FieldConvert allows the user to manipulate the Nektar++ output binary files (.chk and .fld)
by using the flag `-m`

(which stands for `m`

odule). Specifically, FieldConvert has these additional
functionalities

`C0Projection`

: Computes the C0 projection of a given output file;`CFL`

: Computes the CFL number over the solution domain for Incompressible flow`QCriterion`

: Computes the Q-Criterion for a given output file;`L2Criterion`

: Computes the Lambda 2 Criterion for a given output file;`addcompositeid`

: Adds the composite ID of an element as an additional field;`fieldfromstring`

: Modifies or adds a new field from an expression involving the existing fields;`addFld`

: Sum two .fld files;`combineAvg`

: Combine two Nektar++ binary output (.chk or .fld) field file containing averages of fields (and possibly also Reynolds stresses) into single file;`concatenate`

: Concatenate a Nektar++ binary output (.chk or .fld) field file into single file (deprecated);`dof`

: Count the total number of DOF;`equispacedoutput`

: Write data as equi-spaced output using simplices to represent the data for connecting points;`extract`

: Extract a boundary field;`gradient`

: Computes gradient of fields;`halfmodetofourier`

: Convert`HalfMode`

expansion to`SingleMode`

for further processing;`homplane`

: Extract a plane from 3DH1D expansions;`homstretch`

: Stretch a 3DH1D expansion by an integer factor;`innerproduct`

: take the inner product between one or a series of fields with another field (or series of fields).`interpfield`

: Interpolates one field to another, requires fromxml, fromfld to be defined;`interppointdatatofld`

: Interpolates given discrete data using a finite difference approximation to a fld file given an xml file;`interppoints`

: Interpolates a field to a set of points. Requires fromfld, fromxml to be defined, and a topts, line, plane or box of target points;`interpptstopts`

: Interpolates a set of points to another. Requires a topts, line, plane or box of target points;`isocontour`

: Extract an isocontour of “fieldid” variable and at value “fieldvalue”. Optionally “fieldstr” can be specified for a string definition or “smooth” for smoothing;`jacobianenergy`

: Shows high frequency energy of Jacobian;`qualitymetric`

: Evaluate a quality metric of the underlying mesh to show mesh quality;`mean`

: Evaluate the mean of variables on the domain;`meanmode`

: Extract mean mode (plane zero) of 3DH1D expansions;`pointdatatofld`

: Given discrete data at quadrature points project them onto an expansion basis and output fld file;`printfldnorms`

: Print L2 and LInf norms to stdout;`removefield`

: Removes one or more fields from .fld files;`scalargrad`

: Computes scalar gradient field;`scaleinputfld`

: Rescale input field by a constant factor;`shear`

: Computes time-averaged shear stress metrics: TAWSS, OSI, transWSS, TAAFI, TACFI, WSSG;`streamfunction`

: Calculates stream function of a 2D incompressible flow.`surfdistance`

: Computes height of a prismatic boundary layer mesh and projects onto the surface (for e.g. y^{+}calculation).`vorticity`

: Computes the vorticity field.`wss`

: Computes wall shear stress field.`phifile`

: Computes the Φ function representing a body defined in an`.stl`

file. Useful for the Smoothed Profile Method solver.`wallNormalData`

: Interpolate values for a set of points in the wall-normal direction (for e.g. extract boundary layer profiles).

The module list above can be seen by running the command

In the following we will detail the usage of each module.

To smooth the data of a given .fld file one can use the `C0Projection`

module of FieldConvert

where the file `test-C0Proj.fld`

can be processed in a similar way as described in section 5.2
to visualise the result either in Tecplot, Paraview or VisIt.

The option `localtoglobalmap`

will do a global gather of the coefficients and then scatter
them back to the local elements. This will replace the coefficients shared between two elements
with the coefficients of one of the elements (most likely the one with the highest id). Although
not a formal projection it does not require any matrix inverse and so is very cheap to
perform.

The option `usexmlbcs`

will enforce the boundary conditions specified in the input xml
file.

