sometimes it is useful to keep variables and functions that are related to one-another close together. This is the main idea behind Object Oriented programming and is present in programming languages such as C++ and fortran, but also in scripting languages like java and python. In this tutorial, you can find a first brief introduction into this topic, focusing on the concept of a class. 

This tutorial is part of a series of tutorials and the code is available via GitHub. As a real life example, used throughout this series, we consider a class for solving a wordle-puzzle.

1. The Python class

A class is a complex variable type, which contains specific methods (or functions) and attributes (or properties). An instance of such a complex variable is called an object, and different objects can have different values for their attributes (and even methods).

To create a class in python the class keyword is used followed by the name you want to assign your class. In our case this is the WordleAssistant class.

class WordleAssistant():

Defining attributes

This WordleAssistant contains the attributes relevant to our puzzle solver. For example, if we want to make a generic solver, two useful attributes would be the wordle word length (WordleSize) and a dictionary of possible words (FullWordset). Unlike fortran or C++, attributes are not defined in the class definition, but can be dynamically created for a class-object. This a feature (or design flaw) gives rise to some dangerous practices such as the runtime (accidental) addition of attributes to an object. For good practices, one should refrain from this and create all attributes by initializing them during the initialization of the class instance. This is done using the __init__() method of the class:

class WordleAssistant():
    def __init__(self, size: int = 5, dictionary: str = None):
        self.WordleSize = size
        if dictionary is None:
            dictionary = "Mydict.txt"
        self.FullWordset = self.readDictionary(dictionary)

Here the WordleSize attribute is defined by setting it to the size parameter of the __init__ method, while the FullWordset attribute is defined by assigning it the result of the readDictionary method of the WordleAssistant class. As is common (and good) practice in OO langues we use the self variable to indicate the instance of the class, binding attributes and methods to the instance. You may also have noted python uses a dot-notation to indicate attributes/methods of a class, similar as C++ (while fortran uses the % symbol with the same effect).

!! NOTE: There also exist “class attributes” which are defined the way one would define instance attributes in fortran or C++. However, in python these attributes are shared by all instances of the class, as such changing them in one object will change them in all objects, creating a mess.

Defining methods

In the previous section, we already defined a first method, the initialization method. As a method is a function, it is constructed as any other function in python using the def keyword, with the body indented. The method itself is indented one level with respect to the class level. Similar as for a usual function, one can indicate the expected type and default value for each function parameter, and if a result is returned the type can be indicated as well, as can be seen in the example below for the readDictionary method.

class WordleAssistant():
    def __init__(self, size: int = 5, dictionary: str = None):
        ...

    def readDictionary(self, wordlist: str = None)->list:
        ...
        return wordlist 

Privacy

Although private attributes and methods don’t technically exist in Python, it is convention that attributes and methods prefixed with a single underscore are to be treated as non-public parts of the API. In addition, using two or more underscores gives rise to name mangling, which gives a practical behavior akin to making attributes and methods private. The __init__ method above is an example. We will come back to this when discussing inheritance and child classes.

2. The Python Object

Once the class is implemented, it can be used in a script by creating instances of the class. These instances are called Objects.

WA = WordleAssistant()

The above command creates an object WA which is of the class WordleAssistant. The object is initialized through a call to the __init__ method, which is performed by the assignment above. If defaults are provided for all parameters of the __init__ method, then no variables need to be passed to the WordleAssistant class call. Otherwise the creation of an instance could look like this:

wordleSize = 5
WA = WordleAssistant(size=wordleSize,dictionary='MyWords.txt')

Access to the attributes and methods of the WA object s gained using the dot-notation:

wordsize = WA.WordleSize 
wordlist = WA.FullWordset
Top10Guess = WA.getTop(top = 10)

Within the context of data-encapsulation one should never access attributes directly but use get and set methods instead.

3. Additional sources:

Permanent link to this article: https://dannyvanpoucke.be/python-tutorial-classes/

Wordle-mania: an opportunity for python programming and artificial intelligence.

Over that last few months the wordle game has become increasingly popular, with people sharing their daily feats on Twitter. Currently the game is hosted by the NY times which bought it the end of January 2022 from its creator.  The game is rather straightforward: you have 6 guesses to find a 5-letter English word. Every guess, the game tells you if a letter is (1) not in the word [grey], (2) in the word at a different position [yellow/orange], or (3) in the word at the exact same position [green].

Wordle 242 4/6
⬛⬛🟨⬛⬛
⬛🟨⬛⬛⬛
⬛⬛🟩🟨🟩
🟩🟩🟩🟩🟩
An example of the result (as it looks when shared on Twitter). My first guess was the word “PIANO”, which means the A is in the word but at a different position. My second word, “QUERY”, adds the U to the list of letters that are present. With my third guess, “STUCK”, the position of the U and the K are fixed and we now also know the letter C is involved. At this point, I was also stuck, so I got some help of my wordle-assistant program, which taught me there could only be 1 word matching all the information we had: “CAULK“.

This seamlessly brings me to the central topic of this post: writing a program to help win this game as efficiently as possible. Not terribly original, but it’s a means to an end, as this simple project allows us to explore some more advanced topics in programming in python as well as artificial intelligence.

During this exploration I’ll  be including and updating a set of tutorials as well as this post. The python side of the project will focus on efficiency and easy of use and distribution, while the AI side will focus on smart ways predicting the best possible next guess. For the latter, an important caveat is that this means that the program should also work if you’re the last player living on earth, or if you decide to play wordle in a different language or a different number of letters. This means that creating a distribution of the  tweeted results of other players and comparing this with the complete set of brute-forced distributions to guess the wordle of the day in a single guess, would not satisfy my definition of AI. It is an interesting Big-data kaggle competition though.

Python Tutorials

  • Classes in Python. This tutorial provides a simple introduction in the concept of classes in python.
  • Child Classes. Continuing on the previous we deal now with child classes and the intricacies of function overriding and accessibility.
  • Python Library on Github.
  • Jupyter Notebook examples.
  • Slow Python: Profiling python in Jupyter. We look into profiling a Jupyter notebook script, to find the bottlenecks.
  • Slow Python: speeding up copying.

