docs:tutorial

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So you've installed channelflow. Now what? Well, computational fluid dynamics is a pretty big field, and there's no telling what kinds of ideas you might want to explore. For this reason Channelflow was developed primarily as a *programming language*. If you're using Channelflow for research towards a Ph.D. thesis, you will probably eventually end up writing your own channelflow programs, for example, modifying existing programs to integrate flows and analyze data. Or you might need to modify the time-integration routines to incorporate additional physics (polymer additives, bubbles, etc.)

However, channelflow also includes a number of predefined utility programs that a basic set of important computations, such as time-integration of plane Couette and channel flows and measuring properties of velocity fields. These utilities suffice for the bulk of my own research. Probably the best way to get started with channelflow is to step through a few examples of run-of-the-mill calculations using these utilities. If you want to get right to these examples, skip to Section 3.

Here's a list of current channelflow utilities. The first three are taken out of alphabetical order because they're featured in Section 3, Example Calculations.

program name | purpose |
---|---|

randomfield | build a random initial velocity field, save to disk |

couette | integrate an initial condition, save results to disk |

fieldprops | print out norms, symmetries, geometrical data of a stored field |

makemovie | extract slices of fields in order to make a movie |

addfields | compute sum a_n u_n and store result to disk |

arnoldi | compute the eigenvalues and eigenfunctions of eqbs and orbits |

ascii2field | convert a file of ASCII data to a channelflow FlowField |

changegrid | change the discretization or box size of a field |

field2ascii | convert a channelflow FlowField to a file of ASCII data |

fieldplots | extract a number of 2D slices of the 3D field, good for plots |

findorbit | compute an equilibrium or periodic orbit of plane Couette |

L2Dist | compute the L2 distance between two fields |

L2IP | compute the L2 inner product |

makebasis | construct an orthonormal basis from a set of fields |

makeheatmode | construct a field that decays in time according to Laplace eqn |

makestokesmode | construct a stokes eigenfunction of laminar equilibrium |

perturbfield | add random perturbations to a given field |

projectfields | project a set of fields onto a given basis |

projectseries | project a sequence of fields onto a given basis |

seriesprops | compute statistics on a sequence of data |

symmetrize | find the phase shift of a field that optimize a given symmetry |

symmetryop | apply a given symmetry to a field |

The utilities are stand-alone command-line programs that are run from the Unix shell. You can get brief built-in help information on each utility by running it with a -h or –help option. For example, running “couette –help” produces

gibson@akbar$ couette --help couette : integrate an initial condition and save velocity fields to disk.

options : -T0 --T0 <real> default == 0 start time -T1 --T1 <real> default == 100 end time -vdt --variabledt adjust dt for CFL -dt --dt <real> default == 0.03125 timestep -dtmin --dtmin <real> default == 0.001 minimum time step -dtmax --dtmax <real> default == 0.05 maximum time step -dT --dT <real> default == 1 save interval -CFLmin --CFLmin <real> default == 0.4 minimum CFL number -CFLmax --CFLmax <real> default == 0.6 maximum CFL number -ts --timestepping <string> default == sbdf3 timestepping algorithm ... -p --pressure print pressure grad <flowfield> (trailing arg 1) initial condition

The built-in help gives a brief description of each utility's purpose

and a list of its command-line options and arguments. Channelflow utilities are invoked at the command line with syntax like

utility -opt1 value -opt2 value -flag1 arg3 arg2 arg1

or concretely

couette -T0 0 -T1 -vdt -dt 0.02 -ts sbdf4 u0.ff

“Options” (e.g. -opt1 value) are used to reset default values of parameters. For options, the first two columns in the built-in help give the short and long form of the option (e.g. -ts and –timestepping), the third column indicates the type of parameter expected (e.g. real, int, bool, string), and the fourth gives the the default value. For example, “couette -dt 0.02 -ts cnab2” sets the time stepping method to 2nd order Crank-Nicolson Adams-Bashforth with dt=0.02.

“Flags” simply turn on boolean options that would otherwise be set to false. For example, calling “couette -vdt” turns on variable-dt timestepping, which adjusts dt at fixed intervals to keep the CFL number within bounds. For flags the third and fourth columns of built-in help are left blank.

“Arguments” always come after all options and flags. Arguments usually specify the filenames of binary velocity fields that the utility will load and operate on. Most channelflow programs have one required argument (e.g. “couette u0.ff”) some two (e.g. “L2Dist u0.ff u2.ff”). Others take a variable number of arguments (e.g. makebasis u0 u1 u2“). Unfortunately it's difficult to document variable-number arguments properly in the four-column option system, so variable-number arguments are usually documented with a “usage: line right after the description of the utility's purpose.