The option `helmsmoothing=L`

will perform a Helmholtz smoothing projection of the
form

which can be interpreted in a Fourier sense as smoothing the original coefficients using a low pass filter of the form

and so L is the length scale below which the coefficients values are halved or more. Since this form of the Helmholtz operator is not possitive definite, currently a direct solver is necessary and so this smoother is mainly of use in two-dimensions.

This module calculates the CFL number over the domain. It currently only supports
the solution results from the Incompressible flow simulaitons, i.e. the outputs of
`IncNavierStokesSolver`

. To Estimate the CFL number, the user can run

where the file `test-cfl.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt.

To perform the Q-criterion calculation and obtain an output data containing the Q-criterion solution, the user can run

where the file `test-QCrit.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt.

To perform the λ_{2} vortex detection calculation and obtain an output data containing the
values of the λ_{2} eigenvalue, the user can run

where the file `test-L2Crit.fld`

can be processed in a similar way as described in section 5.2
to visualise the result either in Tecplot, Paraview or VisIt.

When dealing with a geometry that has many surfaces, we need to identify the composites to
assign boundary conditions. To assist in this, FieldConvert has a `addcompositeid`

module,
which adds the composite ID of every element as a new field. To use this we simply run

In this case, we have produced a Tecplot file which contains the mesh and a variable that
contains the composite ID. To assist in boundary identification, the input file `mesh.xml`

should
be a surface XML file that can be obtained through the `NekMesh`

`extract`

module (see section
4.5.3).

To modify or create a new field using an expression involving the existing fields, one can use
the `fieldfromstring`

module of FieldConvert

In this case `fieldstr`

is a required parameter describing a function of the coordinates
and the existing variables, and `fieldname`

is an optional parameter defining the
name of the new or modified field (the default is newfield). `file3.fld`

is the output
containing both the original and the new fields, and can be processed in a similar way
as described in section 5.2 to visualise the result either in Tecplot, Paraview or
VisIt.

To sum two .fld files one can use the `addFld`

module of FieldConvert

In this case we use it in conjunction with the command `scale`

which multiply the values of a
given .fld file by a constant `value`

. `file1.fld`

is the file multiplied by `value`

, `file1.xml`

is the
associated session file, `file2.fld`

is the .fld file which is summed to `file1.fld`

and finally
`file3.fld`

is the output which contain the sum of the two .fld files. `file3.fld`

can be
processed in a similar way as described in section 5.2 to visualise the result either in Tecplot,
Paraview or VisIt.

To combine two .fld files obtained through the AverageFields or ReynoldsStresses filters, use
the `combineAvg`

module of FieldConvert

`file3.fld`

can be processed in a similar way as described in section 5.2 to visualise the result
either in Tecplot, Paraview or VisIt.

To concatenate `file1.fld`

and `file2.fld`

into `file-conc.fld`

one can run the following
command

where the file `file-conc.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt. The `concatenate`

module
previously used for this purpose is not required anymore, and will be removed in a future
release.

To count the number of DOF in a solution file, one can run the following command

This module interpolates the output data to a truly equispaced set of points (not equispaced along the collapsed coordinate system). Therefore a tetrahedron is represented by a tetrahedral number of poinst. This produces much smaller output files. The points are then connected together by simplices (triangles and tetrahedrons).

or

The boundary region of a domain can be extracted from the output data using the following command line

The option `bnd`

specifies which boundary region to extract. Note this is different to NekMesh
where the parameter `surf`

is specified and corresponds to composites rather boundaries. If `bnd`

is not provided, all boundaries are extracted to different fields. The output will
be placed in test-boundary_b2.fld. If more than one boundary region is specified
the extension _b0.fld, _b1.fld etc will be outputted. To process this file you will
need an xml file of the same region. This can be generated using the command:

The surface to be extracted in this command is the composite number and so needs to correspond to the boundary region of interest. Finally to process the surface file one can use

This will obviously generate a Tecplot output if a .dat file is specified as last argument. A .vtu extension will produce a Paraview or VisIt output.

To compute the spatial gradients of all fields one can run the following command

where the file `file-grad.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt.

