# User Guide

For information on how to install PyFR see Installation.

## Running PyFR

PyFR 1.15.0 uses three distinct file formats:

`.ini`

— configuration file`.pyfrm`

— mesh file`.pyfrs`

— solution file

The following commands are available from the `pyfr`

program:

`pyfr import`

— convert a Gmsh .msh file into a PyFR .pyfrm file.Example:

pyfr import mesh.msh mesh.pyfrm

`pyfr partition`

— partition an existing mesh and associated solution files.Example:

pyfr partition 2 mesh.pyfrm solution.pyfrs .

`pyfr run`

— start a new PyFR simulation. Example:pyfr run mesh.pyfrm configuration.ini

`pyfr restart`

— restart a PyFR simulation from an existing solution file. Example:pyfr restart mesh.pyfrm solution.pyfrs

`pyfr export`

— convert a PyFR`.pyfrs`

file into an unstructured VTK`.vtu`

or`.pvtu`

file. If a`-k`

flag is provided with an integer argument then`.pyfrs`

elements are converted to high-order VTK cells which are exported, where the order of the VTK cells is equal to the value of the integer argument. Example:pyfr export -k 4 mesh.pyfrm solution.pyfrs solution.vtu

If a

`-d`

flag is provided with an integer argument then`.pyfrs`

elements are subdivided into linear VTK cells which are exported, where the number of sub-divisions is equal to the value of the integer argument. Example:pyfr export -d 4 mesh.pyfrm solution.pyfrs solution.vtu

If no flags are provided then

`.pyfrs`

elements are converted to high-order VTK cells which are exported, where the order of the cells is equal to the order of the solution data in the`.pyfrs`

file.

### Running in Parallel

PyFR can be run in parallel. To do so prefix `pyfr`

with
`mpiexec -n <cores/devices>`

. Note that the mesh must be
pre-partitioned, and the number of cores or devices must be equal to
the number of partitions.

## Configuration File (.ini)

The .ini configuration file parameterises the simulation. It is written
in the INI format.
Parameters are grouped into sections. The roles of each section and
their associated parameters are described below. Note that both `;`

and
`#`

may be used as comment characters. Additionally, all parameter
values support environment variable expansion.

### Backends

The backend sections detail how the solver will be configured for a range of different hardware platforms. If a hardware specific backend section is omitted, then PyFR will fall back to built-in default settings.

#### [backend]

Parameterises the backend with

`precision`

— number precision:`single`

|`double`

`rank-allocator`

— MPI rank allocator:`linear`

|`random`

`collect-wait-times`

— If to track MPI request wait times or not:`True`

|`False`

`collect-wait-times-len`

— Size of the wait time history buffer:*int*

Example:

```
[backend]
precision = double
rank-allocator = linear
```

#### [backend-cuda]

Parameterises the CUDA backend with

`device-id`

— method for selecting which device(s) to run on:*int*|`round-robin`

|`local-rank`

|`uuid`

`mpi-type`

— type of MPI library that is being used:`standard`

|`cuda-aware`

`cflags`

— additional NVIDIA realtime compiler (`nvrtc`

) flags:*string*

Example:

```
[backend-cuda]
device-id = round-robin
mpi-type = standard
```

#### [backend-hip]

Parameterises the HIP backend with

`device-id`

— method for selecting which device(s) to run on:*int*|`local-rank`

|`uuid`

`mpi-type`

— type of MPI library that is being used:`standard`

|`hip-aware`

Example:

```
[backend-hip]
device-id = local-rank
mpi-type = standard
```

#### [backend-opencl]

Parameterises the OpenCL backend with

`platform-id`

— for selecting platform id:*int*|*string*`device-type`

— for selecting what type of device(s) to run on:`all`

|`cpu`

|`gpu`

|`accelerator`

`device-id`

— for selecting which device(s) to run on:*int*|*string*|`local-rank`

|`uuid`

`gimmik-max-nnz`

— cutoff for GiMMiK in terms of the number of non-zero entires in a constant matrix:*int*

Example:

```
[backend-opencl]
platform-id = 0
device-type = gpu
device-id = local-rank
gimmik-max-nnz = 512
```

#### [backend-openmp]

Parameterises the OpenMP backend with

`cc`

— C compiler:*string*`cflags`

— additional C compiler flags:*string*`alignb`

— alignment requirement in bytes; must be a power of two and at least 32:*int*`schedule`

— OpenMP loop scheduling scheme:`static`

|`dynamic`

|`dynamic, n`

|`guided`

|`guided, n`

where

*n*is a positive integer.

