# Source code for espressomd.accumulators

# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
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#
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
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from .script_interface import ScriptObjectRegistry, ScriptInterfaceHelper, script_interface_register
import numpy as np

[docs]@script_interface_register
class MeanVarianceCalculator(ScriptInterfaceHelper):

"""
Accumulates results from observables.

Parameters
----------
obs : :class:espressomd.observables.Observable
delta_N : :obj:int
Number of timesteps between subsequent samples for the auto update mechanism.

Methods
-------
update()
Update the accumulator (get the current values from the observable).

"""
_so_name = "Accumulators::MeanVarianceCalculator"
_so_bind_methods = (
"update",
"get_mean",
"get_variance"
)
_so_creation_policy = "LOCAL"

[docs]@script_interface_register
class TimeSeries(ScriptInterfaceHelper):

"""
Records results from observables.

Parameters
----------
obs : :class:espressomd.observables.Observable
delta_N : :obj:int
Number of timesteps between subsequent samples for the auto update mechanism.

Methods
-------
update()
Update the accumulator (get the current values from the observable).
clear()
Clear the data

"""
_so_name = "Accumulators::TimeSeries"
_so_bind_methods = (
"update",
"time_series",
"clear"
)
_so_creation_policy = "LOCAL"

[docs]@script_interface_register
class Correlator(ScriptInterfaceHelper):

"""
Calculates correlations based on results from observables.

Parameters
----------
obs1 : :class:espressomd.observables.Observable
The observable :math:A to be correlated with :math:B (obs2).
If obs2 is omitted, autocorrelation of obs1 is calculated by
default.

obs2 : :class:espressomd.observables.Observable, optional
The observable :math:B to be correlated with :math:A (obs1).

corr_operation : :obj:str
The operation that is performed on :math:A(t) and
:math:B(t+\\tau) to obtain :math:C(\\tau). The
following operations are currently available:

* "scalar_product": Scalar product of :math:A and
:math:B, i.e., :math:C=\\sum\\limits_{i} A_i B_i

* "componentwise_product": Componentwise product of
:math:A and :math:B, i.e., :math:C_i = A_i B_i

* "square_distance_componentwise": Each component of
the correlation vector is the square of the difference
between the corresponding components of the observables, i.e.,
:math:C_i = (A_i-B_i)^2. Example: when :math:A is
:class:espressomd.observables.ParticlePositions, it produces the
mean square displacement (for each component separately).

* "tensor_product": Tensor product of :math:A and
:math:B, i.e., :math:C_{i \\cdot l_B + j} = A_i B_j
with :math:l_B the length of :math:B.

* "fcs_acf": Fluorescence Correlation Spectroscopy (FCS)
autocorrelation function, i.e.,

.. math::

G_i(\\tau) =
\\frac{1}{N} \\left< \\exp \\left(
- \\frac{\\Delta x_i^2(\\tau)}{w_x^2}
- \\frac{\\Delta y_i^2(\\tau)}{w_y^2}
- \\frac{\\Delta z_i^2(\\tau)}{w_z^2}
\\right) \\right>

where :math:N is the average number of fluorophores in the
illumination area,

.. math::

\\Delta x_i^2(\\tau) = \\left( x_i(0) - x_i(\\tau) \\right)^2

is the square displacement of particle
:math:i in the :math:x direction, and :math:w_x
is the beam waist of the intensity profile of the
exciting laser beam,

.. math::

W(x,y,z) = I_0 \\exp
\\left( - \\frac{2x^2}{w_x^2} - \\frac{2y^2}{w_y^2} -
\\frac{2z^2}{w_z^2} \\right).