 

Artificial Intelligence

  • Distributions of words and letters.
  • Information theory of wordle?

 

The WordleAssistant Library and notebooks.

All tutorial code and jupyter notebooks can be found in this github repository.

Permanent link to this article: https://dannyvanpoucke.be/wordle-mania-an-opportunity-for-python-programming-and-artificial-intelligence/

Parallel Python in classes…now you are in a pickle

In the past, I discussed how to create a python script which runs your calculations in parallel.  Using the multiprocessing library, you can circumvent the GIL and employing the async version of the multiprocessing functions, calculations are even performed in parallel. This works quite well, however, when using this within a python class you may run into some unexpected behaviour and errors due to the pickling performed by the multiprocessing library.

For example, if the doOneRun function is a class function defined as

class MyClass:
...
    def doOneRun(self, id:int):
       return id**3
...

and you perform some parallel calculation in another function of your class as

class MyClass:
...
    def ParallelF(self, NRuns:int):
       import multiprocessing as mp

       nproc=10
       pool=mp.Pool(processes=nprocs) 
       drones=[pool.apply_async(self.doOneRun, args=(nr,)) for nr in range(NRuns)] 

       for drone in drones: 
           Results.collectData(drone.get()) 
       pool.close() 
       pool.join() 
       
...

you may run into a runtime error complaining that a function totally unrelated to the parallel work (or even to the class itself) can not be pickled. 😯

So what is going on? In the above setup, you would expect the pool.apply_async function to take just a function pointer to the doOneRun function. However, as it is provided by a the call self.doOneRun, the pool-function grabs the entire class and everything it contains, and tries to pickle it to distribute it to all the processes.  In addition to the fact that such an approach is hugely inefficient, it has the side-effect that any part associated to your class needs to be pickleable, even if it is a class-function of a class used to generate an object which is just a property of the MyClass Class above.

So both for reasons of efficiency and to avoid such side-effects, it is best to make the doOneRun function independent of a class, and even placing it outside the class.

def doOneRun(id:int):
    return id**3
  
class MyClass:
...
    def ParallelF(self, NRuns:int):
       import multiprocessing as mp

       nproc=10
       pool=mp.Pool(processes=nprocs) 
       drones=[pool.apply_async(doOneRun, args=nr) for nr in range(NRuns)] 

       for drone in drones: 
           Results.collectData(drone.get()) 
       pool.close() 
       pool.join() 
       
...

This way you avoid pickling the entire class, reducing initialization times of the processes and the  unnecessary communication-overhead between processes. As a bonus, you also reduce the risk of unexpected crashes unrelated to the calculation performed.

Permanent link to this article: https://dannyvanpoucke.be/parallel-python-classes-pickle/

Tutorial OOP(V): Documenting Fortran 2003 Classes

In the previous sessions of this tutorial on Object Oriented Programming in Fortran 2003, the basics of OO programming, including the implementation of constructors and destructors as well as operator overloading were covered. The resulting classes have already become quite extended (cf. github source). Although at this point it is still very clear what each part does and why certain choices were made, memory fades. One year from now, when you revisit your work, this will no longer be the case. Alternately, when sharing code, you don’t want to have to dig through every line of code to figure out how to use it. These are just some of the reasons why code documentation is important. This is a universal habit of programming which should be adopted irrespective of the programming-language and-paradigm, or size of the code base (yes, even small functions should be documented).

In Fortran, comments can be included in a very simple fashion: everything following the “!” symbol (when not used in a string) is considered a comment, and thus ignored by the compiler. This allows for quick and easy documentation of your code, and can be sufficient for single functions. However, when dealing with larger projects retaining a global overview and keeping track of interdependencies becomes harder. This is where automatic documentation generation software comes into play.  These tools parse specifically formatted comments to construct API documentation and user-guides. Over the years, several useful tools have been developed for the Fortran language directly, or as a plugin/extension to a more general tool:

  • ROBODoc : A tool capable of generating documentation (many different formats) for any programming/script language which has comments.  The latest update dates from 2015.
  • Doctran : This tool is specifically aimed at free-format (≥ .f90 ) fortran, and notes explicitly the aim to deal with object oriented f2003. It only generates html documentation, and is currently proprietary with license costs of 30£ per plugin. Latest update 2016.
  • SphinxFortran : This extension to SphinxFortran generates automatic documentation for f90 source (no OO fortran) and generates an html manual. This package is written in python and requires you to construct your config file in python as well.
  • f90doc / f90tohtml : Two tools written in Perl, which transform f90 code into html webpages.
  • FotranDOC : This tool (written in Fortran itself) aims to generate documentation for f95 code, preferably in a single file, in latex. It has a simple GUI interface, and the source of the tool itself is an example of how the fortran code should be documented. How nice is that?
  • FORD : Ford is a documentation tool written in python, aimed at modern fortran (i.e. ≥ f90).
  • Doxygen :  A multi-platform automatic documentation tool developed for C++, but extended to many other languages including fortran. It is very flexible, and easy to use and can produce documentation in html, pdf, man-pages, rtf,… out of the box.

As you can see, there is a lot to choose from, all with their own quirks and features. One unfortunate aspect is the fact that most of these tools use different formatting conventions, so switching from one to the another is not an exercise to perform lightly. In this tutorial, the doxygen tool is used, as it provides a wide range of options, is multi-platform,  supports multiple languages and multiple output formats.

As you might already expect, Object Oriented Fortran (f2003) is a bit more complicated to document than  procedural Fortran, but with some ingenuity doxygen can be made to provide nice documentation even in this case.

1. Configuring Doxygen

Before you can start you will need to install doxygen:

  1. Go the the doxygen-download page and find the distribution which is right for you (Windows-users: there are binary installers, no hassle with compilations 🙂 ).
  2. Follow the installation instructions, also install GraphViz, this will allow you to create nicer graphics using the dot-tool.
  3. Also get a pdf version of the manual (doxygen has a huge number of options)

With a nicely installed doxygen, you can make use of the GUI to setup a configuration suited to your specific needs and generate the documentation for your code automatically. For Object Oriented Fortran there are some specific settings you should consider:GUI interface of doxygen.

