Synopsis

This analyzer calculates structure factors using a specified set of "mode" vectors, which define weighting factors for different atom types, and a specified set of reciprocal lattice wavevectors.

See the McMd::StructureFactor class documentation for a precise mathematical definition of the structure factor, and an explanation of the notion of "modes". Also see the example input file below.

See also: McMd::StructureFactor; Util::IntVector

Parameters

The parameter file format is:

StructureFactor{ 
   interval           int
   outputFileName     string
   nMode              int
   modes              Matrix<double> [nMode x nAtomType]
   nWave              int
   waveIntVectors     Array<IntVector> [nWave]
}

in which

interval	number of steps between data samples
outputFileName	name of output file
nMode	number of modes (vectors in space of dimension nAtomType)
modes	Each row is a vector of dimension nAtomType, which specifies a set of weight factors for different atom types in the calcultation of Fourier modes.
nWave	number of reciprocal lattice wavevectors.
waves	array of reciprocal lattice vectors, each specified on a separate line by 3 integer indices (Miller indices)

Example

Consider a system with nAtomType = 2, with two monomer types 0 and 1. The correlation function for the monomer density can be calculted using a mode vector (1,1). The correlation function for the difference between the A and B monomer concentrations can be calculated using the mode vector (1,-1). A parameter file input for simultaneously calculating the density and composition mode correlation functions for 5 wavevectors along the x axis in a cubic or orthorhombic unit cell might look like this:

StructureFactor{
   interval                      1000
   outputFileName    StructureFactor
   nMode                            1
   modes                     1      1
                             0     -1
   nWave                            5
   waveIntVectors     8      0      0
                      9      0      0 
                     10      0      0 
                     11      0      0 
                     12      0      0 
}

Output Files

At the end of a simulation, all of the structure factors are output in a file {outputFileName}.dat Each line in this file contains the results for a single wavevector. Each line contains the 3 Miller indices of a wavevector, the absolute magnitude of the wavevector, and a list of structure factor values for that wavevector, one for each mode.