Synopsis

This analyzer calculates the radii of gyration of blocks of atoms of the same type within a molecule and the mean-squared distanced between the center of mass of different blocks, for a specified species of molecule. This was written for use with block copolymers, but the definition of a "block" used here operationally mean "a set of all atoms of a specific atom type", without regard to whether they form a contiguous block within the molecular structure.

KNOWN BUG: The algorithm appears to assume that the chosen species will contain at least one atom every type of atom in the simulation (i.e., at least one atom of each type 0,...,nAtomType). This is correct only for a few situations, such as a melt of AB diblock copolymers, and will probably crash if this assumption is not correct.

Parameters

The parameter file format is:

BlockRadiusGyration{ 
   interval           int
   outputFileName     string
   samplePerBlock     int
   speciesId          int
}

in which

interval	number of steps between data samples
outputFileName	name of output file
samplePerBlock	number of samples averaged in each block average
speciesId	integer index of molecular species

Output

If nSamplePerBlock != 0, a time sequence of block average values of these quantities will be output to a file {outputFileName}.dat during the simulation. Final average values with error estimates are output to {outputFileName}.ave.