  1.  Wizard tab

    • Project Topic : Fill out the different fields. In a multi-file project, with source stored in a folder structure, don’t forget to select the tick-box “Scan recursively” .
    • Mode Topic : Select “Optimize for Fortran output”.
    • Output Topic : Select one or more output formats you wish to generate: html, Latex (pdf), map-pages, RTF, and XML
    • Diagrams Topic: Select which types of diagrams you want to generate.
  2. Expert tab

    (Provides access each single configuration option to set in doxygen, so I will only highlight a few. Look through them to get a better idea of the capabilities of doxygen.)

    • Project Topic :
      • EXTENSION_MAPPING: You will have to tell doxygen which fortran extensions you are using by adding them, and identifying it as free format fortran: e.g. f03=FortranFree (If you are also including text-files to provide additional documentation, it is best to add them here as well as free format fortran).
    • Build Topic:
      • CASE_SENSE_NAMES: Even though Fortran itself is not case sensitive, it may be nice to keep the type of casing you use in your code in your documentation. Note, however, that even though the output may have upper-case names, the documentation itself will require lower-case names in references.
    • Messages Topic:
      • WARN_NO_PARAMDOC: Throw a warning if documentation is missing for a function variable. This is useful to make sure you have a complete documentation.
    • Source Browser Topic:
      • SOURCE_BROWSER: Complete source files are included in the documentation.
      • INLINE_SOURCES: Place the source body with each function directly in the documentation.
    • HTML Topic:
      • FORMULA_FONTSIZE: The fontsize used for generated formulas. If 10 pts is too small to get a nice effect of formulas embedded in text.
    • Dot Topic:
      • HAVE_DOT & DOT_PATH: If you installed GraphViz
      • DOT_GRAPH_MAX_NODES: Maximum number of nodes to draw in a relation graph. In case of larger projects, 50 may be too small.
      • CALL_GRAPH & CALLER_GRAPH: Types of relation graphs to include.
  3. Run tab

    • Press “Run doxygen” and watch how your documentation is being generated. For larger projects this may take some time. Fortunately, graphics are not generated anew if they are present from a previous run, speeding things up. (NOTE: If you want to generate new graphics (and equations with larger font size), make sure to delete the old versions first.) Any warnings and errors are also shown in the main window.
    • Once doxygen was run successfully, pressing the button “Show HTML output” will open a browser and take you to the HTML version of the documentation.

 

Once you have a working configuration for doxygen, you can save this for later use. Doxygen allows you to load an old configuration file and run immediately. The configuration file for the Timer-class project is included in the docs folder, together with the pdf-latex version of the generated documentation.  Doxygen generates all latex files required for generating the pdf. To generate the actual pdf, a make.bat file needs to be run (i.e. double-click the file, and watch it run) in a Windows environment.

2. Documenting Fortran (procedural)

Let us start with some basics for documenting Fortran code in a way suitable for doxygen. Since doxygen has a very extensive set of options and features, not all of them can be covered. However, the manual of more than 300 pages provides all the information you may need.

With doxygen, you are able to document more or less any part of your code: entire files, modules, functions or variables. In each case, a similar approach can be taken. Let’s consider the documentation of the TimeClass module:

  1. !++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
  2. !> \brief The <b>TimeClass module</b> contains the
  3. !! \link ttime TTime class\endlink used by the
  4. !! \link timerclass::ttimer TTimer class\endlink for practical timing.
  5. !!
  6. !! @author  Dr. Dr. Danny E. P. Vanpoucke
  7. !! @version 2.0-3  (upgrades deprecated timing module)
  8. !! @date    19-03-2020
  9. !! @copyright https://dannyvanpoucke.be
  10. !!
  11. !! @warning Internally, Julian Day Numbers are used to compare dates. As a
  12. !! result, *negative* dates are not accepted. If such dates are created
  13. !! (*e.g.*, due to a subtraction), then the date is set to zero.
  14. !!
  15. !! This module makes use of:
  16. !! - nothing; this module is fully independent
  17. !<-----------------------------------------------------------------------
  18. module TimeClass
  19.     implicit none
  20.     private

The documentation is placed in a standard single or multi-line fortran comment.  In case of multi-line documentation, I have the personal habit turning it into a kind of banner starting with a “!+++++++++” line and closing with a “!<——————-” line.  Such choices are your own, and are not necessary for doxygen documentation. For doxygen, a multi-line documentation block starts with “!>” and ends with “!<“ . The documentation lines in between can be indicated with “!!”. This is specifically for fortran documentation in doxygen. C/C++ and other languages will have slightly different conventions, related to their comment section conventions.

In the block above, you immediately see certain words are preceded by an “@”-symbol or a “\”, this indicates these are special keywords. Both the “@” and “\” can be used interchangeably for most keywords, the preference is again personal taste.  Furthermore, doxygen supports both html and markdown notation for formatting, providing a lot of flexibility. The multi-line documentation is placed before the object being documented (here an entire module).

Some keywords:

  • \brief : Here you can place a short description of the object. This description is shown in parts of the documentation that  provide an overview. Note that this is also the first part of the full documentation of the object itself. After a blank line, the \details(this keyword does not need to provided explicitly) section starts, providing further details on the object. This information is only visible in the documentation of the object itself.
  • \link … \endlink, or \ref : These are two option to build links between parts of your documentation. You can either use \ref nameobject or \link nameobject FormattedNameObject \endlink. Note that for fortran, doxygen uses an all non-capitalized namespace, so YourObject needs to be referenced as \ref yourobject or you will end up with an error and a missing link. So if you want your documentation to show YourObject as a link instead of yourobject, you can use the \link … \endlink construction.
  • “::”  : Referring to an element of an object can be done by linking the element and the object via two colons:  object::element . Here it is important to remember that your module is an object, so linking to an element of a module from outside that module requires you to refer to it in this way.
  • @author : Provide information on the author.
  • @version : Provide version information.
  • @date : Provide information on the date.
  • @copyright : Provide information on the copyright.
  • @warning : Provides a highlighted section with warning information for the user of your code (e.g., function kills the program when something goes wrong).
  • @todo[not shown] If you still have some things to do with regard to this object you can use this keyword. More interestingly, doxygen will also create a page where all to-do’s of the entire project are gathered, and link back to the specific code fragments.