To obtain full Fourier expansion form a `HalfMode`

result, use the comand:

FieldConvert -m halfmodetofourier:realmodetoimag=value1,value2 file.xml half_mode_file.fld single_mode_file.fld

In linear stability analysis with halfmode expansion, the variable w, whose variable number is
2, is a imaginary mode but it is output as a real mode in the eigenvector field file.
By setting option `realmodetoimag=2`

, w can be transformed to a imaginary mode
correctly.

To obtain a 2D expansion containing one of the planes of a 3DH1D field file, use the command:

If the option `wavespace`

is used, the Fourier coefficients corresponding to `planeid`

are
obtained. The command in this case is:

The output file `file-plane.fld`

can be processed in a similar way as described in section 5.2
to visualise it either in Tecplot or in Paraview.

To stretch a 3DH1D expansion in the z-direction, use the command:

The number of modes in the resulting field can be chosen using the command-line parameter
`--output-points-hom-z`

.

The output file `file-stretch.fld`

can be processed in a similar way as described in section
5.2 to visualise it either in Tecplot or in Paraview.

You can take the inner product of one field with another field using the following command:

This command will load the `file1.fld`

and `file2.fld`

assuming they both are spatially
defined by `files.xml`

and determine the inner product of these fields. The input option
`fromfld`

must therefore be specified in this module.

Optional arguments for this module are `fields`

which allow you to specify the fields that you
wish to use for the inner product, i.e.

will only take the inner product between the variables 0,1 and 2 in the two fields files. The default is to take the inner product between all fields provided.

Additional options include `multifldids`

and `allfromflds`

which allow for a series of fields to
be evaluated in the following manner:

will take the inner product between a file names field1_0.fld, field1_1.fld, field1_2.fld and field1_3.fld with respect to field2.fld.

Analogously including the options `allfromflds`

, i.e.

FieldConvert -m innerproduct:fromfld=file1.fld:multifldids="0-3":\

allfromflds file2.xml file2.fld out.stdout

allfromflds file2.xml file2.fld out.stdout

Will take the inner product of all the from fields, i.e. field1_0.fld,field1_1.fld,field1_2.fld and field1_3.fld with respect to each other. This option essentially ignores file2.fld. Only the unique inner products are evaluated so if four from fields are given only the related trianuglar number 4 × 5∕2 = 10 of inner products are evaluated.

This option can be run in parallel.

To interpolate one field to another, one can use the following command:

This command will interpolate the field defined by `file1.xml`

and `file1.fld`

to the new
mesh defined in `file2.xml`

and output it to `file2.fld`

. The `fromxml`

and `fromfld`

must be
specified in this module. In addition there are two optional arguments `clamptolowervalue`

and `clamptouppervalue`

which clamp the interpolation between these two values. Their
default values are -10,000,000 and 10,000,000.

If the fromfld is a 3DH1D field and uses HalfMode expansion, you can use
`realmodetoimag=n`

to transform the n_{1},n_{2},...,n_{m}_{1},n_{2},...,n_{m}th variables from real modes to
imaginary modes. Variable index starts from 0.

To interpolate discrete point data to a field, use the interppointdatatofld module:

or alternatively for csv data:

This command will interpolate the data from `file1.pts`

(`file1.csv`

) to the mesh and
expansions defined in `file1.xml`

and output the field to `file1.fld`

. The file `file.pts`

must
be of the form:

1<?xml version="1.0" encoding="utf-8" ?>

2<NEKTAR>

3 <POINTS DIM="1" FIELDS="a,b,c">

4 1.0000 -1.0000 1.0000 -0.7778

5 2.0000 -0.9798 0.9798 -0.7980

6 3.0000 -0.9596 0.9596 -0.8182

7 4.0000 -0.9394 0.9394 -0.8384

8 </POINTS>

9</NEKTAR>

2<NEKTAR>

3 <POINTS DIM="1" FIELDS="a,b,c">

4 1.0000 -1.0000 1.0000 -0.7778

5 2.0000 -0.9798 0.9798 -0.7980

6 3.0000 -0.9596 0.9596 -0.8182

7 4.0000 -0.9394 0.9394 -0.8384

8 </POINTS>

9</NEKTAR>

where `DIM="1" FIELDS="a,b,c`

specifies that the field is one-dimensional and contains three
variables, a, b, and c. Each line defines a point, while the first column contains its
x-coordinate, the second one contains the a-values, the third the b-values and so on. In case of
n-dimensional data, the n coordinates are specified in the first n columns accordingly. An
equivalent csv file is:

# x, a, b, c

1.0000,-1.0000,1.0000,-0.7778

2.0000,-0.9798,0.9798,-0.7980

3.0000,-0.9596,0.9596,-0.8182

4.0000,-0.9394,0.9394,-0.8384

1.0000,-1.0000,1.0000,-0.7778

2.0000,-0.9798,0.9798,-0.7980

3.0000,-0.9596,0.9596,-0.8182

4.0000,-0.9394,0.9394,-0.8384

In order to interpolate 1D data to a nD field, specify the matching coordinate in the output
field using the `interpcoord`

argument:

This will interpolate the 1D scattered point data from `1D-file1.pts`

to the y-coordinate of
the 3D mesh defined in `3D-file1.xml`

. The resulting field will have constant values along the
x and z coordinates. For 1D Interpolation, the module implements a quadratic scheme
and automatically falls back to a linear method if only two data points are given.
A modified inverse distance method is used for 2D and 3D interpolation. Linear
and quadratic interpolation require the data points in the `.pts`

-file to be sorted by
their location in ascending order. The Inverse Distance implementation has no such
requirement.

You can interpolate one field to a series of given points using the following command:

This command will interpolate the field defined by `file1.xml`

and `file1.fld`

to the points
defined in `file2.pts`

and output it to `file2.dat`

. The `fromxml`

and `fromfld`

must be
specified in this module. The format of the file `file2.pts`

is of the same form as for the
interppointdatatofld module:

1<?xml version="1.0" encoding="utf-8" ?>

2<NEKTAR>

3 <POINTS DIM="2" FIELDS="">

4 0.0 0.0

5 0.5 0.0

6 1.0 0.0

7 </POINTS>

8</NEKTAR>

2<NEKTAR>

3 <POINTS DIM="2" FIELDS="">

4 0.0 0.0

5 0.5 0.0

6 1.0 0.0

7 </POINTS>

8</NEKTAR>

Similar to the interppointdatatofld module, the `.pts`

file can be interchanged with a `.csv`

file
(the output can also be written to `.csv`

):

There are three optional arguments `clamptolowervalue`

, `clamptouppervalue`

and
`defaultvalue`

the first two clamp the interpolation between these two values and the third
defines the default value to be used if the point is outside the domain. Their default values are
-10,000,000, 10,000,000 and 0.

In addition, instead of specifying the file `file2.pts`

, a module list of the form

can be specified where `npts`

is the number of equispaced points between (x_{0},y_{0}) to (x_{1},y_{1}).
This also works in 3D, by specifying (x_{0},y_{0},z_{0}) to (x_{1},y_{1},z_{1}).

An extraction of a plane of points can also be specified by

FieldConvert -m interppoints:fromxml=file1.xml:fromfld=file1.fld:\

plane=npts1,npts2,x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3 file2.dat

plane=npts1,npts2,x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3 file2.dat

where `npts1,npts2`

is the number of equispaced points in each direction and (x_{0},y_{0},z_{0}),
(x_{1},y_{1},z_{1}), (x_{2},y_{2},z_{2}) and (x_{3},y_{3},z_{3}) define the plane of points specified in a clockwise or
anticlockwise direction.

In addition, an extraction of a box of points can also be specified by

FieldConvert -m interppoints:fromxml=file1.xml:fromfld=file1.fld:\

box=npts1,npts2,npts3,xmin,xmax,ymin,ymax,zmin,zmax file2.dat

box=npts1,npts2,npts3,xmin,xmax,ymin,ymax,zmin,zmax file2.dat

where `npts1,npts2,npts3`

is the number of equispaced points in each direction and
(x_{min},y_{min},z_{min}) and (x_{max},y_{max},z_{max}) define the limits of the box of points.