The values of :math:w_x, :math:w_y, and :math:w_z
are passed to the correlator as args. The correlator calculates

.. math::

C_i(\\tau) =
\\exp \\left(
- \\frac{\\Delta x_i^2(\\tau)}{w_x^2}
- \\frac{\\Delta y_i^2(\\tau)}{w_y^2}
- \\frac{\\Delta z_i^2(\\tau)}{w_z^2}
\\right)

Per each 3 dimensions of the
observable, one dimension of the correlation output
is produced. If "fcs_acf" is used with other observables than
:class:espressomd.observables.ParticlePositions, the physical
meaning of the result is unclear.

The above equations are a
generalization of the formula presented by Hoefling
et. al. :cite:hofling11a. For more information, see
references therein.

delta_N : :obj:int
Number of timesteps between subsequent samples for the auto update mechanism.

tau_max : :obj:float
This is the maximum value of :math:\\tau for which the
correlation should be computed.  Warning: Unless you are using
the multiple tau correlator, choosing tau_max of more than
100 * dt will result in a huge computational overhead.  In a
multiple tau correlator with reasonable parameters, tau_max
can span the entire simulation without too much additional cpu time.

tau_lin : :obj:int
The number of data-points for which the results are linearly spaced
in tau. This is a parameter of the multiple tau correlator. If you
want to use it, make sure that you know how it works. tau_lin must
be divisible by 2. By setting tau_lin such that
tau_max >= dt * delta_N * tau_lin, the
multiple tau correlator is used, otherwise the trivial linear
correlator is used. By setting tau_lin = 1, the value will be
overridden by tau_lin = ceil(tau_max / (dt * delta_N)), which
will result in either the multiple or linear tau correlator.
In many cases, tau_lin=16 is a
good choice but this may strongly depend on the observables you are
ref. :cite:ramirez10a or to perform your own tests.

compress1 : :obj:str
These functions are used to compress the data when
going to the next level of the multiple tau
correlator. This is done by producing one value out of two.
The following compression functions are available:

* "discard2": (default value) discard the second value from the time series, use the first value as the result

* "discard1": discard the first value from the time series, use the second value as the result

* "linear": make a linear combination (average) of the two values

If only compress1 is specified, then
the same compression function is used for both
observables. If both compress1 and compress2 are specified,
then compress1 is used for obs1 and compress2 for obs2.

Both discard1 and discard2 are safe for all
observables but produce poor statistics in the
tail. For some observables, "linear" compression
can be used which makes an average of two
neighboring values but produces systematic
errors.  Depending on the observable, the
systematic error using the "linear" compression
can be anything between harmless and disastrous.
:cite:ramirez10a or to perform your own tests.

compress2 : :obj:str, optional
See compress1.

args: :obj:float of length 3
Three floats which are passed as arguments to the correlation
function. Currently it is only used by "fcs_acf", which
will square these values in the core; if you later decide to
update these weights with obs.args = [...], you'll have to
provide already squared values! Other correlation operations
will ignore these values.
"""

_so_name = "Accumulators::Correlator"
_so_bind_methods = (
"update",
"finalize")
_so_creation_policy = "LOCAL"

[docs]    def result(self):
"""
Returns
-------

numpy.ndarray
The result of the correlation function as a 2d-array.
The first column contains the values of the lag time tau.
The second column contains the number of values used to
perform the averaging of the correlation. Further columns contain
the values of the correlation function. The number of these columns
is the dimension of the output of the correlation operation.
"""
res = np.array(self.call_method("get_correlation"))
return res.reshape((self.n_result, 2 + self.dim_corr))

[docs]@script_interface_register
class AutoUpdateAccumulators(ScriptObjectRegistry):

"""
Class for handling the auto-update of accumulators used by
:class:espressomd.system.System.

"""
_so_name = "Accumulators::AutoUpdateAccumulators"
_so_creation_policy = "LOCAL"

"""
Adds an accumulator instance to the auto-update list.

"""

[docs]    def remove(self, accumulator):
"""
Removes an accumulator from the auto-update list.

"""
self.call_method("remove", object=accumulator)

[docs]    def clear(self):
"""
Removes all accumulators from the auto-update list.
"""
self.call_method("clear")