src/README

Solvers

Saint-Venant

\displaystyle \partial_t \int_{\Omega} \mathbf{q} d \Omega = \int_{\partial \Omega} \mathbf{f} ( \mathbf{q}) \cdot \mathbf{n}d \partial \Omega - \int_{\Omega} hg \nabla z_b \displaystyle \mathbf{q} = \left(\begin{array}{c} h\\ hu_x\\ hu_y \end{array}\right), \;\;\;\;\;\; \mathbf{f} (\mathbf{q}) = \left(\begin{array}{cc} hu_x & hu_y\\ hu_x^2 + \frac{1}{2} gh^2 & hu_xu_y\\ hu_xu_y & hu_y^2 + \frac{1}{2} gh^2 \end{array}\right)

• Semi-implicit scheme
• Multiple layers \displaystyle \partial_th + \partial_x\sum_{l=0}^{nl-1}h_lu_l = 0

\displaystyle \partial_t(h\mathbf{u}_l) + \nabla\cdot\left(h\mathbf{u}_l\otimes\mathbf{u}_l + \frac{gh^2}{2}\mathbf{I}\right) = - gh\nabla z_b - \partial_z(h\mathbf{u}w) + \nu h\partial_{z^2}\mathbf{u}

• Green-Naghdi \displaystyle \partial_t \int_{\Omega} \mathbf{q} d \Omega = \int_{\partial \Omega} \mathbf{f} ( \mathbf{q}) \cdot \mathbf{n}d \partial \Omega - \int_{\Omega} hg \nabla z_b + h \left( \frac{g}{\alpha}\nabla \eta - D \right) \displaystyle \alpha h\mathcal{T} \left( D \right) + hD = b \displaystyle b = \left[ \frac{g}{\alpha} \nabla \eta +\mathcal{Q}_1 \left( u \right) \right]

• Multilayer hydrostatic

\displaystyle \begin{aligned} \partial_t h_k + \mathbf{{\nabla}} \cdot \left( h \mathbf{u} \right)_k & = 0,\\ \partial_t \left( h \mathbf{u} \right)_k + \mathbf{{\nabla}} \cdot \left( h \mathbf{u} \mathbf{u} \right)_k & = - gh_k \mathbf{{\nabla}} (\eta) \end{aligned}

Systems of conservation laws

\displaystyle \partial_t\left(\begin{array}{c} s_i\\ \mathbf{v}_j\\ \end{array}\right) + \nabla\cdot\left(\begin{array}{c} \mathbf{F}_i\\ \mathbf{T}_j\\ \end{array}\right) = 0

• Compressible gas dynamics
• All Mach compressible flows

\displaystyle \partial_t\mathbf{q} + \nabla\cdot(\mathbf{q}\mathbf{u}) = - \nabla p + \nabla\cdot(\mu\nabla\mathbf{u}) + \rho\mathbf{a} \displaystyle \partial_t p + \mathbf{u}\cdot\nabla p = -\rho c^2\nabla\cdot\mathbf{u}

• All Mach compressible two-phase flows

\displaystyle \frac{\partial (f \rho_i)}{\partial t } + \nabla \cdot (f \rho_i \mathbf{u}) = 0 \displaystyle \frac{\partial (\rho_i \mathbf{u})}{\partial t } + \nabla \cdot ( \rho_i \mathbf{u} \mathbf{u}) = -\nabla p + \nabla \cdot \tau_i' \displaystyle \frac{\partial [\rho_i (e_i + \mathbf{u}^2/2)]}{\partial t } + \nabla \cdot [ \rho_i \mathbf{u} (e_i + \mathbf{u}^2/2)] = -\nabla \cdot (\mathbf{u} p_i) + \nabla \cdot \left( \tau'_i \mathbf{u} \right)

