Tuesday 31 March 2009

To get:

Effect of flow on the acoustic resonances of an open-ended duct
J. Acoust. Soc. Am. Volume 58, Issue 4, pp. 788-793 (October 1975)
Issue Date: October 1975

Acoustic waves in ducts with sinusoidally perturbed walls and mean flow
Nayfeh, A. H.
Acoustical Society of America, Journal, vol. 57, May 1975, p. 1036-1039.

Title:
Standing acoustic waves in a low Mach number shear flow
Authors:
Wang, Meng; Kassoy, David R.

@ARTICLE{art:Yeh64,
author = "Y. Yeh and H. Z. Cummins",
title = "Localised flow measurements with an He-Ne laser spectrometer",
journal = "Applied Physics Letters",
year = "1964",
volume = "4",
pages = "176",
note = "I can't get this one online",
}

DIsplay elements / polar setup, PAFEC




Copy the Python code into an interpreter, execute it. Copy the output to a NODES
section. First the display, then, an uncoupled BE, over a circular region, raised slightly from
z=0.


c cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c DISPLAY
c cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c Python script for node generation.
c from math import *
c def n():
c r, o, n0 = 0.025, [0, 0, 2E-3], 100 # radius, origin, 0th node.
c for i in xrange(360 + 1):
c x = o[0] + r * cos(0.5 * i * 2 * pi / 360)
c y = o[1] + 0
c z = o[2] + r * sin(0.5 * i * 2 * pi / 360)
c print n0 + i, x, y, z
c print n0 + i + 1, o[0] + r / 2, o[1], o[2]
c print n0 + i + 2, o[0] + r / 2, o[1], o[2] + r / 2
c print n0 + i + 3, o[0] + 0 / 2, o[1], o[2] + r / 2
c print n0 + i + 4, o[0] - r / 2, o[1], o[2] + r / 2
c print n0 + i + 5, o[0] - r / 2, o[1], o[2]
c print n0 + i + 6, o[0], o[1], o[2]
c print

c for i in xrange(360 + 1):
c x = o[0] + 0
c y = o[1] + r * cos(0.5 * i * 2 * pi / 360)
c z = o[2] + r * sin(0.5 * i * 2 * pi / 360)
c print 400 + n0 + i, x, y, z
c print 400 + n0 + i + 1, o[0], o[1] + r / 2, o[2]
c print 400 + n0 + i + 2, o[0], o[1] + r / 2, o[2] + r / 2
c print 400 + n0 + i + 3, o[0], o[1] + 0 / 2, o[2] + r / 2
c print 400 + n0 + i + 4, o[0], o[1] - r / 2, o[2] + r / 2
c print 400 + n0 + i + 5, o[0], o[1] - r / 2, o[2]
c print 400 + n0 + i + 6, o[0], o[1], o[2]
c print

c for i in xrange(360 + 1):
c x = o[0] + r * cos(0.5 * i * 2 * pi / 360)
c y = o[1] + r * sin(0.5 * i * 2 * pi / 360)
c z = o[2] + 0
c print 800 + n0 + i, x, y, z
c print 800 + n0 + i + 1, o[0] + r / 2, o[1], o[2]
c print 800 + n0 + i + 2, o[0] + r / 2, o[1] + r / 2, o[2]
c print 800 + n0 + i + 3, o[0] + 0 / 2, o[1] + r / 2, o[2]
c print 800 + n0 + i + 4, o[0] - r / 2, o[1] + r / 2, o[2]
c print 800 + n0 + i + 5, o[0] - r / 2, o[1], o[2]
c print 800 + n0 + i + 6, o[0], o[1], o[2]


PAFBLOCKS
BLOCK GROUP ELEMENT.TYPE PROP N1 N2 TOPO
1 1 24720 11 <'dm'> <'dm'> 462 190 461 100 0 0 145
2 1 24720 11 <'dm'> <'dm'> 280 190 463 462 235
3 1 24720 11 <'dm'> <'dm'> 370 280 464 463 325
4 1 24720 11 <'dm'> <'dm'> 370 464 460 465 0 415
5 1 24720 11 <'dm'> <'dm'> 463 462 466 461
6 1 24720 11 <'dm'> <'dm'> 464 463 465 466