Example:

```
[backend-openmp]
cc = gcc
```

### Systems

These sections of the input file setup and control the physical system being solved, as well as charateristics of the spatial and temporal schemes to be used.

#### [constants]

Sets constants used in the simulation

`gamma`

— ratio of specific heats for`euler`

|`navier-stokes`

:*float*`mu`

— dynamic viscosity for`navier-stokes`

:*float*`nu`

— kinematic viscosity for`ac-navier-stokes`

:*float*`Pr`

— Prandtl number for`navier-stokes`

:*float*`cpTref`

— product of specific heat at constant pressure and reference temperature for`navier-stokes`

with Sutherland’s Law:*float*`cpTs`

— product of specific heat at constant pressure and Sutherland temperature for`navier-stokes`

with Sutherland’s Law:*float*`ac-zeta`

— artificial compressibility factor for`ac-euler`

|`ac-navier-stokes`

*float*

Other constant may be set by the user which can then be used throughout the
`.ini`

file.

Example:

```
[constants]
; PyFR Constants
gamma = 1.4
mu = 0.001
Pr = 0.72
; User Defined Constants
V_in = 1.0
P_out = 20.0
```

#### [solver]

Parameterises the solver with

`system`

— governing system:`euler`

|`navier-stokes`

|`ac-euler`

|`ac-navier-stokes`

where

`navier-stokes`

requires`viscosity-correction`

— viscosity correction:`none`

|`sutherland`

`shock-capturing`

— shock capturing scheme:`none`

|`artificial-viscosity`

`order`

— order of polynomial solution basis:*int*`anti-alias`

— type of anti-aliasing:`flux`

|`surf-flux`

|`flux, surf-flux`

Example:

```
[solver]
system = navier-stokes
order = 3
anti-alias = flux
viscosity-correction = none
shock-capturing = artificial-viscosity
```

#### [solver-time-integrator]

Parameterises the time-integration scheme used by the solver with

`formulation`

— formulation:`std`

|`dual`

where

`std`

requires`scheme`

— time-integration scheme`euler`

|`rk34`

|`rk4`

|`rk45`

|`tvd-rk3`

`tstart`

— initial time*float*`tend`

— final time*float*`dt`

— time-step*float*`controller`

— time-step controller`none`

|`pi`

where

`pi`

only works with`rk34`

and`rk45`

and requires`atol`

— absolute error tolerance*float*`rtol`

— relative error tolerance*float*`errest-norm`

— norm to use for estimating the error`uniform`

|`l2`

`safety-fact`

— safety factor for step size adjustment (suitable range 0.80-0.95)*float*`min-fact`

— minimum factor by which the time-step can change between iterations (suitable range 0.1-0.5)*float*`max-fact`

— maximum factor by which the time-step can change between iterations (suitable range 2.0-6.0)*float*`dt-max`

— maximum permissible time-step*float*

`dual`

requires`scheme`

— time-integration scheme`backward-euler`

|`sdirk33`

|`sdirk43`

`pseudo-scheme`

— pseudo time-integration scheme`euler`

|`rk34`

|`rk4`

|`rk45`

|`tvd-rk3`

|`vermeire`

`tstart`

— initial time*float*`tend`

— final time*float*`dt`

— time-step*float*`controller`

— time-step controller`none`

`pseudo-dt`

— pseudo time-step*float*`pseudo-niters-max`

— minimum number of iterations*int*`pseudo-niters-min`

— maximum number of iterations*int*`pseudo-resid-tol`

— pseudo residual tolerance*float*`pseudo-resid-norm`

— pseudo residual norm`uniform`

|`l2`

`pseudo-controller`

— pseudo time-step controller`none`

|`local-pi`

where

`local-pi`

only works with`rk34`

and`rk45`

and requires`atol`

— absolute error tolerance*float*`safety-fact`

— safety factor for pseudo time-step size adjustment (suitable range 0.80-0.95)*float*`min-fact`