There is also an additional optional argument `cp=p0,q`

which adds to the interpolated fields
the value of c_{p} = (p-p0)∕q and c_{p0} = (p-p0 + 0.5u^{2})∕q where p0 is a reference pressure and
q is the free stream dynamics pressure. If the input does not contain a field “p” or a velocity
field “u,v,w” then cp and cp0 are not evaluated accordingly.

If the fromfld is a 3DH1D field and uses HalfMode expansion, you can use
`realmodetoimag=n`

to transform the n_{1},n_{2},...,n_{m}_{1},n_{2},...,n_{m}th variables from real modes to
imaginary modes. Variable index starts from 0.

You can interpolate one set of points to another using the following command:

This command will interpolate the data in `file1.pts`

to a new set of points defined in
`file2.pts`

and output it to `file2.dat`

.

Similarly to the interppoints module, the target point distribution can also be specified
using the `line`

, `plane`

or `box`

options. The optional arguments `clamptolowervalue`

,
`clamptouppervalue`

, `defaultvalue`

and `cp`

are also supported with the same meaning as in
interppoints.

One useful application for this module is with 3DH1D expansions, for which currently the interppoints module does not work. In this case, we can use for example

FieldConvert file1.xml file1.fld -m interpptstopts:\

plane=npts1,npts2,x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3 \

file2.dat

plane=npts1,npts2,x0,y0,z0,x1,y1,z1,x2,y2,z2,x3,y3,z3 \

file2.dat

With this usage, the equispacedoutput module will be automatically called to interpolate the field to a set of equispaced points in each element. The result is then interpolated to a plane by the interpptstopts module.

Extract an isocontour from a field file. This option automatically take the field to an
equispaced distribution of points connected by linear simplicies of triangles or tetrahedrons.
The linear simplices are then inspected to extract the isocontour of interest. To specify the
field `fieldid`

can be provided giving the id of the field of interest and `fieldvalue`

provides
the value of the isocontour to be extracted.

Alternatively `fieldstr="u+v"`

can be specified to calculate the field u + v and extract its
isocontour. You can also specify `fieldname="UplusV"`

to define the name of the isocontour in
the .dat file, i.e.

FieldConvert -m isocontour:fieldstr="u+v":fieldvalue=0.5:\

fieldname="UplusV" test.xml test.fld test-isocontour.dat

fieldname="UplusV" test.xml test.fld test-isocontour.dat

Optionally `smooth`

can be specified to smooth the isocontour with default values
`smoothnegdiffusion`

=0.495, `smoothnegdiffusion`

=0.5 and `smoothiter`

=100. This option
typically should be used wiht the `globalcondense`

option which removes multiply defined
verties from the simplex definition which arise as isocontour are generated element by element.
The `smooth`

option preivously automatically called the `globalcondense`

option but this has
been depracated since it is now possible to read isocontour files directly and so it is useful to
have these as separate options.

In addition to the `smooth`

or `globalcondense`

options you can specify `removesmallcontour`

=100
which will remove separate isocontours of less than 100 triangles.

The option `topmodes`

can be used to specify the number of top modes to keep.

The output file `jacenergy.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt.

The `qualitymetric`

module assesses the quality of the mesh by calculating a per-element
quality metric and adding an additional field to any resulting output. This does not require
any field input, therefore an example usage looks like

Two quality metrics are implemented that produce scalar fields Q:

- By default a metric outlined in [14] is produced, where all straight sided elements have quality Q = 1 and Q < 1 shows the deformation between the curved element and the straight-sided element. If Q = 0 then the element is invalid. Note that Q varies over the volume of the element but is not guaranteed to be continuous between elements.
- Alternatively, if the
`scaled`

option is passed through to the module, then the scaled Jacobian(i.e. the ratio of the minimum to maximum Jacobian of each element) is calculated. Again Q = 1 denotes an ideal element, but now invalid elements are shown by Q < 0. Any elements with Q near zero are determined to be low quality.