7 2 24720 11 <'dm'> <'dm'> <462+400> <190+400> <461+400> <100+400> 0 0 <145+400>
8 2 24720 11 <'dm'> <'dm'> <280+400> <190+400> <463+400> <462+400> <235+400>
9 2 24720 11 <'dm'> <'dm'> <370+400> <280+400> <464+400> <463+400> <325+400>
10 2 24720 11 <'dm'> <'dm'> <370+400> <464+400> <460+400> <465+400> 0 <415+400>
11 2 24720 11 <'dm'> <'dm'> <463+400> <462+400> <466+400> <461+400>
12 2 24720 11 <'dm'> <'dm'> <464+400> <463+400> <465+400> <466+400>

c 13 3 24720 11 <'xm'> <'xm'> <462+800> <190+800> <461+800> <100+800> 0 0 <145+800>
c 14 3 24720 11 <'xm'> <'xm'> <280+800> <190+800> <463+800> <462+800> <235+800>
c 15 3 24720 11 <'xm'> <'xm'> <370+800> <280+800> <464+800> <463+800> <325+800>
c 16 3 24720 11 <'xm'> <'xm'> <370+800> <464+800> <460+800> <465+800> 0 <415+800>
c 17 3 24720 11 <'xm'> <'xm'> <463+800> <462+800> <466+800> <461+800>
c 18 3 24720 11 <'xm'> <'xm'> <464+800> <463+800> <465+800> <466+800>

c cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c BE
c cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
c r, z0 = 4.75E-3, 1E-3
c def n2():
c for i in xrange(17):
c print i+1, r * cos (i/16. * 2 * pi), r * sin (i/16. * 2 * pi), z0
c print 17, r/2, 0, z0
c print 18, r/2, r/2, z0
c print 19, 0, r/2, z0
c print 20, -r/2, r/2, z0
c print 21, -r/2, 0, z0
c print 22, -r/2, -r/2, z0
c print 23, 0, -r/2, z0
c print 24, r/2, -r/2, z0
c print 25, 0, 0, z0
c for i in xrange(31, 46 + 1):
c print i, r * cos ((i - 31) / 16. * 2 * pi), r * sin ((i - 31) / 16. * 2 * pi), 0



PAFBLOCKS
BOUNDARY.ELEMENT = 1000
GROUP ELEMENT.TYPE PROP N1 N2 TOPO
c top face
4 24620 11 <'xm'> <'xm'> 18 3 17 1 0 0 2
4 24620 11 <'xm'> <'xm'> 5 3 19 18 4
4 24620 11 <'xm'> <'xm'> 7 5 20 19 6
4 24620 11 <'xm'> <'xm'> 7 20 9 21 0 8
4 24620 11 <'xm'> <'xm'> 9 21 11 22 0 10
4 24620 11 <'xm'> <'xm'> 22 23 11 13 0 0 0 12
4 24620 11 <'xm'> <'xm'> 23 24 13 15 0 0 0 14
4 24620 11 <'xm'> <'xm'> 17 1 24 15 0 0 16
4 24620 11 <'xm'> <'xm'> 19 18 25 17
4 24620 11 <'xm'> <'xm'> 20 19 21 25
4 24620 11 <'xm'> <'xm'> 21 25 22 23
4 24620 11 <'xm'> <'xm'> 25 17 23 24
c side face
4 24620 11 <'xm'> 1 1 3 31 33 2 0 0 32
4 24620 11 <'xm'> 1 <1+1*2> <3+1*2> <31+1*2> <33+1*2> <2+1*2> 0 0 <32+1*2>
4 24620 11 <'xm'> 1 <1+2*2> <3+2*2> <31+2*2> <33+2*2> <2+2*2> 0 0 <32+2*2>
4 24620 11 <'xm'> 1 <1+3*2> <3+3*2> <31+3*2> <33+3*2> <2+3*2> 0 0 <32+3*2>
4 24620 11 <'xm'> 1 <1+4*2> <3+4*2> <31+4*2> <33+4*2> <2+4*2> 0 0 <32+4*2>
4 24620 11 <'xm'> 1 <1+5*2> <3+5*2> <31+5*2> <33+5*2> <2+5*2> 0 0 <32+5*2>
4 24620 11 <'xm'> 1 <1+6*2> <3+6*2> <31+6*2> <33+6*2> <2+6*2> 0 0 <32+6*2>
4 24620 11 <'xm'> 1 <1+7*2> 1 <31+7*2> 31 <2+7*2> 0 0 <32+7*2>