• Thermal effects for all Mach compressible two-phase flows

\displaystyle \rho_ic_{p,i}\frac{DT_i}{Dt} = \beta_iT_i\frac{Dp_i}{Dt} - \nabla\cdot\mathbf{q}_i \displaystyle \left(\frac{\gamma_i}{\rho_ic_i^2} - \frac{\beta_i^2T_i}{\rho_ic_{p,i}}\right)\frac{Dp_i}{Dt} = -\frac{\beta_i}{\rho_ic_{p,i}}\nabla\cdot\mathbf{q}_i - \nabla\cdot\mathbf{u}_i

Navier–Stokes

• Streamfunction–Vorticity formulation \displaystyle \partial_t\omega + \mathbf{u}\cdot\nabla\omega = \nu\nabla^2\omega \displaystyle \nabla^2\psi = \omega

• “Markers-And-Cells” (MAC or “C-grid”) formulation
• Centered formulation \displaystyle \partial_t\mathbf{u}+\nabla\cdot(\mathbf{u}\otimes\mathbf{u}) = \frac{1}{\rho}\left[-\nabla p + \nabla\cdot(2\mu\mathbf{D})\right] + \mathbf{a} \displaystyle \nabla\cdot\mathbf{u} = 0
  • Azimuthal velocity for axisymmetric flows \displaystyle \partial_t w + u_x \partial_x w + u_y \partial_y w + \frac{u_y w}{y} = \frac{1}{\rho y} \left[ \nabla \cdot (\mu y \nabla w) - w \left( \frac{\mu}{y} + \partial_y \mu \right) \right]
• Two-phase interfacial flows
  • Momentum conservation option
• Momentum-conserving two-phase interfacial flows

• Multilayer incompressible Euler/Navier-Stokes equations with a free-surface

\displaystyle \begin{aligned} \partial_t h_k + \mathbf{{\nabla}} \cdot \left( h \mathbf{u} \right)_k & = 0,\\ \partial_t \left( h \mathbf{u} \right)_k + \mathbf{{\nabla}} \cdot \left( h \mathbf{u} \mathbf{u} \right)_k & = - gh_k \mathbf{{\nabla}} (\eta) - \mathbf{{\nabla}} (h \phi)_k + \left[ \phi \mathbf{{\nabla}} z \right]_k,\\ \partial_t (hw)_k + \mathbf{{\nabla}} \cdot \left( hw \mathbf{u} \right)_k & = - [\phi]_k,\\ \mathbf{{\nabla}} \cdot \left( h \mathbf{u} \right)_k + \left[ w - \mathbf{u} \cdot \mathbf{{\nabla}} z \right]_k & = 0 \end{aligned}

Electrohydrodynamics

• Ohmic conduction \displaystyle \partial_t\rho_e = \nabla \cdot(K \nabla \phi) \displaystyle \nabla \cdot (\epsilon \nabla \phi) = - \rho_e
• Ohmic conduction of charged species \displaystyle \partial_tc_i = \nabla \cdot( K_i c_i \nabla \phi)
• Electrohydrodynamic stresses \displaystyle M_{ij} = \varepsilon (E_i E_j - \frac{E^2}{2}\delta_{ij})

Viscoelasticity

• The log-conformation method for some viscoelastic constitutive models

\displaystyle \rho\left[\partial_t\mathbf{u}+\nabla\cdot(\mathbf{u}\otimes\mathbf{u})\right] = - \nabla p + \nabla\cdot(2\mu_s\mathbf{D}) + \nabla\cdot\mathbf{\tau}_p + \rho\mathbf{a} \displaystyle \mathbf{\tau}_p = \frac{\mu_p \mathbf{f_s}(\mathbf{A})}{\lambda} \displaystyle \Psi = \log\mathbf{A} \displaystyle D_t \Psi = (\Omega \cdot \Psi -\Psi \cdot \Omega) + 2 \mathbf{B} + \frac{e^{-\Psi} \mathbf{f}_r (e^{\Psi})}{\lambda}