— minimum factor by which the local pseudo time-step can change between iterations (suitable range 0.98-0.998)*float*`max-fact`

— maximum factor by which the local pseudo time-step can change between iterations (suitable range 1.001-1.01)*float*`pseudo-dt-max-mult`

— maximum permissible local pseudo time-step given as a multiplier of`pseudo-dt`

(suitable range 2.0-5.0)*float*

Example:

```
[solver-time-integrator]
formulation = std
scheme = rk45
controller = pi
tstart = 0.0
tend = 10.0
dt = 0.001
atol = 0.00001
rtol = 0.00001
errest-norm = l2
safety-fact = 0.9
min-fact = 0.3
max-fact = 2.5
```

#### [solver-dual-time-integrator-multip]

Parameterises multi-p for dual time-stepping with

`pseudo-dt-fact`

— factor by which the pseudo time-step size changes between multi-p levels:*float*`cycle`

— nature of a single multi-p cycle:`[(order,nsteps), (order,nsteps), ... (order,nsteps)]`

where

`order`

in the first and last bracketed pair must be the overall polynomial order used for the simulation, and`order`

can only change by one between subsequent bracketed pairs

Example:

```
[solver-dual-time-integrator-multip]
pseudo-dt-fact = 2.3
cycle = [(3, 1), (2, 1), (1, 1), (0, 2), (1, 1), (2, 1), (3, 3)]
```

#### [solver-interfaces]

Parameterises the interfaces with

`riemann-solver`

— type of Riemann solver:`rusanov`

|`hll`

|`hllc`

|`roe`

|`roem`

where

`hll`

|`hllc`

|`roe`

|`roem`

do not work with`ac-euler`

|`ac-navier-stokes`

`ldg-beta`

— beta parameter used for LDG:*float*`ldg-tau`

— tau parameter used for LDG:*float*

Example:

```
[solver-interfaces]
riemann-solver = rusanov
ldg-beta = 0.5
ldg-tau = 0.1
```

#### [solver-source-terms]

Parameterises solution, space (x, y, [z]), and time (t) dependent source terms with

`rho`

— density source term for`euler`

|`navier-stokes`

:*string*`rhou`

— x-momentum source term for`euler`

|`navier-stokes`

:*string*`rhov`

— y-momentum source term for`euler`

|`navier-stokes`

:*string*`rhow`

— z-momentum source term for`euler`

|`navier-stokes`

:*string*`E`

— energy source term for`euler`

|`navier-stokes`

:*string*`p`

— pressure source term for`ac-euler`

|`ac-navier-stokes`

:*string*`u`

— x-velocity source term for`ac-euler`

|`ac-navier-stokes`

:*string*`v`

— y-velocity source term for`ac-euler`

|`ac-navier-stokes`

:*string*`w`

— w-velocity source term for`ac-euler`

|`ac-navier-stokes`

:*string*

Example:

```
[solver-source-terms]
rho = t
rhou = x*y*sin(y)
rhov = z*rho
rhow = 1.0
E = 1.0/(1.0+x)
```

#### [solver-artificial-viscosity]

Parameterises artificial viscosity for shock capturing with

`max-artvisc`

— maximum artificial viscosity:*float*`s0`

— sensor cut-off:*float*`kappa`

— sensor range:*float*

Example:

```
[solver-artificial-viscosity]
max-artvisc = 0.01
s0 = 0.01
kappa = 5.0
```

#### [soln-filter]

Parameterises an exponential solution filter with

`nsteps`

— apply filter every`nsteps`

:*int*`alpha`

— strength of filter:*float*`order`

— order of filter:*int*`cutoff`

— cutoff frequency below which no filtering is applied:*int*

Example:

```
[soln-filter]
nsteps = 10
alpha = 36.0
order = 16
cutoff = 1
```

### Boundary and Initial Conditions

These sections allow users to set the boundary and initial conditions of calculations.