 

  1. !++++++++++++++++++++++++++++++++++++++++++++++
  2. !>\brief Function to subtract two \link ttime TTime\endlink instance
  3. !! via the "-" operator. This is the function
  4. !! performing the actual operator overloading.
  5. !!
  6. !! \b usage:
  7. !! \code{.f03}
  8. !! Total = this - that
  9. !! \endcode
  10. !! This line also calls the \link copy assignment operator\endlink.
  11. !!
  12. !! \note The result should remain a positive number.
  13. !!
  14. !! @param[in] this The \link ttime TTime\endlink instance before
  15. !!                 the "-" operator.
  16. !! @param[in] that The \link ttime TTime\endlink instance after
  17. !!                 the "-" operator.
  18. !! \return Total The \link ttime TTime\endlink instance representing
  19. !!               the difference.
  20. !<---------------------------------------------
  21.     pure function subtract(this,that) Result(Total)
  22.         class(TTime), intent(in) :: this, that
  23.         Type(TTime) :: total

When documenting functions and subroutines there are some addition must-have keywords.

  • @param[in] , @param[out] ,or@param[in,out] : Provide a description for each of the function parameters, including their  intent: “in”, “out”, or “in,out” (note the comma!).
  • \return : Provides information on the return value of the function.
  • \b, \i : The next word is bold or italic
  • \n : Start a newline, without starting a new paragraph.
  • \note : Add a special note in your documentation. This section will be high lighted in a fashion similar to @warning.
  • \code{.f03}…\endcode :  This environment allows you to have syntax highlighted code in your documentation. The language can be indicated via the “extension” typical for said language. In this case: fortran-2003.
  • \f$ … \f$, or \f[ … \f] : Sometimes equations are just that much easier to convey your message. Doxygen also supports latex formatting for equations. These tags can be used to enter a latex $…$ or \[ \] math environments. The equations are transformed into small png images upon documentation generation, to be included in the html of your documentation. There are two important aspects to consider when using this option:
    1. Font size of the equation: Check if this is sufficient and don’t be afraid to change the font size to improve readability.
    2. Compilation is not halted upon an error: If the latex compiler encounters an error in your formula it just tries to continue. In case of failure, the end result may be missing or wrong. Debugging latex equations in doxygen documentation can be quite challenging as a result. So if you are using large complex equations, it may be advised to run them in a pure latex environment, and only past them in the documentation once you are satisfied with the result.

 

3. Documenting Fortran Classes

With the knowledge of the previous section, it is relatively easy to document most fortran code. Also the type of object orientation available in fortran 95, in which a fortran module is refurbished as a class. True fortran classes in contrast tend to give a few unexpected issues to deal with. Lets have a look at the documentation of the TTime class of the TimeClass module:

  1. !+++++++++++++++++++++++++++++++++++++++
  2. !> @class ttime
  3. !! \brief The TTime class contains all time functionality
  4. !! with regard to a single time stamp.
  5. !<-------------------------------------
  6.     type, public :: TTime
  7.       private
  8.         integer :: year    !< @private The year
  9.         integer :: month   !< @private The month (as integer).
  10.         ...
  11.     contains
  12.       private
  13.         procedure, pass(this),public :: SetTime       !<          @copydoc timeclass::settime
  14.         procedure, pass(this)        :: CalculateJDN  !< @private @copydoc timeclass::calculatejdn
  15.         procedure, pass(this)        :: SetJDN        !< @private @copydoc timeclass::setjdn
  16.         ...
  17.         procedure, pass(this)        :: copy          !< @private @copydoc timeclass::copy
  18.         ...
  19.         generic, public :: assignment(=) => copy      !<          @copydoc timeclass::copy
  20.         !> @{ @protected
  21.         final :: destructor !< @copydoc timeclass::destructor
  22.         !> @}
  23.     end type TTime
  24.  
  25.     ! This is the only way a constructor can be created,
  26.     ! as no "initial" exists, emulates the C++ constructor behavior
  27.     interface TTime
  28.         module procedure constructor
  29.     end interface TTime

To make sure doxygen generates a class-like documentation for our fortran class, it needs to be told it is a class. This can be done by documenting the class itself and using the keyword @class nameclass, with nameclass the name doxygen will use for this class (so you can choose something different from the actual class name). Unfortunately, doxygen will call this a “module” in the documentation (just poor luck in nomenclature). On the module page for the ttime class a listing is provided of all elements given in the class definition. The documentation added to each member (e.g.,:

  1. integer :: year !< @private The year

is shown as “\brief” documentation. By default all members of our function are considered as public. Adding the @private, @public, or @protected keyword instructs doxygen explicitly to consider these members as private, public or protected. (I used protected in the ttime code not as it should be used in fortran, but as a means of indicating the special status of the final subroutine (i.e. protected in a C++ way).)

However, there seems to be something strange going on. When following the links in the documentation, we do not end up with the documentation provided for the functions/subroutines in the body of our timeclass module. Doxygen seems to consider these two distinct things. The easiest way to link the correct information is by using the keyword @copydoc functionreference . The documentation is (according to doxygen) still for two distinctly different objects, however, this time they have the exact same documentation (unless you add more text on the member documentation line). In this context, it interesting to know there is also @copybrief and @copydetails which can be used to only copy the brief/details section.

In this example, the constructor interface is not documented, as this created confusion in the final  documentation since doxygen created a second ttime module/object linked to this interface. However, not documenting this specific instance of the constructor does not create such a large issue, as the module(the fortran module) function itself is documented already.

Conclusion

Documenting fortran classes can be done quite nicely with doxygen. It provides various modes of output: from a fully working website with in-site search engine to a hyperlinked pdf or RTF document. The flexibility and large number of options may be a bit daunting at first, but you can start simple, and work your way up.

As Fortran is supported as an extension, you will need to play around with the various options to find which combination gives the effect you intended. This is an aspect present in all automated code documentation generation tools, since object oriented Fortran is not that widely used. Nonetheless, doxygen provides a very powerful tool worth your time and effort.

