Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/ianhinder/Kranc

A Mathematica package for generating code for solving time dependent partial differential equations
https://github.com/ianhinder/Kranc

Last synced: about 1 month ago
JSON representation

A Mathematica package for generating code for solving time dependent partial differential equations

Awesome Lists containing this project

README 

        

========================================

    KRanc Assembles Numerical Codes

========================================



What is Kranc?

--------------



Kranc is a set of Mathematica scripts to convert systems of time

evolution PDEs into code for numerical simulations using the Cactus

infrastructure.  You need Mathematica in order to use Kranc.



NOTE: This README has not been updated for use with modern versions of

Kranc and the instructions below will not work.



What is here?

-------------



README           This file



COPYING          Licensing information - Kranc is licensed under the GPL



Tools            Mathematica packages used in the conversion of a PDE system

                 to a numerical code



Examples         Worked out examples (massive scalar field, Maxwell equations, ADM

                 formulation of general relativity) -- Not currently included



Auxiliary        Auxiliary code required for compilation of the code produced

                 by the scripts



Getting up and running with the examples

----------------------------------------



For the following instructions, we assume that you are working

on a Unix-type system, and that you have Mathematica and a C compiler

installed.  We have tested with Mathematica version 8.

The example for the Einstein equations requires a Fortran 90 compiler, as it

relies on existing Fortran code for initial data.



We assume that your Kranc directory lives in your home directory, so

that this file is ~/Kranc/README.  If this is not the case, modify the

pathnames given in the following accordingly.  We will be creating a

standard Cactus directory as well, as ~/Cactus.  These instructions

are for the Klein-Gordon example, which is the simplest example.

There are also notes at the end on things you need if you want to try

out the other examples.



Building the Massive Klein-Gordon arrangement

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



Change into the directory appropriate for this example:



  cd ~/Kranc/Examples/KleinGordon



Invoke a Mathematica command line session with input from the source

file (this relies on the Kranc packages being found in the correct

place relative to the current directory):



  math < MKGTT.m



There will be some output, and an arrangement directory MKG will be

created containing the thorns.  A thorn list will also be created as

MKG/MKG.th



Installing the Cactus flesh and the required standard thorns

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



Login to the cactusdevcvs repository (you only need to do this once;

the login information is cached in your home directory):



cvs -d :pserver:[email protected]:/cactusdevcvs login



Enter the password "anon".



Check out the Cactus "flesh" from CVS.  This command will check out

the beta 14 version.



  cvs -d :pserver:[email protected]:/cactusdevcvs co -r Cactus_4_0_Beta_14 Cactus



Change into the Cactus directory:



  cd Cactus



You can use this Cactus directory for all the examples, and all your

work with Kranc.



Make a directory for your thornlists:



  mkdir thornlists



Link the MKG.th thornlist into this directory (replace with the

correct path to your thornlist):



  ln -s ~/Kranc/Examples/KleinGordon/MKG/MKG.th thornlists/MKG.th



Run the program used for checking out public thorns:



  gmake checkout



Enter "arr" to download thorns by arrangement, choose default option to

download all arrangements. Press q to quit the checkout program.



For consistency with the Cactus 4.0 Beta14 release, you need to

checkout the MoL thorns separately. Enter the Cactus/arrangements directory

and issue the command 



  cvs -d :pserver:[email protected]:/cactusdevcvs co -r Cactus_4_0_Beta_14 AlphaThorns/MoL



Verify that the thorns have been downloaded into the Cactus/arrangements

directory.



Linking the extra thorns into your Cactus installation

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



You should have a ~/Cactus/arrangements directory into which the

standard Cactus thorns have been downloaded.



Create a symbolic link from the MKG arrangement to here:



  ln -s ~/Kranc/Examples/KleinGordon/MKG ~/Cactus/arrangements/MKG



Create a symbolic link from the KrancNumericalTools arrangement to here:



  ln -s ~/Kranc/Auxiliary/Cactus/KrancNumericalTools ~/Cactus/arrangements/KrancNumericalTools



Building a Cactus configuration

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~



You need to create a Cactus "configuration"; this is a directory in

Cactus/configs in which a particular set of thorns (in this case those

listed in MKG.th) are compiled.  For simplicity, you may like to use a

new configuration for each of the examples.  However, it is also

possible to manually merge the thornlists generated from many

different Kranc arrangements and create just one configuration for all

of them.



gmake mkg-config THORNLIST=thornlists/MKG.th



Now compile the configuration:



gmake mkg



An executable program called cactus_mkg should be created in the

Cactus/exe directory.  See the Cactus documentation for instructions

concerning how to compile using optimization.



Running the examples

~~~~~~~~~~~~~~~~~~~~



Create a directory to run Cactus in for the MKG example:



  mkdir MKG

  cd MKG



Run the cactus_mkg executable with the example parameter file.



  ~/Cactus/exe/cactus_mkg ~/Kranc/Examples/KleinGordon/MKG100.par



A directory MKG_100 will be created containing output from the run.



Viewing the output

~~~~~~~~~~~~~~~~~~



Cactus based codes can generate output in many formats.  For getting

started we recommend ygraph (http://www.aei.mpg.de/~pollney/ygraph) to

look at 1D data.



ygraph MKG_100/phi_x_\[6]\[6].xg



Running the other examples

--------------------------



We also supply Maxwell's equations and the ADM form of the Einstein

equations as examples.  To run the ADM example, you will need an extra

thorn ("Exact") which is not part of Cactus.



cd ~/Cactus



Login to the numrelcvs repository



cvs -d :pserver:[email protected]:/numrelcvs login

Password: anon



Check out the necessary thorns:



cvs -d :pserver:[email protected]:/numrelcvs co AEIThorns/Exact



Link the AEIThorns arrangement into your Cactus/arrangements directory:



ln -s ~/Cactus/AEIThorns ~/Cactus/arrangements/AEIThorns



You also have to add the following thorns to the thornlist KrancADM.th:



AEIThorns/Exact

CactusEinstein/ADMCoupling

CactusEinstein/CoordGauge

CactusEinstein/StaticConformal



NB: You will need a Fortran 90 compiler to compile the Exact thorn,

and several of the standard Cactus thorns needed for Einstein's

equations.  We recommend the Intel Fortran Compiler, version 8 as of

the time of writing.  See the Cactus documentation for details about

telling Cactus which compiler to use for a particular configuration.



Contributing to Kranc

---------------------



In order to contribute a patch to Kranc, first ensure that you are

working with a clone of the Kranc repository, obtained by



  git clone http://github.com/ianhinder/kranc



Commit your patches to your local working copy, preferably with each

new feature in a separate patch, and make sure the repository is up to

date by using



  git pull --rebase



every so often.  The --rebase makes sure that your commits are moved

to the end of the history.  It is wise to do this frequently to avoid

complicated merging.  When your patches are ready, use



  git format-patch origin



which will output numbered .patch files, one per commit, to the

current directory.  Commits which are present in your repository but

not in the public repository you cloned from (origin) will be output.



Email these to the maintainers for review and inclusion.



Authors:

--------



Sascha Husa



Christiane Lechner



Ian Hinder



  Max Planck Institute for Gravitational Physics / Albert Einstein Institute

  Am Muehlenberg 1

  14476 Potsdam

  Germany



  http://numrel.aei.mpg.de