#### [soln-bcs-*name*]

Parameterises constant, or if available space (x, y, [z]) and time (t)
dependent, boundary condition labelled *name* in the .pyfrm file with

`type`

— type of boundary condition:`ac-char-riem-inv`

|`ac-in-fv`

|`ac-out-fp`

|`char-riem-inv`

|`no-slp-adia-wall`

|`no-slp-isot-wall`

|`no-slp-wall`

|`slp-adia-wall`

|`slp-wall`

|`sub-in-frv`

|`sub-in-ftpttang`

|`sub-out-fp`

|`sup-in-fa`

|`sup-out-fn`

where

`ac-char-riem-inv`

only works with`ac-euler`

|`ac-navier-stokes`

and requires`ac-zeta`

— artificial compressibility factor for boundary (increasing`ac-zeta`

makes the boundary less reflective allowing larger deviation from the target state)*float*`niters`

— number of Newton iterations*int*`p`

— pressure*float*|*string*`u`

— x-velocity*float*|*string*`v`

— y-velocity*float*|*string*`w`

— z-velocity*float*|*string*

`ac-in-fv`

only works with`ac-euler`

|`ac-navier-stokes`

and requires`u`

— x-velocity*float*|*string*`v`

— y-velocity*float*|*string*`w`

— z-velocity*float*|*string*

`ac-out-fp`

only works with`ac-euler`

|`ac-navier-stokes`

and requires`p`

— pressure*float*|*string*

`char-riem-inv`

only works with`euler`

|`navier-stokes`

and requires`rho`

— density*float*|*string*`u`

— x-velocity*float*|*string*`v`

— y-velocity*float*|*string*`w`

— z-velocity*float*|*string*`p`

— static pressure*float*|*string*

`no-slp-adia-wall`

only works with`navier-stokes`

`no-slp-isot-wall`

only works with`navier-stokes`

and requires`u`

— x-velocity of wall*float*`v`

— y-velocity of wall*float*`w`

— z-velocity of wall*float*`cpTw`

— product of specific heat capacity at constant pressure and temperature of wall*float*

`no-slp-wall`

only works with`ac-navier-stokes`

and requires`u`

— x-velocity of wall*float*`v`

— y-velocity of wall*float*`w`

— z-velocity of wall*float*

`slp-adia-wall`

only works with`euler`

|`navier-stokes`

`slp-wall`

only works with`ac-euler`

|`ac-navier-stokes`

`sub-in-frv`

only works with`navier-stokes`

and requires`rho`

— density*float*|*string*`u`

— x-velocity*float*|*string*`v`

— y-velocity*float*|*string*`w`

— z-velocity*float*|*string*

`sub-in-ftpttang`

only works with`navier-stokes`

and requires`pt`

— total pressure*float*`cpTt`

— product of specific heat capacity at constant pressure and total temperature*float*`theta`

— azimuth angle (in degrees) of inflow measured in the x-y plane relative to the positive x-axis*float*`phi`

— inclination angle (in degrees) of inflow measured relative to the positive z-axis*float*

`sub-out-fp`

only works with`navier-stokes`

and requires`p`

— static pressure*float*|*string*

`sup-in-fa`

only works with`euler`

|`navier-stokes`

and requires`rho`

— density*float*|*string*`u`

— x-velocity*float*|*string*`v`

— y-velocity*float*|*string*`w`

— z-velocity*float*|*string*`p`

— static pressure*float*|*string*

`sup-out-fn`

only works with`euler`

|`navier-stokes`

Example:

```
[soln-bcs-bcwallupper]
type = no-slp-isot-wall
cpTw = 10.0
u = 1.0
```

Simple periodic boundary conditions are supported; however, their behaviour
is not controlled through the `.ini`

file, instead it is handled at
the mesh generation stage. Two faces may be taged with
`periodic_x_l`

and `periodic_x_r`

, where `x`

is a unique
identifier for the pair of boundaries. Currently, only periodicity in a
single cardinal direction is supported, for example, the planes
`(x,y,0)``

and `(x,y,10)`

.

