PROFASI  Version 1.5
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SimTempRun Class Reference

Simulated tempering with profasi. More...

#include <SimTempRun.hh>

Inheritance diagram for SimTempRun:
Inheritance graph

Additional Inherited Members

- Public Member Functions inherited from BasicMCRun
int parseCommands (std::list< InstructionString > &cmds)
 Execute commands collected with getCommands.
- Protected Member Functions inherited from BasicMCRun
virtual void writeConf ()
 Write program state to PROFASI binary configuration file.
int recover (unsigned rcyc=(unsigned)-1)
 Restore the state of the run to a given point of a previous run.
FILE * open_segment (std::string prfx)
 Open a new conf.data___ file for a new simulation segment.
- Protected Attributes inherited from BasicMCRun
PopulationHandler PH
 A population handler.
ObsHandler H
 An observable handler.
RandomNumberHandler ranh
 A handler object for random numbers.
FFHandler ffh
 A force field handler.

Detailed Description

The class definition here looks a bit thin. It does not even have an explicit Run function. But it inherits a large number of properties from the class BasicMCRun. Most of the steps required during a simulated tempering run are also required in a simple cannonical MC run. There are only a few extra steps. This class implements only those differences relative to BasicMCRun. In simulated tempering, the temperature is a dynamic variable, and changes during the simulation. The algorithm defines a specific way in which the temperature is updated, which is implemented in the update_T() function. The Run function of the BasicMCRun class calls an update_T function at a suitable point. That has no meaning for a cannonical MC run, but gives a way to implement other algorithms without repeating too much code. The parseCommands function here only processes commands that are specific to simulated annealing.

The documentation for this class was generated from the following files:

PROFASI: Protein Folding and Aggregation Simulator, Version 1.5
© (2005-2016) Anders Irbäck and Sandipan Mohanty
Documentation generated on Mon Jul 18 2016 using Doxygen version 1.8.2