PyFR 1.6.0 has a hard dependency on Python 3.3+ and the following Python packages:

1. appdirs >= 1.4.0
2. gimmik >= 2.0
3. h5py >= 2.6
4. mako >= 1.0.0
5. mpi4py >= 2.0
6. numpy >= 1.8
7. pytools >= 2016.2.1

Note that due to a bug in numpy PyFR is not compatible with 32-bit Python distributions.

The CUDA backend targets NVIDIA GPUs with a compute capability of 2.0 or greater. The backend requires:

1. CUDA >= 4.2
2. pycuda >= 2015.1

The MIC backend targets Intel Xeon Phi co-processors. The backend requires:

1. ICC >= 14.0
2. Intel MKL >= 11.1
3. Intel MPSS >= 3.3
4. pymic >= 0.7 (post commit 4d8a2da)

The OpenCL backend targets a range of accelerators including GPUs from AMD and NVIDIA. The backend requires:

1. OpenCL
2. pyopencl >= 2015.2.4
3. clBLAS

The OpenMP backend targets multi-core CPUs. The backend requires:

1. GCC >= 4.9
2. A BLAS library compiled as a shared library (e.g. OpenBLAS)
3. Optionally libxsmm >= 1.6 compiled as a shared library (STATIC=0) with BLAS=0

To partition meshes for running in parallel it is also necessary to have one of the following partitioners installed:

1. metis >= 5.0
2. scotch >= 6.0

To import CGNS meshes it is necessary to have the following installed:

1. CGNS >= 3.3 (develop branch post commit e0faea6)

pyfr can be run in parallel. To do so prefix pyfr with mpirun -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.

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.

Parameterises the backend with

1. precision — number precision:

   single | double

2. rank-allocator — MPI rank allocator:

   linear | random

Example:

[backend]
precision = double
rank-allocator = linear

Parameterises the CUDA backend with

1. device-id — method for selecting which device(s) to run on:

   int | round-robin | local-rank

2. gimmik-max-nnz — cutoff for GiMMiK in terms of the number of non-zero entires in a constant matrix:

   int

3. mpi-type — type of MPI library that is being used:

   standard | cuda-aware

4. block-1d — block size for one dimensional pointwise kernels:

   int

5. block-2d — block size for two dimensional pointwise kernels:

   int, int

Example:

[backend-cuda]
device-id = round-robin
gimmik-max-nnz = 512
mpi-type = standard
block-1d = 64
block-2d = 128, 2

Parameterises the MIC backend with

1. device-id — for selecting which device(s) to run on:

   int | local-rank

2. mkl-root — path to MKL root directory:

   string

Parameterises the OpenCL backend with

1. platform-id — for selecting platform id:

   int | string

2. device-type — for selecting what type of device(s) to run on:

   all | cpu | gpu | accelerator

3. device-id — for selecting which device(s) to run on:

   int | string | local-rank

4. gimmik-max-nnz — cutoff for GiMMiK in terms of the number of non-zero entires in a constant matrix:

   int

5. local-size-1d — local work size for one dimensional pointwise kernels:

   int

6. local-size-2d — local work size for two dimensional pointwise kernels:

   int, int

Example:

[backend-opencl]
platform-id = 0
device-type = gpu
device-id = local-rank
gimmik-max-nnz = 512
local-size-1d = 16
local-size-2d = 128, 1

Parameterises the OpenMP backend with

1. cc — C compiler:

   string

2. cflags — additional C compiler flags:

   string

3. alignb — alignment requirement in bytes; must be a power of two and at least 32:

   int

4. cblas — path to shared C BLAS library:

   string

5. cblas-type — type of BLAS library:

   serial | parallel

6. gimmik-max-nnz — cutoff for GiMMiK in terms of the number of non-zero entires in a constant matrix:

   int

7. libxsmm-block-sz — blocking factor to use for libxsmm; must be a multiple of 16:

   int

8. libxsmm-max-sz — cutoff for libxsmm in terms of the number of entires in a constant matrix:

   int

Example:

[backend-openmp]
cc = gcc
cblas= example/path/libBLAS.dylib
cblas-type = parallel