#### [soln-ics]

Parameterises space (x, y, [z]) dependent initial conditions with

`rho`

— initial density distribution for`euler`

|`navier-stokes`

:*string*`u`

— initial x-velocity distribution for`euler`

|`navier-stokes`

|`ac-euler`

|`ac-navier-stokes`

:*string*`v`

— initial y-velocity distribution for`euler`

|`navier-stokes`

|`ac-euler`

|`ac-navier-stokes`

:*string*`w`

— initial z-velocity distribution for`euler`

|`navier-stokes`

|`ac-euler`

|`ac-navier-stokes`

:*string*`p`

— initial static pressure distribution for`euler`

|`navier-stokes`

|`ac-euler`

|`ac-navier-stokes`

:*string*

Example:

```
[soln-ics]
rho = 1.0
u = x*y*sin(y)
v = z
w = 1.0
p = 1.0/(1.0+x)
```

### Nodal Point Sets

Solution point sets must be specified for each element type that is used and flux point sets must be specified for each interface type that is used. If anti-aliasing is enabled then quadrature point sets for each element and interface type that is used must also be specified. For example, a 3D mesh comprised only of prisms requires a solution point set for prism elements and flux point set for quadrilateral and triangular interfaces.

#### [solver-interfaces-line{-mg-p*order*}]

Parameterises the line interfaces, or if -mg-p*order* is suffixed the
line interfaces at multi-p level *order*, with

`flux-pts`

— location of the flux points on a line interface:`gauss-legendre`

|`gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing on a line interface:*int*`quad-pts`

— name of quadrature rule for anti-aliasing on a line interface:`gauss-legendre`

|`gauss-legendre-lobatto`

Example:

```
[solver-interfaces-line]
flux-pts = gauss-legendre
quad-deg = 10
quad-pts = gauss-legendre
```

#### [solver-interfaces-tri{-mg-p*order*}]

Parameterises the triangular interfaces, or if -mg-p*order* is
suffixed the triangular interfaces at multi-p level *order*, with

`flux-pts`

— location of the flux points on a triangular interface:`williams-shunn`

`quad-deg`

— degree of quadrature rule for anti-aliasing on a triangular interface:*int*`quad-pts`

— name of quadrature rule for anti-aliasing on a triangular interface:`williams-shunn`

|`witherden-vincent`

Example:

```
[solver-interfaces-tri]
flux-pts = williams-shunn
quad-deg = 10
quad-pts = williams-shunn
```

#### [solver-interfaces-quad{-mg-p*order*}]

Parameterises the quadrilateral interfaces, or if -mg-p*order* is
suffixed the quadrilateral interfaces at multi-p level *order*, with

`flux-pts`

— location of the flux points on a quadrilateral interface:`gauss-legendre`

|`gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing on a quadrilateral interface:*int*`quad-pts`

— name of quadrature rule for anti-aliasing on a quadrilateral interface:`gauss-legendre`

|`gauss-legendre-lobatto`

|`witherden-vincent`

Example:

```
[solver-interfaces-quad]
flux-pts = gauss-legendre
quad-deg = 10
quad-pts = gauss-legendre
```

#### [solver-elements-tri{-mg-p*order*}]

Parameterises the triangular elements, or if -mg-p*order* is suffixed
the triangular elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a triangular element:`williams-shunn`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a triangular element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a triangular element:`williams-shunn`

|`witherden-vincent`

Example:

```
[solver-elements-tri]
soln-pts = williams-shunn
quad-deg = 10
quad-pts = williams-shunn
```