An alternative approach is to get PAFEC to generate the
nodes, and use triangles.



c polar extraction. Define three nodes, for arc definition. 1 node per dgree.
NODES
NODE AXIS X Y
300 3 0.018 0 c on axis.
345 3 0.018 45
390 3 0.018 90 c 90 degrees off axis
391 3 0.000 0 c on axis, 0 radius, for display elements.
ARC.NODES
LIST.OF.NODES.ON.ARC
300 301 302 303 304 305 306 307 308 309
* 310 311 312 313 314 315 316 317 318 319
* 320 321 322 323 324 325 326 327 328 329
* 330 331 332 333 334 335 336 337 338 339
* 340 341 342 343 344 345 346 347 348 349
* 350 351 352 353 354 355 356 357 358 359
* 360 361 362 363 364 365 366 367 368 369
* 370 371 372 373 374 375 376 377 378 379
* 380 381 382 383 384 385 386 387 388 389
* 390

c observation elements.
PAFBLOCKS
BLOCK TYPE GROUP ELEMENT PROP N1 N2 N3 TOPO
56 2 7 24710 13 15 15 15 391 300 390 0 345

Monday 30 March 2009

translating nodes in PAFEC

Given a data file, with nodes defined:


a = file('ct1b.DAT')
b = a.readlines()
c = b[36:500] # only node entries
d = [i.strip('\n').split(' ') for i in c]
e = []
for i in d:
tmp = [float(j) for j in i]
e.append(tmp)
f = array(e)
f[:, 2] = f[:, 2] + 0.001 # apply offset
for i in f:
print str(i).strip('[]') # copy and paste.

Thursday 26 March 2009

Formatting in this blog

Leading spaces tend to be lost. Add < p r e > to the start, and < / p r e > to the end, to preserve them.

Python scripts called from $

An example:


import sys
if __name__ == '__main__':
# Executed, only if called from command line.
args = sys.argv

if len(args) == 1:
print 'No argument specified. call as filename.py '
exit()
else:
print 'Argument(s) provided: ', args

Tuesday 24 March 2009

PGFplots error bars.


\documentclass{article}
\usepackage{pgfplots}
%
\begin{document}
\thispagestyle{empty}
\begin{tikzpicture}
\begin{axis}
\addplot plot[error bars/.cd,
y dir=both, y explicit,
x dir=both, x explicit]
coordinates {
(0,0) +- (0.5, 0.1)
(1,1) +- (0.2, 0.3)
};
\end{axis}
\end{tikzpicture}

\end{document}

Building Engrid on Ubuntu Hardy

from https://sourceforge.net/mailarchive/forum.php?forum_name=engrid-users&max_rows=100&style=nested&viewmonth=200903&viewday=3

First, make sure you have the build dependencies:
/================
sudo apt-get install libvtk5 libvtk5-dev libvtk5-qt4 libvtk5-qt4-dev
libqt4-dev
================
/
Second, if you have qt3 dev files installed too, there might be a
conflict with qmake-qt3. So just run one of the following commands:
(I used the second command on my laptop. I'm not sure if the first one
works, but it should based on what I've read.)
/================
update-alternatives --install /usr/bin/qmake qmake "/usr/bin/qmake-qt4"
"50" --slave /usr/share/man/man1/qmake.1.gz qmake.1.gz
"/usr/share/man/man1/qmake-qt4.1.gz"
================
/or
/================
ln -sf /usr/bin/qmake-qt4 /usr/bin/qmake
================
/
To make sure the rest will work, check that /usr/bin/qmake is a link to
/usr/bin/qmake-qt4:
/================
[29][~]$ ls -l /usr/bin/qmake
lrwxrwxrwx 1 root root 18 Mar 3 12:04 /usr/bin/qmake -> /usr/bin/qmake-qt4
================
/
Check out the CVS:
/================
cvs -d:pserver:anonymous@en...:/cvsroot/engrid login
cvs -d:pserver:anonymous@en...:/cvsroot/engrid co src
cd src
================
/
Then you'll need to set up the environment before running qmake:
/================
export VTKLIBDIR=/usr/lib/
export VTKINCDIR=/usr/include/vtk-5.0/
export LD_LIBRARY_PATH=$VTKLIBDIR:$LD_LIBRARY_PATH
================
/I wrote a convenience script for this, which you can use instead if you
wish:
/================
source ./setup_paths.sh ubuntu
================
/
And finally, build netgen and engrid:
/================
./build-nglib.sh
qmake
make
================
/