PS:

Permanent link to this article: https://dannyvanpoucke.be/oop-fortran-tut6-en/

Tutorial OOP(IV) : Operator and Assignment Overloading

In the previous tutorial, we created a constructor and destructor for our TTimer class.  Next, we extend our class with overloaded operators. Depending on the type of object your class represents, you may want to define an addition/subtraction/multiplication/… operator. In addition, the assignment operator deserves some extra attention as you may want to have a clear control over this operation  (e.g.deep copy vs shallow copy). The full source of this tutorial and the previous, can be downloaded from my github-page.

Let us start with the latter: the assignment operator. As with all other operators, it is possible to overload the assignment operator in modern fortran.

1. Assignment (=) operator overloading

When dealing with objects and classes—or extended data-structures in general—, their properties often are (implicit) pointers to the actual data-structure. This brings an interesting source of possible bugs due to shallow copies being made while deep copies are expected (although the problem may be less pronounced in Fortran than it is in Python).

In a fortran object, the assignment of a pointer component (i.e., an explicit pointer variable, or a component which is an object itself) happens via a shallow copy (or pointer assignment). In contrast, for an allocatable component, the assignment operation performs by default a deep copy (i.e., space is allocated, and values are copied). Shallow copies are very useful with regard to quickly creating new handles to the same data-structure. However, if you want to make a true copy, which you can modify without changing the original, then a deep copy is what you want. By implementing assignment overloading for your own classes, you have more control over the actual copying process, and you can make sure you are creating deep copies if those are preferred.

The implementation of overloading for the assignment operator is not too complicated. It requires two lines in your class definition:

type, public :: TTimer
        private
        ...
    contains
        private
        procedure, pass(this) :: Copy                   !< Make a copy of a timer object
        generic, public       :: assignment(=) => Copy  !< This is how copy is used.
        ...
end type TTimer

First, you need to define a class method which performs a copy-operation—which in a fit or original though we decided to call “copy” ;-).  As you can see this function is private, so it will not be accessible to the user of your class via a call like :

call MyTimer%Copy()

Secondly, you link this class method via the “=>” to the assignment-operator.  It is a generic interface, which means the assignment operator could be linked to different functions, of which the relevant one will be determined and used during run-time. This generic is also public  (otherwise you would not be able to use it).

The implementation of the class method follows the standard rules of any class method and could look like

pure subroutine Copy(this,from)
        class(TTimer), intent(inout) :: this
        class(TTimer), intent(in) :: from

    this%firstProperty = from%firstProperty
    ...
    !make explicit copies of all properties and components
    ...

end subroutine Copy

The “this” object which we passed to our class method is the object on the left side of the assignment operator, while the “from” object is the one on the right side. Note that both objects are defined as “class” and not as “type”. Within the body of this method you are in charge of copying the data from the “from”-object to the “this”-object, giving you control over deep/shallow copying.

In practice the overloaded operator is used as:

type(TTimer):: TimerThis, TimerFrom

TimerFrom = TTimer() ! initialization of the timers
TimerThis = TTimer() ! (cf., previous tutorial on constructors and destructors)
... 
! do stuff with TimerFrom
...
TimerThis = TimerFrom ! although you type "=", the overloading causes this to be implemented as-if you wrote
                      ! call TimerThis%copy(TimerFrom)

2. Operator (+,-,*,/,…) overloading

Just as you can overload the assignment operator above, you can also overload all other fortran operators. However, be careful to keep things intuitive.  For example, an addition operation on our TTimer class is strange. What would it mean to add one timer to another? How would you subtract one chronometer from another? In contrast, inside our TTimer class we have a list of TTime objects which can be used to represent a date and time, as-well-as a time interval.[1]  For the remainder of this tutorial, we will assume the TTime class only represents time-intervals. For such a class, it makes sense to be able to add and subtract time intervals.

Let us start with the basic definition of our TTime-class:

type, public :: TTime
  private
   ...
   ! the properties of the TTime class
   ...
contains
  private
   ...
   ! the methods of the TTime class
   ... 
   procedure, pass(this)        :: copy          ! Copy content from other TTime instance,  
                                                 ! private, accessed via the assignment statement
   procedure, pass(this)        :: add           ! Add two TTime instances.
   procedure, pass(this)        :: subtract      ! subtract two TTime instances.
   generic, public :: assignment(=) => copy      ! This is how copy is used.
   generic, public :: operator(+)   => add       ! This is how add is used.
   generic, public :: operator(-)   => subtract  ! This is how subtract is used.
   final :: destructor
end type TTime

interface TTime
   module procedure constructor
end interface TTime

The TTime class has a constructor and destructor, implemented as we discussed before. The assignment operator is over-loaded as well. The overloading of the “+” and “” operator follows the same setup as for the assignment operator. First, you define a class method where you will implement the addition or subtraction. Second, you link this class method to the operator as a generic. The main difference with overloading the assignment operator is that you need to use the keyword operator instead of assignment, during the second step. The class methods are private, while the generic link is public. The only thing left to do is to implement the class methods. In case of operator overloading, the class methods are functions.

pure function add(this,that) Result(Total)
     class(TTime), intent(in) :: this, that
     Type(TTime) :: total

total = TTime()
...
! implementation of the addition of the properties of 
! this to the properties of that, and storing them in 
! Total
! e.g.: Total%seconds = this%seconds + that%seconds        
...
end function add

The returned object need to be defined as a type, and the further implementation of the function follows the standard fortran rules. It is important to note that for a function-header like this one, the object to the left of the operator will be the one calling the overloaded operator function, so:

Total = this + that

and not

Total = that + this

This may not seem this important, as we are adding two objects of the same class, but that is not necessarily always the case. Imagine that you want to overload the multiplication operator, such that you could multiply your time-interval with any possible real value. On paper

Δt * 3.5 = 3.5 * Δt

but for the compiler in the left product “this” would be a TTime object and “that” would be a real, while in the right product “this” is the real, and “that” is the TTime object. To deal with such a situation, you need to implement two class methods, which in practice only differ in their header:

pure function MultLeft(this,that) Result(Total) 
    class(TTime), intent(in) :: this
    real, intent(in) :: that 
    Type(TTime) :: total

and

pure function MultRight(that, this) Result(Total) 
    class(TTime), intent(in) :: this
    real, intent(in) :: that 
    Type(TTime) :: total

In the class definition both functions are linked to the operator as

procedure, pass(this) ::  MultLeft
procedure, pass(this) ::  MultRight
generic, public :: operator(*) => MultLeft, MultRight

With this in mind, we could also expand our implementation of the “+” and “” operator, by adding functionality that allows for the addition and subtraction of reals representing time-intervals. Also here, the left and right versions would need to be implemented.