So, as you read work through the Example Calculations, you can run the suggested command with a –help option to clarify what the options are doing and what other options are possible.

gibson@akbar$ randomfield -Nx 48 -Ny 35 -Nz 48 -lx 0.875 -lz 0.6 -m 0.20 u0.ff

This command generates a no-slip, divergence-free velocity field with random spectral coefficients on a 48 x 35 x 48 grid, on [0, 2pi] x [-1, 1] x [0, pi], with magnitude 1/V \integral_V |u|^2 dx = 0.2. The field is a perturbation from the laminar flow –by default, velocity fields in channelflow are differences from laminar. The spectral coefficients are random within an exponentially decaying envelope, roughly similar to turbulent fields. The velocity field is saved to disk in binary format in file u0.ff (the .ff stands for “FlowField”, the name of the C++ class for velocity, pressure and tensor fields in channelflow). The channelflow binary format stores the spectral coefficients, the geometry, and all discretization information so the field can be reconstructed entirely from the data in the file. You can list this information and some dynamical properties of the field by running

gibson@akbar$ fieldprops u0.ff

gibson@akbar$ couette -T0 0 -T1 200 -l2 -o data u0.ff

This command load the velocity field u0.ff from disk and integrates it in time (using the default integration algorithm and parameters) from t=T0=0 to t=T1=200, and saves the time varying velocity field to disk at the interval dT=1.0 (the default save interval) in a directory named data/. The -l2 option prints out the L2 norm of u as well as the Chebyshev-weighted norm.

After this command finishes, look in the data/ directory, and you will see u0.ff u1.ff u2.ff etc. The integer label is the time (remember the save interval is dT=1.0). If you choose a noninteger save interval, the filenames will be something like u0.000.ff u0.975.ff etc.

gibson@akbar$ movieframes -T0 0 -T1 200 -d data -o frames

The movieframes program reads in the series of files data/u0.ff, data/u1.ff, etc. and extracts a number of 2D slices of the 3D fields that are good for visualizing the flow. These 2D slices are stored in the frames/ directory with filenames like u0_yz_slice.asc.

To make a movie using channelflow's existing visualization tools, you need Matlab. (If you would like to write similar tools for another visualization package, please do so and send them to me!). Start up Matlab. Get all the scripts in channelflow/matlab into your Matlab path. Do this either by copying the scripts into the current directory, by copying them to wherever you store your Matlab scripts, or by putting channelflow/matlab in your Matlab path. You can do that by typing 'addpath /home/larry/channelflow-1.3.2/matlab' at the Matlab prompt (changing the directory as appropriate).

Then, within Matlab change to the directory that where you ran the couette programs, the one with data/ and frames/ subdirectories. Within Matlab run

makemovie(0,1,200,0,1,10, 'couette.avi');

This will construct a movie of the 3D velocity field as it evolves in time and store the result in file couette.avi, in AVI format. Running 'help makemovie' will give you a help string about the makemovie script and its arguments; briefly, here the arguments are

0 starting frame number int 1 frame interval int 200 ending frame number int 0 starting time float 1 time interval float 10 frames per second int 'couette.avi' output filename string

further optional arguments are

title printed this in the upper-left corner string credit printed this in the lower-right corner string xstride plot every xstride-th gridpoint int ystride plot every ystride-th gridpoint int zstride plot every zstride-th gridpoint int perspect do a perspective plot 0 or 1 (false or true) framedir directory containing frame data string (default='frames')

Note: The Matlab scripts provided with channelflow are kludgy. I cobbled them together in order to get the plots I want. Some things, like the position of the title and credit strings, must be positioned manually by editing values in the script files. Improvements in the scripts and alternatives for systems other than matlab are welcome.

Matlab produces only uncompressed AVI files on Linux. You will probably want to
compress the AVI file and convert it to another format. On Linux you can do this with
`mencoder`

, which is part of the MPlayer package. For example, this command will
convert `couette.avi`

file to a flash video file `couette.flv`

.

gibson@akbar$ mencoder couette.avi -nosound -of lavf -lavopts format=flv -ovc lavc -lavcopts vcodec=flv:vmax_b_frames=0:vbitrate=1600 -o couette.flv

Adjust the bitrate to balance filesize and video quality.

The Nagata (1990) “lower-branch” equilibrium has a one-dimensional unstable manifold. Here we compute the unstable manifold by integrating two 1d trajectories

using several channelflow utilities:

`fieldprops`

`arnoldi`

`addfields`

`couette`

`seriesprops`

`makebasis`

`projectseries`

…from the channelflow database. `LB`

stands for 'lower-branch'.

wget http://channelflow.org/database/a1.14_g2.5_Re400/LB.ff

The `fieldprops`

utility will print out basic information about the field. For example,

fieldprops -g LB

prints out the field's geometrical properties: cell size, grid size, etc. Try `–help`

to get a list of other options. Channelflow adds a `.ff`

file extension to `LB`

if you leave it off.

Visualization of fluid velocity fields is an art in itself. Channelflow provides a few scripts for plotting the velocity field on certain slices of the rectangular domain. I've found these plots useful, but if you have better ideas please adapt the scripts accordingly.

Plotting take two steps. First you extract some 2D slices from the 3D field with a channelflow utility, like this

fieldplots -o plot LB

That saves the 2D slices as ASCII data files in a plot/ directory. Then within Matlab, go to the plot/ driectory and run

plotbox('LB')

The matlab `plotbox`

script has a number of default parameters that you can change.
Try `help plotbox`

within Matlab for more information.