To evaluate the mean of variables on the domain one can use the `mean`

module of FieldConvert

This module does not create an output file which is reinforced by the out.stdout option. The integral and mean for each field variable are then printed to the stdout.

To obtain a 2D expansion containing the mean mode (plane zero in Fourier space) of a 3DH1D field file, use the command:

The output file `file-mean.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot or in Paraview or VisIt.

To project a series of points given at the same quadrature distribution as the .xml file and write out a .fld file use the pointdatatofld module:

This command will read in the points provided in the `file.pts`

and assume these are
given at the same quadrature distribution as the mesh and expansions defined in
`file.xml`

and output the field to `file.fld`

. If the points do not match an error will be
dumped.

The file `file.pts`

which is assumed to be given by an interpolation from another source is of
the form:

1<?xml version="1.0" encoding="utf-8" ?>

2<NEKTAR>

3 <POINTS DIM="3" FIELDS="p">

4 1.70415 -0.4 -0.0182028 -0.106893

5 1.70415 -0.395683 -0.0182028 -0.106794

6 1.70415 -0.3875 -0.0182028 -0.106698

7 1.70415 -0.379317 -0.0182028 -0.103815

8 </POINTS>

9</NEKTAR>

2<NEKTAR>

3 <POINTS DIM="3" FIELDS="p">

4 1.70415 -0.4 -0.0182028 -0.106893

5 1.70415 -0.395683 -0.0182028 -0.106794

6 1.70415 -0.3875 -0.0182028 -0.106698

7 1.70415 -0.379317 -0.0182028 -0.103815

8 </POINTS>

9</NEKTAR>

where `DIM="3" FIELDS="p`

specifies that the field is three-dimensional and contains one
variable, p. Each line defines a point, the first, second, and third columns contains the
x,y,z-coordinate and subsequent columns contain the field values, in this case the p-value So
in the general case of n-dimensional data, the n coordinates are specified in the first n columns
accordingly followed by the field data. Alternatively, the `file.pts`

can be interchanged with a
csv file.

The default argument is to use the equispaced (but potentially collapsed) coordinates which can be obtained from the command.

In this case the pointdatatofld module should be used without the `–noequispaced`

option. However this can lead to problems when peforming an elemental forward
projection/transform since the mass matrix in a deformed element can be singular
as the equispaced points do not have a sufficiently accurate quadrature rule that
spans the polynomial space. Therefore it is advisable to use the set of points given
by

which produces a set of points at the gaussian collapsed coordinates.

Finally the option `setnantovalue=0`

can also be used which sets any nan values in the
interpolation to zero or any specified value in this option.

This module does not create an output file which is reinforced by the out.stdout option. The L2 and LInf norms for each field variable are then printed to the stdout.

This module allows to remove one or more fields from a .fld file:

where the file `test-removed.fld`

can be processed in a similar way as described in section 5.2
to visualise the result either in Tecplot, Paraview or VisIt. The lighter resulting file speeds up
the postprocessing of large files when not all fields are required.

The scalar gradient of a field is computed by running:

The option `bnd`

specifies which boundary region to extract. Note this is different to NekMesh
where the parameter `surf`

is specified and corresponds to composites rather boundaries. If `bnd`

is not provided, all boundaries are extracted to different fields. To process this file you will
need an xml file of the same region.

To scale a .fld file by a given scalar quantity, the user can run:

The argument `scale=value`

rescales of a factor `value`

`test.fld`

by the factor value. The
output file `file-scal.fld`

can be processed in a similar way as described in section 5.2 to
visualise the result either in Tecplot, Paraview or VisIt.

Time-dependent wall shear stress derived metrics relevant to cardiovascular fluid dynamics research can be computed using this module. They are

- TAWSS: time-averaged wall shear stress;
- OSI: oscillatory shear index;
- transWSS: transverse wall shear stress;
- TACFI: time-averaged cross-flow index;
- TAAFI: time-averaged aneurysm formation index;
- |WSSG|: wall shear stress gradient.

