Filters are a method for calculating a variety of useful quantities from the field variables as the
solution evolves in time, such as time-averaged fields and extracting the field variables at
certain points inside the domain. Each filter is defined in a FILTER
tag inside a
FILTERS
block which lies in the main NEKTAR
tag. In this section we give an overview
of the modules currently available and how to set up these filters in the session
file.
Here is an example FILTER
:
A filter has a name – in this case, FilterName
– together with parameters which are set to
user-defined values. Each filter expects different parameter inputs, although where
functionality is similar, the same parameter names are shared between filter types for
consistency. Numerical filter parameters may be expressions and so may include session
parameters defined in the PARAMETERS
section.
Some filters may perform a large number of operations, potentially taking up a
significant percentage of the total simulation time. For this purpose, the parameter
IO_FiltersInfoSteps
is used to set the number of steps between successive total filter CPU
time stats are printed. By default it is set to 10 times IO_InfoSteps
. If the solver is run with
the verbose -v
flag, further information is printed, detailing the CPU time of each individual
filter and percentage of time integration.
In the following we document the filters implemented. Note that some filters are solver-specific and will therefore only work for a given subset of the available solvers.
When analysing certain time-dependent problems, it might be of interest to activate a filter in a specific physical phase and with a certain period (for instance, to carry out phase averaging). The simulation time can be written as t = mT + nT T , where m is an integer representing the number of periods T elapsed, and 0 ≤ nT ≤ 1 is the phase. This feature is not a filter in itself and it is activated by adding the parameters below to the filter of interest:
Option name | Required | Default | Description |
PhaseAverage | ✓ | Feature activation |
|
PhaseAveragePeriod | ✓ | Period T |
|
PhaseAveragePhase | ✓ | Phase nT . |
|
For instance, to activate phase averaging with a period of T = 10 at phase nT = 0.5:
Since this feature monitors nT every SampleFrequency
, for best results it is recommended to
set SampleFrequency
= 1.
The maximum error in sampling phase is nT ,tol = ⋅ SampleFrequency
, which is
displayed at the beginning of the simulation if the solver is run with the verbose -v
option.
The number of periods elapsed is calculated based on simulation time. Caution is therefore
recommended when modifying time information in the restart field, because if the new
time does not correspond to the same phase, the feature will produce erroneous
results.
This filter evaluates the aerodynamic forces along a specific surface. The forces are projected along the Cartesian axes and the pressure and viscous contributions are computed in each direction.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the forces are written. |
Frequency | ✗ | 1 | Number of timesteps after which output is written. |
Boundary | ✓ | - | Boundary surfaces on which the forces are to be evaluated. |
PivotPoint | ✗ | (0. 0. 0.) | Pivot Point around which the Moments are calculated. If Doesn’t explicitly defined by user, the moments will be calculated around the point X = (0. 0. 0.) |
An example is given below:
During the execution a file named DragLift.fce
will be created and the value of the
aerodynamic forces on boundaries 1 and 2, defined in the GEOMETRY
section, will be output
every 10 time steps.
The lack of physical boundaries in the Smoothed Profile Method requires an alternative formulation to calculate the aerodynamic forces. Since the method imposes the boundary geometry by adding an impulse to the flow proportional to the difference between the flow velocity and the expected velocity of the immersed bodies, the forces in this filter are computed by integrating this difference where Φ≠0 [26]:
|
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the forces are written. |
Frequency | ✗ | 1 | Number of timesteps after which the output is written. |
StartTime | ✗ | 0 | Forces before this instant are not written to the output. |
For instance, a block like the following
will generate a file called Forces.fce
with the values of the forces in the (X,Y,Z) directions,
that must be scaled with the density of the fluid to get the real values. It is important
to remark that the computed values are the sum of all the boundaries defined by
Φ.
Filter Benchmark
records spatially distributed event times for activation and repolarisation
(recovert) during a simulation, for undertaking benchmark test problems.
ThresholdValue
specifies the value above which tissue is considered to be
depolarised and below which is considered repolarised.
InitialValue
specifies the initial value of the activation or repolarisation time
map.
OutputFile
specifies the base filename of activation and repolarisation maps
output from the filter. This name is appended with the index of the event and the
suffix ‘.fld‘.
StartTime
(optional) specifies the simulation time at which to start detecting
events.
Filter CellHistoryPoints
writes all cell model states over time at fixed points. Can be used
along with the HistoryPoints
filter to record all variables at specific points during a
simulation.
OutputFile
specifies the filename to write history data to.
OutputFrequency
specifies the number of steps between successive outputs.
Points
lists coordinates at which history data is to be recorded.
Filter CheckpointCellModel
checkpoints the cell model. Can be used along with
the Checkpoint
filter to record complete simulation state and regular intervals.
OutputFile
(optional) specifies the base filename to use. If not specified, the
session name is used. Checkpoint files are suffixed with the process ID and the
extension ‘.chk‘.
OutputFrequency
specifies the number of timesteps between checkpoints.
