Extended dynamics for harmonic restraints

[fhh2626]

As mentioned in issues #874 and #649, this PR enables the use of a harmonic restraint as a collective variable (CV). This allows enhanced sampling algorithms to calculate the free-energy change associated with creating or removing such a harmonic restraint. Specifically, I reimplemented the algorithm and adapted the interface suggested by Jerome:

colvarsTrajFrequency      500              
colvarsRestartFrequency   50000            

colvar {
  name d
  distance {
    group1 {
      atomnumbers   4759
    }
    group2 {
      dummyAtom (-2.543, 1.510, 0.364)    
    }
  }
}

colvar {
  name k_cv

  extendedLagrangian on
  extendedMass 1500000
  extendedLangevinDamping 5000

  lowerBoundary      0.0
  upperBoundary      1.0
  width 0.05
  
  reflectinglowerboundary  on
  reflectingupperboundary  on
  
  subtractAppliedForce     on
  
  harmonicForceConstant {
  }
}

harmonic {
  name       harm
  colvars       d
  centers       0
  forceConstant 10
  dynamicForceConstantLambda k_cv
  dynamicForceConstantExponent 4.0
}


 abf {
   colvars k_cv
   fullSamples 1000
   outputFreq  100000
   historyFreq 100000
}
metadynamics {
    colvars             k_cv
    hillWeight          0.05
    hillWidth           3.0
    wellTempered        on
    biasTemperature     3000
    keepFreeEnergyFiles on
    outputFreq   100000
}