To compute these, the user can run:

The argument `N`

and `fromfld`

are compulsory arguments that respectively define the number
of `fld`

files corresponding to the number of discrete equispaced time-steps, and the first `fld`

file which should have the form of `test_id_b0.fld`

where the first underscore in the name
marks the starting time-step file ID.

The input `.fld`

files are the outputs of the wss module. If they do not contain the surface
normals (an optional output of the wss modle), then the shear module will not compute the
last metric, |WSSG|.

The streamfunction module calculates the stream function of a 2D incompressible flow, by solving the Poisson equation

where ω is the vorticity. Note that this module applies the same boundary conditions specified
for the y-direction velocity component `v`

to the stream function, what may not be the most
appropriate choice.

To use this module, the user can run

where the file `test-streamfunc.fld`

can be processed in a similar way as described in section
5.2.

The surface distance module computes the height of a boundary layer formed by quadrilaterals
(in 2D) or prisms and hexahedrons (in 3D) and projects this value onto the surface of the
boundary, in a similar fashion to the `extract`

module. In conjunction with a mesh of the
surface, which can be obtained with `NekMesh`

, and a value of the average wall shear stress, one
potential application of this module is to determine the distribution of y^{+} grid spacings for
turbulence calculations.

To compute the height of the prismatic layer connected to boundary region 3, the user can issue the command:

Note that no `.fld`

file is required, since the mesh is the only input required in order to
calculate the element height. This produces a file `output_b3.fld`

, which can be visualised
with the appropriate surface mesh from `NekMesh`

.

To perform the vorticity calculation and obtain an output data containing the vorticity solution, the user can run

where the file `test-vort.fld`

can be processed in a similar way as described in section
5.2.

To obtain the wall shear stres vector and magnitude, the user can run:

The option `bnd`

specifies which boundary region to extract. Note this is different to NekMesh
where the parameter `surf`

is specified and corresponds to composites rather boundaries. If `bnd`

is not provided, all boundaries are extracted to different fields. The `addnormals`

is an optional
command argument which, when turned on, outputs the normal vector of the extracted
boundary region as well as the shear stress vector and magnitude. This option is
off by default. To process the output file(s) you will need an xml file of the same
region.

The output fields are wall shear stress in streamwise direction (`Shear_s`

), normal direction
(`Shear_n`

) and magnitude of the wall shear stress vector (`Shear_mag`

) for 2D simulations. For
3D simulations, wall shear stress in the spanwise direction (`Shear_z`

) is also included in the
output fileds. Note that the streamwise and normal directions are local at each point on the
corresponding boundary.

`.stl`

files, errors may occur if triangles are placed exactly at
90This FieldConvert module converts a binary `.stl`

CAD file into `.fld`

or `.vtu`

/`.dat`

files
that can be used as inputs for the Smoothed Profile Method solver. Running the
command:

will generate an output file `geom.fld`

with all the information required to define a shape
function Φ representing the geometry specified in `geom.stl`

. The option `scale`

sets the value
of ξ as it is described in the Synopsis chapter of the Incompressible N-S solver. If the output
file gets the extension `.vtu`

or `.dat`

, the module will produce a graphical representation of the
shape function; however, the recommended way to proceed is to generate an `.fld`

file and
then, use FieldConvert to obtain the `.vtu`

or `.dat`

files if needed for visualisation purposes:

FieldConvert -m phifile:file=geom.stl:scale=value session.xml geom.fld

FieldConvert session.xml geom.fld geom.vtu

FieldConvert session.xml geom.fld geom.vtu

This module can also be used to produce a `.fld`

and `.vtu`

/ `.dat`

file of shapes defined
directly in the session file through an analytical expression. In this case, the commands
simplify to:

The algorithm computes an octree for the triangles that define the 3D object in the `.stl`

file,
and then loops over all the nodes of the computational mesh looking for the shortest distance
to the 3D object. Since this module is currently in experimental phase, it only runs in serial
and therefore its performance in computing the shape function from the `.stl`

file is limited,
especially in 3D cases. In addition to this, it is recommended to make sure that the angles
between triangles are not strictly equal to 90^{∘}, since the algorithm will probably fail to find
the real Φ function.

