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			*** OPT-MHM ***




SOFTWARE INFORMATION :
======================

@author : Tristan Bereau
          ([email protected])

@contact: Department of Physics
          Carnegie Mellon University
          Pittsburgh, PA 15213 USA

@date   : March 2010

@version: 1.8

@license: GNU GENERAL PUBLIC LICENSE
          Please share feedback, bugs, code extensions to [email protected]
		  


PROGRAM :
=========

The multiple histogram method is used to compute temperature averages, as well
as free energy profiles. It relies on any number of simulations taken at
various temperatures, such as a parallel tempering simulation. One (or
optionally two) order parameter(s) is (are) used as input, as well as the
current energy. Hamiltonian Replica Exchange analysis is implemented. There is
no support for Umbrella sampling (though it's easily extendable).


References :
============

 * Ferrenberg and Swendsen, PRL, 61, 1988
   -> Histogram reweighting

 * Kumar et al., Journal of Computational Chemistry, 13, 1992, 
   -> Weighted Histogram Analysis Method (WHAM), or Multiple Histogram Method
   (MHM)

 * Bereau and Swenden, Journal of Computational Physics, 228, 2009
   -> Optimized convergence for the free energy differences between
   simulations. Algorithm implemented in optimizedf() in 'opt-mhm.c'.
   Describes the acronyms for DI and SINH algorithm used in the code.

 * Affentranger et al., JCTC, 2, 2006
   -> Hamiltonian Replica Exchange combined with WHAM.

GETTING STARTED :
=================

System Requirements : 
Compiler            : gcc/icc. This code was tested with both on a Linux
                      system. Depending on your compiler, you might want to
                      change the default values by hand. Right now, gcc is
                      used for both the serial and the parallel codes.		
Additional software : None.



INSTALLATION :
==============

Untar. Then type 'make serial' in the opt-mhm directory for a serial version, or
'make openmp' for a threaded version. To compile both at once type 'make all'
or simply 'make'.



QUICK START :
=============

opt-mhm needs a few things :

  * Observable files which contains all data points. The following format should
    be used without any order parameter

    Time		Energy

    for one order parameter:

    Time		Coord			Energy

    and for two order parameters:

    Time		Coord1			Coord2			Energy

    where 
      'Time' shows the advancement of the simulation. It can be in any kind of
      units (MC/MD time, snapshot ID, etc.); 
	  
      'Coord' is the value of the order parameter we're measuring. Again,
      any unit can be used.

      'Energy' is some energy that we use to measure the system, such as
      potential energy, total energy, internal energy, etc. 
      *** The units need to be in k_BT ***


  * A metafile which contains the relative path to all simulations, plus some
    extra information. The folowing format should be used:

    Path_i		Temperature_i		Snapshot_i	  autocor_factor_i

    where
      'Path_i' is the relative path from metafile to the observable file of
      simulation 'i'.

      'Temperature_i' is the temperature at which simulation 'i' was
      performed.
      *** Temperature should be expressed in multiples of k_BT ***

      'Snapshot_i' determines the first snapshot that should be used when
      sampling. This is useful when data was taken before equilibrium was
      reached. This should obviously be compatible with the format used for
      'Time' in the observable file.

      'autocor_factor_i' represents how correlated the data is. It is an
      integer that specifies how many files should be taken into account. For
      example, a factor of 10 means that one data point every 10 will be
      sampled to avoid correlations.


Command line arguments are explained by simply launching the program without
arguments.

Note that one can run Hamiltonian Replica Exchange analyses by replacing
temperatures by force field coupling (as a multiplicative factor of the
original interaction), and the potential energy of the altered
interaction(s). The temperature at which the analysis is done should be given
as an input parameter.

BUGS/NOTES :
============

 * In case only one order parameter is defined, the free energy profile is saved
   in one file containing 2D data: free energy (3rd column in the data file) as a
   function of temperature (1st column) AND the first order parameter (2nd
   column). In order to plot the free energy profile for a given temperature in
   gnuplot, use the following command  

   plot 'OUTPUT_FILE' u 2:3 every :::X::X

   where X is the index corresponding to the temperature 
   (T = T_MIN + X * T_STEP). 

 * Order the simulations inside the metafile such that temperatures are
   numerically sorted. The algorithm assumes that neighboring simulations (as
   ordered in the metafile) have the largest overlap.
 

 * Version 1.8: added bootstrap calculation for entropy.