As you can see, modern object oriented fortran provides you all the tools you need to create powerful classes capable of operator overloading using simple and straightforward implementations.

In our next Tutorial, we’ll look into data-hiding and private/public options in fortran classes.

 

 

[1] You could argue that this is not an ideal choice and that it would be better to keep these two concepts ( absolute and relative time) separate through the use of different classes. 

Permanent link to this article: https://dannyvanpoucke.be/oop-fortran-tut5-en/

Tutorial OOP(III): Constructors and Destructors

In this tutorial on Object Oriented Programming in Fortran 2003, we are going to discuss how to create constructors and destructors for a Fortran class. During this tutorial, I assume that you know how to create a new project and what a class looks like in Fortran 2003.  This tutorial is build around a TimerClass, which I wrote as an upgrade for my initial timing module in HIVE-tools. The full source of this TimerClass can be found and downloaded from github.

Where the former two tutorials were aimed at translating a scientific model into classes within the confines of the Fortran programming language, this tutorial is aimed at consolidating a class using good practices: The creation a constructor and destructor. As the destructor in Fortran classes is most straight forward of the two, we’ll start with it.

1. The destructor.

A destructor is a method (i.e., a class subroutine) which is automatically invoked when the object is destroyed (e.g., by going out of scope).  In case of a Fortran class, this task is performed by the class-method(s) indicated as  final procedure. Hence such methods are also sometimes referred to as finalizers. Although in some languages destructors and finalizers are two distinctly different features (finalizers are then often linked to garbage collecting), within the Fortran context I consider them the same.

Within the definition of our TTimerClass the destructor is implemented as:

  1. module TimerClass
  2. implicit none
  3.  
  4.     type, public :: TTimer
  5.       private
  6.       ! here come the properties
  7.     contains
  8.       private
  9.       ! here come the methods
  10.       final :: destructor
  11.     end type TTimer
  12.    
  13. contains
  14.  
  15.     subroutine destructor(this)
  16.     Type(TTimer) :: this
  17.     ! Do whatever needs doing in the destructor
  18.     end subroutine destructor
  19.    
  20. end module TimerClass

In contrast to a normal class-method, the destructor is called using the final keyword, instead of the usual procedure keyword. This method is private, as it is not intended to be used by the user anyway, only by the compiler upon cleanup of the instance of the class (i.e., the object). Furthermore, although defined as part of the class, a final subroutine is not type-bound, and can thus not be accessed through the type.

The destructor subroutine itself is a normal Fortran subroutine. There is, however, one small difference with a usual class-method, the parameter referring to the object (c.q. “this“) is indicated as a TYPE and not as a CLASS. This is because the destructor is only applicable to properties belonging to this “class” (Note that final subroutines are not inherited by the child-class). For a child-class (also called a derived class), the destructor of the child-class should deal with all the additional properties of the child-class, while the destructor of the parent-class is called to deal with its respective properties. In practice, the destructor of the child-class is called first, after which the destructor of the parent class is called (and recursively further along the class its family tree.)

So what do you put in such a destructor? Anything that needs to be done to allow the object to be gracefully terminated. Most obviously: deallocation of allocatable arrays, pointer components, closing file handles,…

2. The constructor.

Where other programming  languages may provide an initialization section or access to a key-worded constructor. Although Fortran allows for variables to be initialized upon definition, there is no constructor keyword available to be used in its classes. Of course, this does not prevent you from adding an “init()” subroutine which the user should call once the new object is allocated. You could even use a private Boolean property (initialized old style)  to keep track of the fact that an object was initialized when entering any of its methods, and if not, call the init() function there and then. There are many ways to deal with the initialization of a new object.  Furthermore, different approaches also put the burden of doing things right either with the programmer developing the class, or the user, applying the class and creating objects.

Here, I want to present an approach which allows you to present a clear set-up of your class and which resembles the instance creation approach also seen in other languages (and which implicitly shows the “pointer”-nature of objects ):

NewObject = TClass()

In case of our TTimer class this will look like:

Type(TTimer) :: MyTimer

MyTimer = TTimer()

This means we need to have a function with the exact same name as our class (cf., above), which is achieved through the use of an interface to a module procedure.  Just giving this name to the constructor function itself will cause your compiler to complain (“Name ttimer at (1)  is already defined as a generic interface“).  By using a different name for the  function, and wrapping it in an interface, this issue is avoided.

  1. module Timerclass
  2.     implicit none
  3.  
  4.  
  5.     type, public :: TTimer
  6.         private
  7.     ...
  8.     contains
  9.         private
  10.         ...
  11.     end type TTimer
  12.    
  13.     interface TTimer
  14.         module procedure Constructor
  15.     end interface TTimer
  16.  
  17. contains
  18. function Constructor() Result(Timer)
  19.     type(TTimer) :: Timer
  20.    
  21.     !initialize variables directly
  22.     Timer%x=...
  23.     ! or through method calls
  24.     call Timer%setTime(now)
  25.     ...
  26.  
  27. end function Constructor
  28.  
  29. end module TimerClass

Note that the constructor function is not part of the class definition, and as such the object is not passed to the constructor function. In addition, the Timer object being created is defined as a Type(TTimer) not Class(TTimer), also because this function is not part of the class definition.

That is all there is to it. Simple and elegant.

In our next Tutorial, we’ll have a look at operator and assignment overloading. Combined with a constructor and destructor as presented here, you are able to create powerful and intuitive classes (even in Fortran).

Permanent link to this article: https://dannyvanpoucke.be/oop-fortran-tut4-en/

Fortran dll’s and libraries: a Progress bar

In the previous fortran tutorials, we learned the initial aspects of object oriented programming (OOP) in fortran 2003. And even though our agent-based opinion-dynamics-code is rather simple, it can quickly take several minutes for a single run of the program to finish. Two tools which quickly become of interest for codes that need more than a few minutes to run are: (1) a progress bar, to track the advance of the “slow” part of the code and prevent you from killing the program 5 seconds before it is to finish, and (2) a timer, allowing you to calculate the time needed to complete certain sections of code, and possibly make predictions of the expected total time of execution.