#### [solver-elements-quad{-mg-p*order*}]

Parameterises the quadrilateral elements, or if -mg-p*order* is
suffixed the quadrilateral elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a quadrilateral element:`gauss-legendre`

|`gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a quadrilateral element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a quadrilateral element:`gauss-legendre`

|`gauss-legendre-lobatto`

|`witherden-vincent`

Example:

```
[solver-elements-quad]
soln-pts = gauss-legendre
quad-deg = 10
quad-pts = gauss-legendre
```

#### [solver-elements-hex{-mg-p*order*}]

Parameterises the hexahedral elements, or if -mg-p*order* is suffixed
the hexahedral elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a hexahedral element:`gauss-legendre`

|`gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a hexahedral element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a hexahedral element:`gauss-legendre`

|`gauss-legendre-lobatto`

|`witherden-vincent`

Example:

```
[solver-elements-hex]
soln-pts = gauss-legendre
quad-deg = 10
quad-pts = gauss-legendre
```

#### [solver-elements-tet{-mg-p*order*}]

Parameterises the tetrahedral elements, or if -mg-p*order* is suffixed
the tetrahedral elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a tetrahedral element:`shunn-ham`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a tetrahedral element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a tetrahedral element:`shunn-ham`

|`witherden-vincent`

Example:

```
[solver-elements-tet]
soln-pts = shunn-ham
quad-deg = 10
quad-pts = shunn-ham
```

#### [solver-elements-pri{-mg-p*order*}]

Parameterises the prismatic elements, or if -mg-p*order* is suffixed
the prismatic elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a prismatic element:`williams-shunn~gauss-legendre`

|`williams-shunn~gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a prismatic element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a prismatic element:`williams-shunn~gauss-legendre`

|`williams-shunn~gauss-legendre-lobatto`

|`witherden-vincent`

Example:

```
[solver-elements-pri]
soln-pts = williams-shunn~gauss-legendre
quad-deg = 10
quad-pts = williams-shunn~gauss-legendre
```

#### [solver-elements-pyr{-mg-p*order*}]

Parameterises the pyramidal elements, or if -mg-p*order* is suffixed
the pyramidal elements at multi-p level *order*, with

`soln-pts`

— location of the solution points in a pyramidal element:`gauss-legendre`

|`gauss-legendre-lobatto`

`quad-deg`

— degree of quadrature rule for anti-aliasing in a pyramidal element:*int*`quad-pts`

— name of quadrature rule for anti-aliasing in a pyramidal element:`witherden-vincent`

Example:

```
[solver-elements-pyr]
soln-pts = gauss-legendre
quad-deg = 10
quad-pts = witherden-vincent
```

### Plugins

Plugins allow for powerful additional functionality to be swapped in and out. It is possible to load multiple instances of the same plugin by appending a tag, for example:

```
[soln-plugin-writer]
...
[soln-plugin-writer-2]
...
[soln-plugin-writer-three]
...
```

#### [soln-plugin-writer]

Periodically write the solution to disk in the pyfrs format. Parameterised with

`dt-out`

— write to disk every`dt-out`

time units:*float*`basedir`

— relative path to directory where outputs will be written:*string*`basename`

— pattern of output names:*string*`post-action`

— command to execute after writing the file:*string*`post-action-mode`

— how the post-action command should be executed:`blocking`

|`non-blocking`

`region`

— region to be written, specified as either the entire domain using`*`

, a combination of the geometric shapes specified in Regions, or a sub-region of elements that have faces on a specific domain boundary via the name of the domain boundary:`*`

|`shape(args, ...)`

|*string*

Example:

```
[soln-plugin-writer]
dt-out = 0.01
basedir = .
basename = files-{t:.2f}
post-action = echo "Wrote file {soln} at time {t} for mesh {mesh}."
post-action-mode = blocking
region = box((-5, -5, -5), (5, 5, 5))
```