Following an email from Oliver Gloth, I needed to re-compile. I did this,
as:
-----------------------
export VTKLIBDIR=/usr/lib/
export VTKINCDIR=/usr/include/vtk-5.0/
export LD_LIBRARY_PATH=$VTKLIBDIR:$LD_LIBRARY_PATH

and in ~/downloads/newengrid/src/

make clean
qmake
make

Sunday 22 March 2009

To get:

@ARTICLE{art:Schewe,
AUTHOR = "G. Schewe",
TITLE = "On the force oscillations acting on a circular cylinder in
crossflow from subcritical up to transcritical Reynolds numbers",
YEAR = "1983",
JOURNAL = "J. Fluid Mech",
VOLUME = "133",
PAGES = "265--285",
NOTES = "From art:Travin. Domain length. Couldn't get this, paper copy?",
}

Monday 16 March 2009

String table to list

a = file('filename')
b = a.readlines()
c = b[3:86] # extract relevant rows

# list of lists, assuming space separated values, stripping
# empty strings.

d = [[j for j in i.split(' ') if j != ''] for i in c] # lists of strings
d = [[float(j) for j in i.split(' ') if j != ''] for i in c] # lists of floats

d can be converted to an array, if desired. :)

Wednesday 11 March 2009

list - continuous file cat

#!/bin/bash
# Display the file provided as filename, every second.
while [ 1 ]
do
clear
cat $1
sleep 1
done

Wednesday 4 March 2009

Superimposed plots.



I was so amazed by this accident, I noted it:

\begin{figure}[htbp]\begin{center} % pressure vs x.

\mbox{
%\hspace{-1.5cm}
\tikzstyle{every axis legend}+= [at={(0.98,0.02)},anchor=south east] % im is 0,0 to 1,1
\begin{tikzpicture}
\begin{semilogyaxis}[width=\hplotw,height=\ploth,
ymin = 30, ymax = 300000,
xlabel={$x/l$}, ylabel={$|p|$},grid=major]