In this tutorial, we will focus on the progress bar. Since our (hypothetical) code is intended to run on High-Performance Computing (HPC) systems and is written in the fortran language, there generally is no (or no easy) access to GUI’s. So we need our progress bar class to run in a command line user interface. Furthermore, because it is such a widely useful tool we want to build it into a (shared) library (or dll in windows).progress_1pct

The progress bar class

What do we want out of our progress bar? It needs to be easy to use, flexible and smart enough to work nicely even for a lazy user. The output it should provide is formatted as follows: <string> <% progress> <text progress bar>, where the string is a custom character string provided by the user, while ‘%progress’ and ‘text progress bar’ both show the progress. The first shows the progress as an updating number (fine grained), while the second shows it visually as a growing bar (coarse grained).

  1. type, public :: TProgressBar
  2. private
  3. logical :: init
  4. logical :: running
  5. logical :: done
  6. character(len=255) :: message
  7. character(len=30) :: progressString
  8. character(len=20) :: bar
  9. real :: progress
  10. contains
  11. private
  12. procedure,pass(this),public :: initialize
  13. procedure,pass(this),public :: reset
  14. procedure,pass(this),public :: run
  15. procedure,pass(this),private:: printbar
  16. procedure,pass(this),private:: updateBar
  17. end type TProgressBar

All properties of the class are private (data hiding), and only 3 procedures are available to the user: initialize, run and reset. The procedures, printbar and updatebar are private, because we intend the class to be smart enough to decide if a new print and/or update is required. The reset procedure is intended to reset all properties of the class. Although one might consider to make this procedure private as well, it may be useful to allow the user to reset a progress bar in mid progress.(The same goes for the initialize procedure.)

  1. subroutine run(this,pct,Ix,msg)
  2. class(TProgressBar) :: this
  3. real::pct
  4. integer, intent(in), optional :: Ix
  5. character(len=*),intent(in),optional :: msg
  6.  
  7. if (.not. this%init) call this%initialize(msg)
  8. if (.not. this%done) then
  9. this%running=.true.
  10. this%progress=pct
  11. call this%updateBar(Ix)
  12. call this%printbar()
  13. if (abs(pct-100.0)<1.0E-6) then
  14. this%done=.true.
  15. write(*,'(A6)') "] done"
  16. end if
  17. end if
  18.  
  19. end subroutine run

In practice, the run procedure is the heart of the class, and the only procedure needed in most applications. It takes 3 parameters: The progress (pct), the number of digits to print of pct (Ix),and the <string> message (msg). The later two parameters are even optional, since msg may already have been provided if the initialize procedure was called by the user. If the class was not yet initialized it will be done at the start of the procedure. And while the progress bar has not yet reached 100% (within 1 millionth of a %) updates and prints of the bar are performed. Using a set of Boolean properties (init, running, done), the class keeps track of its status. The update and print procedures just do this: update the progress bar data and print the progress bar. To print the progress bar time and time again on the same line, we need to make use of the carriage return character (character 13 of the ASCII table):

write(*,trim(fm), advance='NO') achar(13), trim(this%message),trim(adjustl(this%progressString)),'%','[',trim(adjustl(this%bar))

The advance=’NO‘ option prevents the write statement to move to the next line. This can sometimes have the unwanted side-effect that the write statement above does not appear on the screen. To force this, we can use the fortran 2003 statement flush(OUTPUT_UNIT), where “OUTPUT_UNIT” is a constant defined in the intrinsic fortran 2003 module iso_fortran_env. For older versions of fortran, several compilers provided a (non standard) flush subroutine that could be called to perform the same action. As such, we now have our class ready to be used. The only thing left to do is to turn it into a dll or shared library.progress_25pct

How to create a library and use it

There are two types of libraries: static and dynamic.

Static libraries are used to provide access to functions/subroutines at compile time to the library user. These functions/subroutines are then included in the executable that is being build. In linux environments these will have the extension “.a”, with the .a referring to archive. In a windows environment the extension is “.lib”, for library.

Dynamic libraries are used to provide access to functions/subroutines at run time. In contrast to static libraries, the functions are not included in the executable, making it smaller in size. In linux environments these will have the extension “.so”, with the .so referring to shared object. In a windows environment the extension is “.dll”, for dynamically linked library.

In contrast to C/C++, there is relatively little information to be found on the implementation and use of libraries in fortran. This may be the reason why many available fortran-“libraries” are not really libraries, in the sense meant here. Instead they are just one or more files of fortran code shared by their author(s), and there is nothing wrong with that. These files can then be compiled and used as any other module file.

So how do we create a library from our Progressbar class? Standard examples start from a set of procedures one wants to put in a library. These procedures are put into a .f or .f90 file. Although they are not put into a module (probably due to the idea of having compatibility with fortran 77) which is required for our class, this is not really an issue. The same goes for the .f03 or .f2003 extension for our file containing a fortran 2003 class. To have access to our class and its procedures in our test program, we just need to add the use progressbarsmodule clause. This is because our procedures and class are incorporated in a module (in contrast to the standard examples). Some of the examples I found online also include compiler dependent pragmas to export and import procedures from a dll. Since I am using gfortran+CB for development, and ifort for creating production code, I prefer to avoid such approaches since it hampers workflow and introduces another possible source of bugs.

The compiler setups I present below should not be considered perfect, exhaustive or fool-proof, they are just the ones that work fine for me. I am, however, always very interested in hearing other approaches and fixes in the comments.progress_52pct

Windows

The windows approach is very easy. We let Code::Blocks do all the hard work.

shared library: PBar.dll

Creating the dll : Start a new project, and select the option “Fortran DLL“. Follow the instructions, which are similar to the setup of a standard fortran executable. Modify/replace/add the fortran source you wish to include into your library and build your code (you can not run it since it is a library).