Other equations

• Hele-Shaw/Darcy flows \displaystyle \mathbf{u} = \beta\nabla p \displaystyle \nabla\cdot(\beta\nabla p) = \zeta
• Advection \displaystyle \partial_tf_i+\mathbf{u}\cdot\nabla f_i=0
  • Volume-Of-Fluid advection
    • Contact angles
• Interfacial forces \displaystyle \phi\mathbf{n}\delta_s
  • Surface tension \displaystyle \sigma\kappa\mathbf{n}\delta_s
  • Reduced gravity \displaystyle [\rho]\mathbf{g}\cdot\mathbf{x}\mathbf{n}\delta_s
  • Surface tension (integral formulation) \displaystyle \sigma^{x x}_i = \left[ \gamma \frac{t^x}{\Delta} + \left\{\begin{array}{ll} s^x (p_{j - 1} - p_j) & \text{if } s^x < 1 / 2\\ (s^x - 1) (p_j - p_{j + 1}) & \text{otherwise} \end{array}\right. \right]_i
• Reaction–Diffusion \displaystyle \theta\partial_tf = \nabla\cdot(D\nabla f) + \beta f + r
• Poisson–Helmholtz \displaystyle \nabla\cdot (\alpha\nabla a) + \lambda a = b
• General spatial linear systems \displaystyle \mathcal{L}(a) = b
• Henry’s law
• Runge–Kutta time integrators \displaystyle \frac{\partial\mathbf{u}}{\partial t} = L(\mathbf{u}, t)
• Signed distance field
• Redistancing of a distance field \displaystyle \left\{\begin{array}{ll} \phi_t + \text{sign}(\phi^{0}) \left(\left| \nabla \phi\right| - 1 \right) = 0\\ \phi(x,0) = \phi^0(x) \end{array} \right.
• Okada fault model
• Hessenberg systems
• Community Ocean Vertical Mixing (CVMix) interface
• A C interface to the General Ocean Turbulence Model

The Basilisk C preprocessor

• qcc: the command line preprocessor/compiler
• The Abstract Syntax Tree (AST) library
• Dimensional Analysis

General orthogonal coordinates

When not written in vector form, some of the equations above will change depending on the choice of coordinate system (e.g. polar rather than Cartesian coordinates). In addition, extra terms can appear due to the geometric curvature of space (e.g. equations on the sphere). An important simplification is to consider only orthogonal coordinates. In this case, consistent finite-volume discretisations of standard operators (divergence etc…) can be obtained, for any orthogonal curvilinear coordinate system, using only a few additional geometric parameters.

Metric scale factors

The face vector fm is the scale factor for the length of a face i.e. the physical length is fm\Delta and the scalar field cm is the scale factor for the area of the cell i.e. the physical area is cm\Delta^2. By default, these fields are constant and unity (i.e. the Cartesian metric).

Several metric spaces/coordinate systems are predefined:

• Axisymmetric
  • Stokes stream function \displaystyle \frac{\partial^2\psi}{\partial z^2} + \frac{\partial^2\psi}{\partial r^2} - \frac{1}{r}\partial_r\psi = - \omega r
• Spherical symmetry
• Spherical
• Radial/cylindrical

Data processing

• Various utility functions: timing, field statistics, slope limiters, etc.
• Tagging connected neighborhoods
• Counting droplets

Output functions

• Multiple fields interpolated on a regular grid (text format)
• Single field interpolated on a regular grid (binary format)
• Portable PixMap (PPM) image output
• Volume-Of-Fluid facets
• Basilisk snapshots
• Gerris simulation format
• ESRI ASCII Grid format
• VTK format

Input functions

• Basilisk snapshots
• Gerris simulation format
• ESRI ASCII Grid format
• Portable Gray Map (PGM) images

Basilisk View

• Javascript interface
• “Dump files” server
• Online

Miscellaneous functions/modules

• Controlling the maximum runtime

Tracking floating-point exceptions

On systems which support signaling NaNs (such as GNU/Linux), Basilisk is set up so that trying to use an unitialised value will cause a floating-point exception to be triggered and the program to abort. This is particularly useful when developing adaptive algorithms and/or debugging boundary conditions.