#### [soln-plugin-fluidforce-*name*]

Periodically integrates the pressure and viscous stress on the boundary
labelled `name`

and writes out the resulting force and moment (if requested)
vectors to a CSV file. Parameterised with

`nsteps`

— integrate every`nsteps`

:*int*`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*`morigin`

— origin used to compute moments (optional):`(x, y, [z])`

Example:

```
[soln-plugin-fluidforce-wing]
nsteps = 10
file = wing-forces.csv
header = true
morigin = (0.0, 0.0, 0.5)
```

#### [soln-plugin-nancheck]

Periodically checks the solution for NaN values. Parameterised with

`nsteps`

— check every`nsteps`

:*int*

Example:

```
[soln-plugin-nancheck]
nsteps = 10
```

#### [soln-plugin-residual]

Periodically calculates the residual and writes it out to a CSV file. Parameterised with

`nsteps`

— calculate every`nsteps`

:*int*`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*

Example:

```
[soln-plugin-residual]
nsteps = 10
file = residual.csv
header = true
```

#### [soln-plugin-dtstats]

Write time-step statistics out to a CSV file. Parameterised with

`flushsteps`

— flush to disk every`flushsteps`

:*int*`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*

Example:

```
[soln-plugin-dtstats]
flushsteps = 100
file = dtstats.csv
header = true
```

#### [soln-plugin-pseudostats]

Write pseudo-step convergence history out to a CSV file. Parameterised with

`flushsteps`

— flush to disk every`flushsteps`

:*int*`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*

Example:

```
[soln-plugin-pseudostats]
flushsteps = 100
file = pseudostats.csv
header = true
```

#### [soln-plugin-sampler]

Periodically samples specific points in the volume and writes them out to a CSV file. The point location process automatically takes advantage of scipy.spatial.cKDTree where available. Parameterised with

`nsteps`

— sample every`nsteps`

:*int*`samp-pts`

— list of points to sample:`[(x, y), (x, y), ...]`

|`[(x, y, z), (x, y, z), ...]`

`format`

— output variable format:`primitive`

|`conservative`

`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*

Example:

```
[soln-plugin-sampler]
nsteps = 10
samp-pts = [(1.0, 0.7, 0.0), (1.0, 0.8, 0.0)]
format = primitive
file = point-data.csv
header = true
```

#### [soln-plugin-tavg]

Time average quantities. Parameterised with

`nsteps`

— accumulate the average every`nsteps`

time steps:*int*`dt-out`

— write to disk every`dt-out`

time units:*float*`tstart`

— time at which to start accumulating average data:*float*`mode`

— output file accumulation mode:`continuous`

|`windowed`

Windowed outputs averages over each

`dt- out`

period. Whereas, continuous outputs averages over all`dt-out`

periods thus far completed within a given invocation of PyFR. The default is`windowed`

.`basedir`

— relative path to directory where outputs will be written:*string*`basename`

— pattern of output names:*string*`precision`

— output file number precision:`single`

|`double`

`region`

— region to be written, specified as either the entire domain using`*`

, a combination of the geometric shapes specified in Regions, or a sub-region of elements that have faces on a specific domain boundary via the name of the domain boundary:`*`

|`shape(args, ...)`

|*string*`avg`

-*name*— expression to time average, written as a function of the primitive variables and gradients thereof; multiple expressions, each with their own*name*, may be specified:*string*`fun-avg`

-*name*— expression to compute at file output time, written as a function of any ordinary average terms; multiple expressions, each with their own*name*, may be specified:*string*As

`fun-avg`

terms are evaluated at write time, these are only indirectly effected by the averaging mode.