The checkpoint filter writes a checkpoint file, containing the instantaneous state of the
solution fields at at given timestep. This can subsequently be used for restarting the
simulation or examining time-dependent behaviour. This produces a sequence of files, by
default named session_*.chk
, where *
is replaced by a counter. The initial condition is
written to session_0.chk
. Existing files are not overwritten, but renamed to e.g.
session_0.bak0.chk
. In case this file already exists, too, the chk
-file is renamed to
session_0.bak*.chk
and so on.
IO_CheckSteps
parameter in the session
file.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the checkpoints are written. |
OutputFrequency | ✓ | - | Number of timesteps after which output is written. |
OutputStartTime | ✗ | 0 | Specifies the simulation time at which to start writing checkpoint files. |
For example, to output the fields every 100 timesteps we can specify:
It is also possible to specify the OutputStartTime
option based on the simulation time step.
For example, if checkpoint files should only be written after 500 time steps, one can write
Filter Electrogram
computes virtual unipolar electrograms at a prescribed set of points.
OutputFile
(optional) specifies the base filename to use. If not specified, the
session name is used. The extension ‘.ecg‘ is appended if not already specified.
OutputFrequency
specifies the number of resolution of the electrogram data.
Points
specifies a list of coordinates at which electrograms are desired. They must
not lie within the domain.
This filter produces a file containing the time-evolution of the L2 and Linf errors. By default
this file is called session.err
where session
is the session name.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the errors are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
An example syntax is given below:
This filter produces a file containing the time-evolution of the integral of the solver variables
on user defined composites. By default this file is called session.int
where session
is the
session name.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the integrals are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
OutputPrecision | ✗ | 7 | Decimal precision with which the output is written. |
Composites | ✓ | - | Composites on which to calculate the integral. |
Multiple composites can be defined together by using ranges with each composite grouping
producing a summed output for each variable in the OutputFile
. For example C[1,3,5-7]
would produce a single integral output for each variable whilst C[1-3], C[4]
would produce
two.
An example syntax is given below:
This filter applies a sequence of FieldConvert modules to the solution, writing an output file.
An output is produced at the end of the simulation into session_fc.fld
, or alternatively
every M timesteps as defined by the user, into a sequence of files session_*_fc.fld
, where *
is replaced by a counter.
Module options are specified as a colon-separated list, following the same syntax as the
FieldConvert
command-line utility (see Section 5).
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session.fld | Output filename. If no extension is provided, it is assumed as .fld |
OutputFrequency | ✗ | NumSteps | Number of timesteps after which output is written, M. |
Modules | ✗ | FieldConvert modules to run, separated by a white space. |
|
As an example, consider:
This will create a sequence of files named MyFile_*_fc.vtu
containing isocontours. The result
will be output every 100 time steps.
The history points filter can be used to evaluate the value of the fields in specific points of the
domain as the solution evolves in time. By default this produces a file called session.his
. For
each timestep, and then each history point, a line is output containing the current solution
time, followed by the value of each of the field variables. Commented lines are created at the
top of the file containing the location of the history points and the order of the
variables.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the checkpoints are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
OutputOneFile | ✗ | true | If |
OutputPlane | ✗ | -1 | If the simulation is homogeneous, the plane on which to evaluate the history point. If set, all points will be reset to lie on this plane. |
WaveSpace | ✗ | false | If the
simulation is homogeneous
and |
Points | ✗ | - | A list of the history points. |
line | ✗ | - |
|
plane | ✗ | - |
|
box | ✗ | - |
|
One of Points
, line
, plane
or box
must be specified.
For example, to output the value of the solution fields at three points (1,0.5,0),
(2,0.5,0) and (3,0.5,0) into a file TimeValues.his
every 10 timesteps, we use the
syntax:
or
The purpose of this filter is to calculate the kinetic energy and enstrophy
where μ(Ω) is the volume of the domain Ω. This produces a file containing the time-evolution
of the kinetic energy and enstrophy fields. By default this file is called session.eny
where
session
is the session name.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session.eny | Output file name to which the energy and enstrophy are written. |
OutputFrequency | ✓ | - | Number of timesteps at which output is written. |
To enable the filter, add the following to the FILTERS
tag:
This filter calculates time-evolution of the averaged velocity components over the flow domain and can be used to track flow rates.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which averaged values are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
An example syntax is given below:
This filter calculates the time-evolution of the kinetic energy. In the case of a two- or three-dimensional simulation this is defined as
However if the simulation is written as a one-dimensional homogeneous expansion so that
then we instead calculate the energy spectrum
Note that in this case, each component of ûk is a complex number and therefore
N = HomModesZ
∕2 lines are output for each timestep. This is a particularly useful tool in
examining turbulent and transitional flows which use the homogeneous extension.