To maximise the “debugging potential” of this approach it is also recommended to use the trash() function to reset any field prior to updates. This will guarantee that older values are not mistakenly reused. Note that this call is quite expensive and needs to be turned on by adding -DTRASH=1 to the compilation flags (otherwise it is just ignored).

Doing

ulimit -c unlimited

before running the code will allow generation of core files which can be used for post-mortem debugging (e.g. with gdb).

Visualising stencils

It is often useful to visualise the values of fields in the stencil which triggered the exception. This can be done using the -catch option of qcc.

We will take this code as an example:

#include "utils.h"

int main()
{
  init_grid (16);
  scalar a[];
  trash ({a});
  foreach()
    a[] = x;
  vector ga[];
  gradients ({a}, {ga});
}

Copy and paste this into test.c, then do

ulimit -c unlimited
qcc -DTRASH=1 -g -Wall test.c -o test -lm
./test

you should get

Floating point exception (core dumped)

Then do

gdb test core

you should get

...
Core was generated by `./test'.
Program terminated with signal 8, Arithmetic exception.
#0  0x0000000000419dbe in gradients (f=0x7fff5f412430, g=0x7fff5f412420)
    at /home/popinet/basilisk/wiki/src/utils.h:203
203		  v.x[] = (s[1,0] - s[-1,0])/(2.*Delta);

i.e. the exception occured in the gradients() function of utils.h.

To visualise the stencil/fields which lead to the exception do

qcc -catch -g -Wall test.c -o test -lm
./test 

you should now get

Caught signal 8 (Floating Point Exception)
Caught signal 6 (Aborted)
Last point stencils can be displayed using (in gnuplot)
  set size ratio -1
  set key outside
  v=0
  plot 'cells' w l lc 0, \
    'stencil' u 1+3*v:2+3*v:3+3*v w labels tc lt 1 title columnhead(3+3*v), \
        'coarse' u 1+3*v:2+3*v:3+3*v w labels tc lt 3 t ''
Aborted (core dumped)

Follow the instructions i.e.

gnuplot
gnuplot> set size ratio -1
gnuplot> set key outside
gnuplot> v=0
gnuplot> plot 'cells' w l lc 0, \
  'stencil' u 1+3*v:2+3*v:3+3*v w labels tc lt 1 title columnhead(3+3*v), \
  'coarse' u 1+3*v:2+3*v:3+3*v w labels tc lt 3 t ''

With some zooming and panning, you should get this picture

Example of stencil/field causing an exception

The red numbers represent the stencil the code was working on when the exception occured. It is centered on the top-left corner of the domain. Cells both inside the domain and outside (i.e. ghost cells) are represented. While the field inside the domain has been initialised, ghost cell values have not. This causes the gradients() function to generate the exception when it tries to access ghost cell values.

To initialise the ghost-cell values, we need to apply the boundary conditions i.e. add

  boundary ({a});

after initialisation. Recompiling and re-running confirms that this fixes the problem.

Note that the blue numbers are the field values for the parent cells (in the quadtree hierarchy). We can see that these are also un-initialised but this is not a problem since we don’t use them in this example.

The v value in the gnuplot script is important. It controls which field is displayed. v=0 indicates the first field allocated by the program (i.e. a[] in this example), accordingly ga.x[] and ga.y[] have indices 1 and 2 respectively.

Tracing permissions

Some recent systems disallow tracing of processes for security reasons. The symptom will be an error message from gdb looking like:

Attaching to process 9351
Could not attach to process.  If your uid matches the uid of the target
process, check the setting of /proc/sys/kernel/yama/ptrace_scope, or try
again as the root user.  For more details, see /etc/sysctl.d/10-ptrace.conf
ptrace: Operation not permitted.

To enable tracing (which weakens your system’s security), you need to do:

sudo sh -c 'echo 0 > /proc/sys/kernel/yama/ptrace_scope'

See also

• Tips
• Built-in profiling
• Built-in memory profiling
• Performance profiling with Paraver
• Profiling round-off errors with CADNA