Sets constants used in the simulation

1. gamma — ratio of specific heats for euler | navier-stokes:

   float

2. mu — dynamic viscosity for navier-stokes:

   float

3. nu — kinematic viscosity for ac-navier-stokes:

   float

4. Pr — Prandtl number for navier-stokes:

   float

5. cpTref — product of specific heat at constant pressure and reference temperature for navier-stokes with Sutherland’s Law:

   float

6. cpTs — product of specific heat at constant pressure and Sutherland temperature for navier-stokes with Sutherland’s Law:

   float

7. ac-zeta — artificial compressibility factor for ac-euler | ac-navier-stokes

   float

Example:

[constants]
gamma = 1.4
mu = 0.001
Pr = 0.72

Parameterises the solver with

1. 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

2. order — order of polynomial solution basis:

   int

3. anti-alias — type of anti-aliasing:

   flux | surf-flux | div-flux | flux, surf-flux | flux, div-flux | surf-flux, div-flux | flux, surf-flux, div-flux

Example:

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

Parameterises the time-integration scheme used by the solver with

1. 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 that the time-step can change between iterations (suitable range 0.1-0.5)

       float

     • max-fact — maximum factor that the time-step can change between iterations (suitable range 2.0-6.0)

       float

   dual requires

   • scheme — time-integration scheme

     backward-euler | bdf2 | bdf3

   • pseudo-scheme — pseudo time-integration scheme

     euler | tvd-rk3 | rk4

   • tstart — initial time

     float

   • tend — final time

     float

   • dt — time-step

     float

   • pseudo-dt — pseudo time-step

     float

   • controller — pseudo time-step controller

     none

     where

     none requires

     • 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

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

Parameterises the interfaces with

1. 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

2. ldg-beta — beta parameter used for LDG:

   float

3. ldg-tau — tau parameter used for LDG:

   float

Example:

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

Parameterises the line interfaces with

1. flux-pts — location of the flux points on a line interface:

   gauss-legendre | gauss-legendre-lobatto

2. quad-deg — degree of quadrature rule for anti-aliasing on a line interface:

   int

3. 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

Parameterises the triangular interfaces with

1. flux-pts — location of the flux points on a triangular interface:

   williams-shunn

2. quad-deg — degree of quadrature rule for anti-aliasing on a triangular interface:

   int

3. 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

Parameterises the quadrilateral interfaces with

1. flux-pts — location of the flux points on a quadrilateral interface:

   gauss-legendre | gauss-legendre-lobatto

2. quad-deg — degree of quadrature rule for anti-aliasing on a quadrilateral interface:

   int

3. 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

Parameterises the triangular elements with

1. soln-pts — location of the solution points in a triangular element:

   williams-shunn

2. quad-deg — degree of quadrature rule for anti-aliasing in a triangular element:

   int

3. 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

Parameterises the quadrilateral elements with

1. soln-pts — location of the solution points in a quadrilateral element:

   gauss-legendre | gauss-legendre-lobatto

2. quad-deg — degree of quadrature rule for anti-aliasing in a quadrilateral element:

   int

3. 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

Parameterises the hexahedral elements with

1. soln-pts — location of the solution points in a hexahedral element:

   gauss-legendre | gauss-legendre-lobatto

2. quad-deg — degree of quadrature rule for anti-aliasing in a hexahedral element:

   int

3. 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

Parameterises the tetrahedral elements with

1. soln-pts — location of the solution points in a tetrahedral element:

   shunn-ham

2. quad-deg — degree of quadrature rule for anti-aliasing in a tetrahedral element:

   int

3. 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

Parameterises the prismatic elements with

1. soln-pts — location of the solution points in a prismatic element:

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

2. quad-deg — degree of quadrature rule for anti-aliasing in a prismatic element:

   int

3. 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

Parameterises the pyramidal elements with

1. soln-pts — location of the solution points in a pyramidal element:

   gauss-legendre | gauss-legendre-lobatto

2. quad-deg — degree of quadrature rule for anti-aliasing in a pyramidal element:

   int

3. 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

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

1. rho — density source term for euler | navier-stokes:

   string

2. rhou — x-momentum source term for euler | navier-stokes :

   string

3. rhov — y-momentum source term for euler | navier-stokes :

   string

4. rhow — z-momentum source term for euler | navier-stokes :

   string

5. E — energy source term for euler | navier-stokes :

   string

6. p — pressure source term for ac-euler | ac-navier-stokes:

   string

7. u — x-velocity source term for ac-euler | ac-navier-stokes:

   string

8. v — y-velocity source term for ac-euler | ac-navier-stokes:

   string

9. 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)

Parameterises artificial viscosity for shock capturing with

1. max-artvisc — maximum artificial viscosity:

   float

2. s0 — sensor cut-off:

   float

3. kappa — sensor range:

   float

Example:

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

Parameterises an exponential solution filter with

1. nsteps — apply filter every nsteps:

   int

2. alpha — strength of filter:

   float

3. order — order of filter:

   int

4. cutoff — cutoff frequency below which no filtering is applied:

   int

Example:

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

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

1. dt-out — write to disk every dt-out time units:

   float

2. basedir — relative path to directory where outputs will be written:

   string

3. basename — pattern of output names:

   string

4. post-action — command to execute after writing the file:

   string

5. post-action-mode — how the post-action command should be executed:

   blocking | non-blocking

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

Periodically integrates the pressure and viscous stress on the boundary labelled name and writes out the resulting force vectors to a CSV file. Parameterised with

1. nsteps — integrate every nsteps:

   int

2. file — output file path; should the file already exist it will be appended to:

   string

3. header — if to output a header row or not:

   boolean

Example:

[soln-plugin-fluidforce-wing]
nsteps = 10
file = wing-forces.csv
header = true

Periodically checks the solution for NaN values. Parameterised with

1. nsteps — check every nsteps:

   int

Example:

[soln-plugin-nancheck]
nsteps = 10

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

1. nsteps — calculate every nsteps:

   int

2. file — output file path; should the file already exist it will be appended to:

   string

3. header — if to output a header row or not:

   boolean

Example:

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

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

1. flushsteps — flush to disk every flushsteps:

   int

2. file — output file path; should the file already exist it will be appended to:

   string

3. header — if to output a header row or not:

   boolean

Example:

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

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

1. flushsteps — flush to disk every flushsteps:

   int

2. file — output file path; should the file already exist it will be appended to:

   string

3. header — if to output a header row or not:

   boolean

Example:

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

Periodically samples specific points in the volume and writes them out to a CSV file. The plugin actually samples the solution point closest to each sample point, hence a slight discrepancy in the output sampling locations is to be expected. A nearest-neighbour search is used to locate the closest solution point to the sample point. The location process automatically takes advantage of scipy.spatial.cKDTree where available. Parameterised with

1. nsteps — sample every nsteps:

   int

2. samp-pts — list of points to sample:

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

3. format — output variable format:

   primitive | conservative

4. file — output file path; should the file already exist it will be appended to:

   string

5. 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 = primative
file = point-data.csv
header = true

Time average quantities. Parameterised with

1. nsteps — accumulate the average every nsteps time steps:

   int

2. dt-out — write to disk every dt-out time units:

   float

3. basedir — relative path to directory where outputs will be written:

   string

4. basename — pattern of output names:

   string

5. avg-name — expression as a function of the primitive variables, time (t), and space (x, y, [z]) to time average; multiple expressions, each with their own name, may be specified:

   string

Example:

[soln-plugin-tavg]
nsteps = 10
dt-out = 2.0
basedir = .
basename = files-{t:06.2f}

avg-p = p
avg-p2 = p*p
avg-vel = sqrt(u*u + v*v)

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

1. type — type of boundary condition:

   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-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-p 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 navier-stokes

Example:

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

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

1. rho — initial density distribution for euler | navier-stokes:

   string

2. u — initial x-velocity distribution for euler | navier-stokes | ac-euler | ac-navier-stokes:

   string

3. v — initial y-velocity distribution for euler | navier-stokes | ac-euler | ac-navier-stokes:

   string

4. w — initial z-velocity distribution for euler | navier-stokes | ac-euler | ac-navier-stokes:

   string

5. 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)