Example:

```
[soln-plugin-tavg]
nsteps = 10
dt-out = 2.0
mode = windowed
basedir = .
basename = files-{t:06.2f}
avg-u = u
avg-v = v
avg-uu = u*u
avg-vv = v*v
avg-uv = u*v
fun-avg-upup = uu - u*u
fun-avg-vpvp = vv - v*v
fun-avg-upvp = uv - u*v
fun-avg-urms = sqrt(uu - u*u + vv - v*v)
```

#### [soln-plugin-integrate]

Integrate quantities over the compuational domain. Parameterised with:

`nsteps`

— calculate the integral every`nsteps`

time steps:*int*`file`

— output file path; should the file already exist it will be appended to:*string*`header`

— if to output a header row or not:*boolean*`quad-deg`

— degree of quadrature rule (optional):`quad-pts-{etype}`

— name of quadrature rule (optional):`region`

— region to integrate, specified as either the entire domain using`*`

or a combination of the geometric shapes specified in Regions:`*`

|`shape(args, ...)`

`int`

-*name*— expression to integrate, written as a function of the primitive variables and gradients thereof, the physical coordinates [x, y, [z]] and/or the physical time [t]; multiple expressions, each with their own*name*, may be specified:*string*

Example:

```
[soln-plugin-integrate]
nsteps = 50
file = integral.csv
header = true
quad-deg = 9
vor1 = (grad_w_y - grad_v_z)
vor2 = (grad_u_z - grad_w_x)
vor3 = (grad_v_x - grad_u_y)
int-E = rho*(u*u + v*v + w*w)
int-enst = rho*(%(vor1)s*%(vor1)s + %(vor2)s*%(vor2)s + %(vor3)s*%(vor3)s)
```

### Regions

Certain plugins are capable of performing operations on a subset of the
elements inside the domain. One means of constructing these element
subsets is through parameterised regions. Note that an element is
considered part of a region if *any* of its nodes are found to be
contained within the region. Supported regions:

- Rectangular cuboid
`box(x0, x1)`

A rectangular cuboid defined by two diametrically opposed vertices. Valid in both 2D and 3D.

- Conical frustum
`conical_frustum(x0, x1, r0, r1)`

A conical frustum whose end caps are at

*x0*and*x1*with radii*r0*and*r1*, respectively. Only valid in 3D.- Cone
`cone(x0, x1, r)`

A cone of radius

*r*whose centre-line is defined by*x0*and*x1*. Equivalent to`conical_frustum(x0, x1, r, 0)`

. Only valid in 3D.- Cylinder
`cylinder(x0, x1, r)`

A circular cylinder of radius

*r*whose centre-line is defined by*x0*and*x1*. Equivalent to`conical_frustum(x0, x1, r, r)`

. Only valid in 3D.- Cartesian ellipsoid
`ellipsoid(x0, a, b, c)`

An ellipsoid centred at

*x0*with Cartesian coordinate axes whose extents in the*x*,*y*, and*z*directions are given by*a*,*b*, and*c*, respectively. Only valid in 3D.- Sphere
`sphere(x0, r)`

A sphere centred at

*x0*with a radius of*r*. Equivalent to`ellipsoid(x0, r, r, r)`

. Only valid in 3D.

Region expressions can also be added and subtracted together
arbitrarily. For example
`box((-10, -10, -10), (10, 10, 10)) - sphere((0, 0, 0), 3)`

will
result in a cube-shaped region with a sphere cut out of the middle.

### Additional Information

The INI file format is very versatile. A feature that can be useful in defining initial conditions is the substitution feature and this is demonstrated in the [soln-plugin-integrate] example.

To prevent situations where you have solutions files for unknown
configurations, the contents of the `.ini`

file are added as an attribute
to `.pyfrs`

files. These files use the HDF5 format and can be
straightforwardly probed with tools such as h5dump.

In several places within the `.ini`

file expressions may be used. As well as
the constant `pi`

, expressions containing the following functions are
supported:

`+, -, *, /`

— basic arithmetic`sin, cos, tan`

— basic trigonometric functions (radians)`asin, acos, atan, atan2`

— inverse trigonometric functions`exp, log`

— exponential and the natural logarithm`tanh`

— hyperbolic tangent`pow`

— power, note`**`

is not supported`sqrt`

— square root`abs`

— absolute value`min, max`

— two variable minimum and maximum functions, arguments can be arrays