The Nagata lower-branch solution is an equilibrium of plane Couette dynamics. You can
compute the eigenvalues and eigenfunctions of the linearized dynamics about the equilbrium
with the `arnoldi`

utility. (Will write documentation on Arnoldi iteration later).

arnoldi --flow LB.ff

This produces a set of (approximate) eigenfunctions `ef1.ff, ef2.ff, …`

and a
file of eigenvalues `lambda.asc`

.

The Nagata lower branch has a single unstable eigenvalue, so its unstable manifold is 1d and can be computed as a trajectory initiated with small perturbations in the +/- directions of the unstable eigenvector/eigenfunction. The following calculates LB +/- 0.01 ef1 and saves the results into files LBp01ef1 and LBm01ef1

addfields 1 LB 0.01 ef1 LBp01ef1 addfields 1 LB -0.01 ef1 LBm01ef1

couette -T0 0 -T1 400 -o data-LBp01 LBp01ef1 couette -T1 0 -T1 400 -o data-LBm01 LBm01ef1

The `seriesprops`

utility computes a few quantities like energy dissipation D and
wall shear I for a time series of stored velocity fields

seriesprops -T0 0 -T1 400 -d data-LBp01ef1 -o props-LBp01ef1 seriesprops -T0 0 -T1 400 -d data-LBm01ef1 -o props-LBm01ef1

The results will be stored in files in props-LBp01ef1/ and props-LBm01ef1/ directories

movieframes -T0 0 -T1 100 -d data-LBp01ef1 -o frames-LBp01ef1 movieframes -T0 0 -T1 100 -d data-LBm01ef1 -o frames-LBm01ef1

From here you can adapt the movie-making instructions from above.

It can be useful to look at the temporal evolution of a fluid as a trajectory in state space. The number of degrees of freedom in a fluid simulation is very high (e.g. 10^5), so it is necessary to project the fields into a low-dimensional basis in order to plot the trajectory and look at it. We have found that good projection bases can be constructed from the “group orbits” of equilibria under the symmetries of plane Couette flow. In simple language, we take linear combinations of equilibria and their translations in x,z to form orthonormal basis sets. For a more detailed description of the logic and mathematics of this approach, see Gibson et al (2007) JFM 611. Here we will just outline how the computation is done using channelflow.

Make a subdirectory and descend into it, so that the following steps don't pollute the current directory with a bunch of extraneous files

mkdir basis-UBtrans cd basis-UBtrans

Download an equilibrium solution of plane Couette flow from the channelflow website, one that is compatible in geometry and discretization. For example, you can get the Nagata upper-branch equilibrium (UB) with the Unix “wget” utility.

wget http://www.channelflow.org/database/a1.14_g2.5_Re400/UB.ff

Compute the half-cell translations of UB in x, in z, and in x,z with the channelflow symmetryop utility:

symmetryop -ax 0.5 UB UBx symmetryop -az 0.5 UB UBz symmetryop -ax 0.5 -az 0.5 UB UBxz

Briefly, symmetryop constructs a symmetry σ parameterized by the options,
applies it to the first FlowField argument, and saves the result to the
second FlowField argument, according to the symmetry parameterization described
in symmetry. Let if τ_{x} be translation by Lx/2, etc.
Then the above lines compute τ_{x} UB, τ_{z}, and
τ_{xz} respectively.

Now construct the following orthogonal linear combinations of the above fields

with the channelflow addfields utility:

addfields 1 UB 1 UBx 1 UBz 1 UBxz UBpppp addfields 1 UB 1 UBx -1 UBz -1 UBxz UBppmm addfields 1 UB -1 UBx 1 UBz -1 UBxz UBpmpm addfields 1 UB -1 UBx -1 UBz 1 UBxz UBpmmp

Finally, use the channelflow makebasis utility to apply Gram-Schmidt orthogonalization on those fields and form an orthonormal basis set:

makebasis UBpppp UBppmm UBpmpm UBpmmp

The output of “makebasis” will be four orthonormal basis elements e0.ff, e1.ff, e2.ff, and e3.ff saved to disk. In this case the input fields are already orthogonal and all “makebasis” does is normalize.

Now pop out of the basis-UBtrans subdirectory

cd ..

Ok. Suppose you have a series of velocity fields u0.ff, u1.ff, etc for t=0,1,2,…1000 in a data/ directory and a set of basis elements e0.ff, e1.ff, e2.ff, e3.ff in a basis-UBtrans/ directory. To project the fields onto the basis, run

projectseries -T0 0 -T1 1000 -d data -b basis-UBtrans -Nb 4 -o a.asc

That will produce an ASCII file a.asc with 4 columns and 1001 rows. The t-th row and jth column is the value of (u(t), ej), where ( , ) signifies the L2 inner product

docs/tutorial.1234538901.txt.gz · Last modified: 2009/02/13 07:28 by gibson