In either case, the resulting output is written into a file called session.mdl
by
default.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the energy spectrum is written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
An example syntax is given below:
This filter MovingBody
is encapsulated in the forcing module to evaluate the aerodynamic
forces along the moving body surface. It is described in detail in section 11.3.4.1
This filter computes the exponential moving average (in time) of fields for each variable defined in the session file. The moving average is defined as:
with 0 < α < 1 and
1 = u1.The same parameters of the time-average filter are supported, with the output file in the form
session_*_movAvg.fld
. In addition, either α or the time-constant τ must be defined. They
are related by:
where ts is the time interval between consecutive samples.
As an example, consider:
This will create a file named MyMovingAverage_movAvg.fld
with a moving average
sampled every 10 time steps. The averaged field is however only output every 100 time
steps.
This filter is designed to output the energy spectrum of one-dimensional elements. It transforms the solution field at each timestep into a orthogonal basis defined by the functions
where Lp is the p-th Legendre polynomial. This can be used to show the presence of, for
example, oscillations in the underlying field due to numerical instability. The resulting output
is written into a file called session.eny
by default. The following parameters are
supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session | Prefix of the output filename to which the energy spectrum is written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
An example syntax is given below:
This filter is an extended version of the time-average fields filter (see Section 3.4.19). It outputs not only the time-average of the fields, but also the Reynolds stresses. The same parameters supported in the time-average case can be used, for example:
By default, this filter uses a simple average. Optionally, an exponential moving average can be used, in which case the output contains the moving averages and the Reynolds stresses calculated based on them. For example:
This filter computes time-averaged fields for each variable defined in the session file. Time
averages are computed by either taking a snapshot of the field every timestep, or alternatively
at a user-defined number of timesteps N. An output is produced at the end of the simulation
into session_avg.fld
, or alternatively every M timesteps as defined by the user,
into a sequence of files session_*_avg.fld
, where *
is replaced by a counter. This
latter option can be useful to observe statistical convergence rates of the averaged
variables.
This filter is derived from FieldConvert filter, and therefore support all parameters available in that case. The following additional parameter is supported:
Option name | Required | Default | Description |
SampleFrequency | ✗ | 1 | Number of timesteps at which the average is calculated, N. |
RestartFile | ✗ | Restart file used as initial average. If no extension is provided, it is assumed as .fld |
|
As an example, consider:
This will create a file named MyAverageField.fld
averaging the instantaneous
fields every 10 time steps. The averaged field is however only output every 100 time
steps.
The threshold value filter writes a field output containing a variable m, defined by the time at
which the selected variable first exceeds a specified threshold value. The default name of the
output file is the name of the session with the suffix _max.fld
. Thresholding is applied based
on the first variable listed in the session by default.
The following parameters are supported:
Option name | Required | Default | Description |
OutputFile | ✗ | session_max.fld | Output filename to which the threshold times are written. |
ThresholdVar | ✗ | first variable name | Specifies the variable on which the threshold will be applied. |
ThresholdValue | ✓ | - | Specifies the threshold value. |
InitialValue | ✓ | - | Specifies the initial time. |
StartTime | ✗ | 0.0 | Specifies the time at which to start recording. |
An example is given below:
which produces a field file threshold_max.fld
.
Performs the same function as the ThresholdMax
filter (see Section ??) but records the time
at which the threshold variable drops below a prescribed value.
This filter computes the local (pointwise) maximum or minimum field for each variable, including the addition variables for compressible flow solver, over the simulation.
The following parameters are supported:
Option name | Required | Default | Description |
MaxOrMin | ✓ | max | Type of fields
to compute. It can be
either |
RestartFile | ✗ | ∓9999 | Restart file used for
initial comparison. If
it is not provided,
-9999 will be used
for the |
OutputFile | ✗ | session_max.fld | Output filename to which the threshold times are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
SampleFrequency | ✗ | 1 | Number of timesteps after which the fields are used to compute max/min. |
An example is given below:
The BodyFittedVelocity
filter projects the velocity fields in the Cartesian coordinate system
into a body-fitted coordinate system. Meanwhile the user can chose to record the local
(pointwise) maximum or minimum for the body-fitted velocity components, or simply output
their original values. This filter is designed for both compressible flow solver and
incompressible flow solver.
The following parameters are supported:
Option name | Required | Default | Description |
BodyFittedCoordinateFile | ✓ | N/A | Body-fitted coordinate system generated by FieldConvert module. See 5.6.40 for reference. |
RestartFile | ✓ | N/A | Restart file for the initial field for body-fitted velocity components ubfc and vbfc (and wbfc for 3D cases). This restart file is necessary in the currtnt filter. The restart file can use the same output of the FieldConvert modul as well. See 5.6.40 for reference |
OriginalOrMaxOrMin | ✗ | original | Type
of fields to
compute.
It can be
|
OutputFile | ✗ | session_max.fld | Output filename to which the threshold times are written. |
OutputFrequency | ✗ | 1 | Number of timesteps after which output is written. |
SampleFrequency | ✗ | 1 | Number of timesteps after which the fields are used to compute original/max/min. |
An example is given below: