Higgs-Yukawa Polynomial Hybrid Monte Carlo (HYpHMC) 

    A collection of C++ utilities for the investiagtion of the lattice Higgs-Yukawa model using Monte-Carlo methods. The bulk of the source code was written by P. Gerhold (arXiv:1002.2569 [hep-lat]) and J. Kallarackal. Changes were made to conform to C++ standards and add the GNU auto-tools framework by J. Bulava. 

1: Obtaining the Code

   We use the GIT revision control system. Before obtaining the package, you 
install GIT, which is present in basically every package management system, or 
can be downloaded from http://git-scm.com/. With git installed, do 

     git clone git://github.com/johnbulava/HYpHMC

which will fetch the repository from github. There should now be a 'HYpHMC' 
directory created where you executed this command. 


2: Compiling 

     From the 'HYpHMC' directory, you first need to run 

		 aclocal
		 autoconf 
		 automake --add-missing 

successfully before proceeding. This will create the (machine-dependent) 
makefiles on your system. Once this has been completed the standard 
compilation chain

                  ./configure 
	          make 
	          make install 

can be performed. 

3: Running the code 

      The executables are found in the 'mainprogs' directory. To generate 
scalar field configurations, one must run `pHMC' in a directory that contains 
the input file `SimulationParameterspHMC.txt'. A sample version of this input 
file can be found in the `input_files' directory. The directory where pHMC is 
run must also have a complicated subdirectory structure. This structure can be 
created with the following commands: 

	mkdir -p dataBase/data/results/pHMC/
	cd dataBase/data/results/pHMC/
        mkdir FACC configurations miscellaneous revers analysis measure     omegaFields states

Hopefully, this will be fixed in future revisions. The 'pHMC' executable can 
now be run in the top dir. that contains 'dataBase'. Note: you probably want 
to make some symbolic link to a central data storage place. 

     Once a simulation has completed and the scalar field configurations have 
been generated, the 'analyzer' executable must be run in the same directory in
which 'pHMC' was run, to analyze the data. The input file 
'AnalyzerToDoList.dat' must be present in this directory. Before running this, 
create the directories 'data' and 'pics' in this directory, and copy the 
scripts 'fixbb' and 'makePlot' from the scripts directory. 

     After the analysis has been completed, the measurements can be analyzed 
using the 'evaluateConfs' executable. This requires the input file 
'EvaluateConfsToDoList.dat', which is identical to 'AnalyzerToDoList.dat', to
be created in the directory containing the 'dataBase' directory. 

     Once this has been completed, a latex summary of the results can be 
obtained by 

    cd dataBase/data/results/pHMC/analysis/subFolder<descriptor> 
    make 
  
4: Adding to the repository. 

   Please don't be afraid to add to the repository! Especially documentation! If you have changed some files (hopefully to add documentation) do 

	 git commit <filename> 

to add these changes to the repository. If you wish to commit all changes, do 

   git commit -a 

If you have created a new file, do 
   
	 git add <filename> 
	
to add it to the repository. After adding a file, you still need to do a 
'git commit <filename>' to commit the change. Note: When moving/renaming files,
'git commit' will delete the old files, but `git add' still must be performed 
to add the new files. Please do not add machine dependent makefiles 
(Makefile.in) to the repository. 

If you have made some changes that you wish to be commited to the central 
repository, please notify me (john.bulava@cern.ch), and I will commit them. 

If you want the latest changes from the central repository do 

        git pull git://github.com/johnbulava/HYpHMC