To obtain the values of an array of points in the wall-normal direction, such as boundary layer profiles, the user can run:

FieldConvert -m wss:bnd=0:xorig="0.5,0,0":projDir="0,1,0":maxDist=0.1:\

distH=0.1:nptsH=0.01:d=0.2 test.xml test.fld test.pts

distH=0.1:nptsH=0.01:d=0.2 test.xml test.fld test.pts

The option `bnd`

specifies the target boundary region, to which the input point specified by
`xorig`

will be projected as the first point in the interpolation points array. The projection
direction is specified by `projDir`

, which does not have to be a unit vector but will be
automatically normalized. The input point and projetion direction must be set carefully to
make sure a projected point can be found on the target boundary. In cases with curved
boundaries on which multiple projected points might exist, the user can use `maxDist`

to
limit the maximum projection distance between the input point to the projected
point.

After the projected point is found, this module will compute the wall-normal direction at the
point, and an array of points will be set in this direction. The number of points is
specified by `nptsH`

, and the parameter `d`

controls the distribution of the points as
follows

where ξ is equally-spaced parametric parameter varying from 0 to 1; H is the distance between
the first point (on the booundary) and the last point, which is specified `distH`

; δ is given by `d`

.
This distribution is employed for 0 < δ ≤ 0.95 while δ > 0.95 for evenly-spaced
distribution.

Finally, this module will interpolate the values at the points from test.fld, and save the result in test.pts.

FieldConvert has support for two modules that can be used in conjunction with the linear elastic solver, as shown in chapter 12. To do this, FieldConvert has an XML output module, in addition to the Tecplot and VTK formats.

The `deform`

module, which takes no options, takes a displacement field and applies it to the
geometry, producing a deformed mesh:

The `displacement`

module is designed to create a boundary condition field file.
Its intended use is for mesh generation purposes. It can be used to calculate the
displacement between the linear mesh and a high-order surface, and then produce a `fld`

file,
prescribing the displacement at the boundary, that can be used in the linear elasticity
solver.

Presently the process is somewhat convoluted and must be used in conjunction with NekMesh
to create the surface file. However the bash input below describes the procedure. Assume the
high-order mesh is in a file called `mesh.xml`

, the linear mesh is `mesh-linear.xml`

that can be
generated by removing the `CURVED`

section from `mesh.xml`

, and that we are interested in the
surface with ID 123.

# Extract high order surface

NekMesh -m extract:surf=123 mesh.xml mesh-surf-curved.xml

# Use FieldConvert to calculate displacement between two surfaces

FieldConvert -m displacement:id=123:to=mesh-surf-curved.xml \

mesh-linear.xml mesh-deformation.fld

# mesh-deformation.fld is used as a boundary condition inside the

# solver to prescribe the deformation conditions.xml contains

# appropriate Nektar++ parameters (mu, E, other BCs, ...)

LinearElasticSolver mesh-linear.xml conditions.xml

# This produces the final field mesh-linear.fld which is the

# displacement field, use FieldConvert to apply it:

FieldConvert-g -m deform mesh-linear.xml mesh-linear.fld mesh-deformed.xml

NekMesh -m extract:surf=123 mesh.xml mesh-surf-curved.xml

# Use FieldConvert to calculate displacement between two surfaces

FieldConvert -m displacement:id=123:to=mesh-surf-curved.xml \

mesh-linear.xml mesh-deformation.fld

# mesh-deformation.fld is used as a boundary condition inside the

# solver to prescribe the deformation conditions.xml contains

# appropriate Nektar++ parameters (mu, E, other BCs, ...)

LinearElasticSolver mesh-linear.xml conditions.xml

# This produces the final field mesh-linear.fld which is the

# displacement field, use FieldConvert to apply it:

FieldConvert-g -m deform mesh-linear.xml mesh-linear.fld mesh-deformed.xml