MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement Class Reference

Public Member Functions
def	__init__ (self, rundirs)
def	getMaximumMeasurementTime (self)
def	getMeanSquareDisplacement (self, deltaT)
def	fitToData (self, function=None, minTime=None, maxTime=None)
def	getMPLAxes (self, showEstimatedStandardDeviation=True, lines=[])

Detailed Description

Analysis class for data on mean square displacement, as produced by
`OpenMPCD::CUDA::MPCFluid::Instrumentation::LogicalEntityMeanSquareDisplacement`.

Unless specified otherwise, all times are measured in units of `measurement
time`, as defined in
`OpenMPCD::CUDA::MPCFluid::Instrumentation::LogicalEntityMeanSquareDisplacement`.

@see OpenMPCD::CUDA::MPCFluid::Instrumentation::LogicalEntityMeanSquareDisplacement

Definition at line 20 of file LogicalEntityMeanSquareDisplacement.py.

Constructor & Destructor Documentation

__init__()

def MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement.__init__	(		self,
			rundirs
	)

    The constructor.

    @throw TypeError
           Throws if `rundir` is not a `str`, or a `list` of `str`.
    @throw ValueError
           Throws if the given `rundir` does not exist, or does not contain
           a readable, valid data file.
    @throw ValueError
           Throws if `rundir` is an empty list.

    @param[in] rundirs
               The run directory, as a `string`. From this directory, the
               file `logicalEntityMeanSquareDisplacement.data` will be read
               as input. If this file does not exist,
               `logicalEntityMeanSquareDisplacement.data.xz` will be read
               instead.
               Alternatively, this can be a list of strings, each element
               of which specifies a directory that is treated as described
               above.

Definition at line 44 of file LogicalEntityMeanSquareDisplacement.py.

Member Function Documentation

fitToData()

def MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement.fitToData	(		self,
			function = None,
			minTime = None,
			maxTime = None
	)

    Fits the data to the given function, and returns the optimal function
    parameters.

    @param[in] function
               A function object suitable to be used as the first argument
               to `scipy.optimize.curve_fit`, or `None`, in which case a
               function of the form \f$ y\left(x\right) = p_1 x^{p_2} \f$
               with parameters \f$ p_1 \f$ and \f$ p_2 \f$ is used.
    @param[in] minTime
               If not `None`, this value specifies the minimum value of the
               measurement time that will be used for the fit.
    @param[in] maxTime
               If not `None`, this value specifies the maximum value of the
               measurement time that will be used for the fit.

Definition at line 158 of file LogicalEntityMeanSquareDisplacement.py.

getMaximumMeasurementTime()

def MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement.getMaximumMeasurementTime

(

self

)

    Returns, in units of `measurement time`, the maximum correlation time
    that was configured to be measured, i.e. \f$ N_A \f$.

Definition at line 107 of file LogicalEntityMeanSquareDisplacement.py.

getMeanSquareDisplacement()

def MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement.getMeanSquareDisplacement	(		self,
			deltaT
	)

    Returns an `OnTheFlyStatisticsDDDA` object that holds information on the
    sample of measured mean square displacements for time difference
    `deltaT`.

    @throw TypeError
           Throws if any of the arguments have invalid types.
    @throw ValueError
           Throws if any of the arguments have invalid values.

    @param[in] deltaT
               The time difference to return results for, measured in
               This argument is to be of type `int`, positive, and at
               most `getMaximumMeasurementTime()`.

Definition at line 128 of file LogicalEntityMeanSquareDisplacement.py.

getMPLAxes()

def MPCDAnalysis.LogicalEntityMeanSquareDisplacement.LogicalEntityMeanSquareDisplacement.getMPLAxes	(		self,
			showEstimatedStandardDeviation = True,
			lines = []
	)

    Returns an `matplotlib.axes.Axes` object that plots the mean square
    displacement against the diffusion time, in units of `measurement time`.

    @throw TypeError
           Throws if any of the arguments have invalid types.
    @throw ValueError
           Throws if any of the arguments have invalid values.

    @param[in] showEstimatedStandardDeviation
               Whether to show, for each data point, the estimated standard
               deviation.
    @param[in] lines
               A list of lines to plot, in addition to the data. Each
               element of this list represents a line and is a list
               containing, in this order:
                 - A list containing `x` and `y` coordinates for the
                   starting point of the line,
                 - Likewise for the ending point.

Definition at line 207 of file LogicalEntityMeanSquareDisplacement.py.

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

• LogicalEntityMeanSquareDisplacement.py