Creating a user program : The program in which you will be using the dll is setup in the usual way. And to get the compilation running smoothly the following steps are required:

  • Add the use myspecificdllmodule clause where needed, with myspecificdllmodule the name of the module included in the dll you wish to use at that specific point.
  • If there are modules included in the dll, the *.mod files need to be present for the compiler to access upon compilation of the user program. (Which results in a limitation with regard to distribution of the dll.)
  • Add the library to the linker settings of the program (project>build options>linker settings), and then add the .dll file.
  • Upon running the program you only need the program executable and the dll.

static library

The entire setup is the same as for the shared library. This time, however, choose the “Fortran Library” option instead of Fortran dll. As the static library is included in the executable, there is no need to ship it with the executable, as is the case for the dll.

Unix

For the unix approach we will be working on the command line, using the intel compiler, since this compiler is often installed at HPC infrastructures.

static library: PBar.a

After having created the appropriate fortran files you wish to include in your library (in our example this is always a single file: PBar.f03, but for multiple files you just need to replace PBar.f03 with the list of files of interest.)

  1. Create the object files:
    ifort -fpic -c -free -Tf Pbar.f03

    Where -fpic tells the compiler to generate position independent code, typical for use in a shared object/library, while -c tells the compiler to create an object file. The -free and -Tf compiler options are there to convince the compiler that the f03 file is actual fortran code to compile and that it is free format.

  2. Use the GNU ar tool to combine the object files into a library:
    ar rc PBarlib.a PBar.o
  3. Compile the program with the library
    ifort TestProgram.f90 PBarlib.a -o TestProgram.exe

    Note that also here the .mod file of our Progressbarsmodule needs to be present for the compilation to be successful.

shared library: PBar.so

For the shared library the approach does not differ that much.

  1. Create the object files:
    ifort -fpic -c -free -Tf Pbar.f03

    In this case the fpic option is not optional in contrast to the static library above. The other options are the same as above.

  2. Compile the object files into a shared library:
    ifort -shared PBar.o -o libPBar.so

    The compiler option -shared creates a shared library, while the -o option allows us to set the name of the library.

  3. Compile the program with the library
    ifort TestProgram.f90 libPBar.so -o TestProgram.exe

    Note that also here the .mod file of our Progressbarsmodule needs to be present for the compilation to be successful. To run the program you also need to add the location of the library file libPBar.so to the environment variable LD_LIBRARY_PATH

One small pickle

HPC systems may perform extensive buffering of data before output, to increase the efficiency of the machine (disk-writes are the slowest memory access option)…and as a result this can sometimes overrule our flush command. The progressbar in turn will not show much progress until it is actually finished, at which point the entire bar will be shown at once. There are options to force the infrastructure not to use this buffering (and the system administrators in general will not appreciate this), for example by setting the compiler flag -assume nobuffered_stdout. So the best solution for HPC applications will be the construction of a slightly modified progress bar, where the carriage return is not used.

progress_100pct

 

Special thanks also to the people of stack-exchange for clarifying some of the issues with the modules.

Source files for the class and test-program can be downloaded here.

 

Permanent link to this article: https://dannyvanpoucke.be/fortran-dlls-en/

Tutorial OOP(II): One problem, different possible classes

additional resources
agent paper: Sobkowicz
source-code: AgentTutorials
Arxiv: Full Tutorial

In the previous tutorial, we saw how to tackle an opinion dynamics problem using agents as a class in an Object Oriented Programming (OOP) approach. In many topics of interest in (socio-)physics and chemistry, we deal with a large number of particles, be it electrons, atoms, agents, stars, … These are contained in a superstructure (electrons⇒atom, atoms⇒molecule/solid, agents⇒population, stars⇒galaxy,…) which is generally represented in the code as an array. As we noted in the previous tutorial, there were several variables which were global to the agents, but we implemented them as properties of the agents anyhow. As a result, a significant amount of additional memory needed to be allocated for storing in essence the same data. This was done to prevent the need of having to provide this information at every function call.

Returning to our problem of interest, we now consider two object classes: The TAgent-class and the TPopulation-class. This leads to several possible ways this problem can be implemented.

  1. Array of TAgents: As was done in the previous tutorial, we only make a class of the agents, and put them in an array.
  2. TPopulation of TAgents: In this case we construct a class called TPopulation of which one property is the set of TAgents. The TPopulation-class also contains some of the global variables as properties, and operations on this set are methods of the TPopulation-class.
  3. TPopulation-class without TAgent-class: In this last case, the agents are dissolved, and their properties are stored in array-properties of the TPopulation-class. The methods of the TAgent-class now become methods of the TPopulation-class. And the global variables become additional properties of the TPopulation-class.

Although the true OOP-programmer may only consider the  second option the way to go, we will consider the third option in this tutorial.

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Tutorial OOP(I): Objects in Fortran 2003

After having set up our new project in the first session of this tutorial, we now come to an important second step: choosing and creating our Objects. In OOP, the central focus is not a (primitive) variable or a function, but “an object”. In Object Oriented Programming (OOP) most if not all variables and functions are incorporated in one or more (types of) objects. An object, is just like a real-life object; It has properties and can do things. For example: a car. It has properties (color, automatic or stick, weight, number of seats,…) and can do things (drive, break down, accelerate,…). In OOP, the variables containing the values that give the color, weight, stick or not,… of the car are called the properties of the car-object. The functions that perform the necessary calculations/modifications of the variables to perform the actions of driving, breaking down,… are called the methods.

Since we are still focusing on the opinion dynamics paper of Sobkowicz, let us use the objects of that paper to continue our tutorial. A simplified version of the research question in the paper could be as follows:

How does the (average) opinion of a population of agents evolve over time?

For our object-based approach, this already contains much of the information we need. It tells us what our “objects” could be: agents. It gives us properties for these objects: opinion. And it also tells us something of the methods that will be involved: opinion…evolve over time.

Let us now put this into Fortran code. A class definition in Fortran uses the TYPE keyword, just like complex data types.

  1. Type, public :: TAgentClass
  2. private
  3. real :: oi !< opinion
  4. contains
  5. private
  6. procedure, pass(this), public :: getOpinion
  7. procedure, pass(this), public :: setOpinion
  8. procedure, pass(this), public :: updateOpinion
  9. end type TAgentClass

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