% Peak search, so use last entry:
% m95acoub3 = mfile.File('m95acoub3.res'); m95acoub3.load()
% m95acoub5 = mfile.File('m95acoub5.res'); m95acoub5.load()
% r1 = m95acoub3.calc_PvX(findex=[-2 + -1*1j], y = -0.005, z = 0)
% r2 = m95acoub5.calc_PvX(findex=[-2 + -1*1j], y = 0, z = 0)
% tmp = reference.dumptex(r1[0] / 0.05, abs(r1[1]))
% tmp = reference.dumptex(r2[0] / 0.05, abs(r2[1]))
% 0 flow:
\addplot[color = black] plot coordinates {(-5.00000e-01,4.68522e+03) (-4.87180e-01,6.14709e+03) (-4.74360e-01,7.63048e+03) (-4.61540e-01,9.06362e+03) (-4.48720e-01,1.04245e+04) (-4.35900e-01,1.17104e+04) (-4.23080e-01,1.29284e+04) (-4.10260e-01,1.40937e+04) (-3.97440e-01,1.52292e+04) (-3.84620e-01,1.63611e+04) (-3.71800e-01,1.75145e+04) (-3.58980e-01,1.87069e+04) (-3.46160e-01,1.99447e+04) (-3.33340e-01,2.12216e+04) (-3.20520e-01,2.25230e+04) (-3.07700e-01,2.38275e+04) (-2.94880e-01,2.51120e+04) (-2.82060e-01,2.63557e+04) (-2.69240e-01,2.75383e+04) (-2.56420e-01,2.86456e+04) (-2.43580e-01,2.96665e+04) (-2.30760e-01,3.05936e+04) (-2.17940e-01,3.14303e+04) (-2.05120e-01,3.21815e+04) (-1.92300e-01,3.28633e+04) (-1.79480e-01,3.34925e+04) (-1.66660e-01,3.40869e+04) (-1.53840e-01,3.46601e+04) (-1.41020e-01,3.52191e+04) (-1.28200e-01,3.57652e+04) (-1.15380e-01,3.62941e+04) (-1.02560e-01,3.67997e+04) (-8.97400e-02,3.72757e+04) (-7.69200e-02,3.77161e+04) (-6.41000e-02,3.81118e+04) (-5.12800e-02,3.84556e+04) (-3.84600e-02,3.87364e+04) (-2.56400e-02,3.89444e+04) (-1.28200e-02,3.90741e+04) (0.00000e+00,3.91589e+04) (1.28200e-02,3.90741e+04) (2.56400e-02,3.89444e+04) (3.84600e-02,3.87364e+04) (5.12800e-02,3.84556e+04) (6.41000e-02,3.81118e+04) (7.69200e-02,3.77161e+04) (8.97400e-02,3.72757e+04) (1.02560e-01,3.67997e+04) (1.15380e-01,3.62941e+04) (1.28200e-01,3.57652e+04) (1.41020e-01,3.52191e+04) (1.53840e-01,3.46601e+04) (1.66660e-01,3.40869e+04) (1.79480e-01,3.34925e+04) (1.92300e-01,3.28633e+04) (2.05120e-01,3.21815e+04) (2.17940e-01,3.14303e+04) (2.30760e-01,3.05936e+04) (2.43580e-01,2.96665e+04) (2.56420e-01,2.86456e+04) (2.69240e-01,2.75383e+04) (2.82060e-01,2.63557e+04) (2.94880e-01,2.51120e+04) (3.07700e-01,2.38275e+04) (3.20520e-01,2.25230e+04) (3.33340e-01,2.12216e+04) (3.46160e-01,1.99447e+04) (3.58980e-01,1.87069e+04) (3.71800e-01,1.75145e+04) (3.84620e-01,1.63611e+04) (3.97440e-01,1.52292e+04) (4.10260e-01,1.40937e+04) (4.23080e-01,1.29284e+04) (4.35900e-01,1.17104e+04) (4.48720e-01,1.04245e+04) (4.61540e-01,9.06362e+03) (4.74360e-01,7.63048e+03) (4.87180e-01,6.14709e+03) (5.00000e-01,4.68522e+03)};
\addplot[color = red] plot coordinates {(-5.00000e-01,3.32899e+02) (-4.87180e-01,3.99514e+02) (-4.74360e-01,4.43786e+02) (-4.61540e-01,4.56559e+02) (-4.48720e-01,4.35594e+02) (-4.35900e-01,3.85809e+02) (-4.23080e-01,3.19156e+02) (-4.10260e-01,2.58352e+02) (-3.97440e-01,2.36882e+02) (-3.84620e-01,2.68063e+02) (-3.71800e-01,3.22661e+02) (-3.58980e-01,3.67617e+02) (-3.46160e-01,3.83471e+02) (-3.33340e-01,3.60929e+02) (-3.20520e-01,2.98806e+02) (-3.07700e-01,2.07038e+02) (-2.94880e-01,1.35031e+02) (-2.82060e-01,2.02836e+02) (-2.69240e-01,3.54802e+02) (-2.56420e-01,5.19014e+02) (-2.43580e-01,6.72321e+02) (-2.30760e-01,8.02972e+02) (-2.17940e-01,9.05292e+02) (-2.05120e-01,9.78824e+02) (-1.92300e-01,1.02744e+03) (-1.79480e-01,1.05767e+03) (-1.66660e-01,1.07661e+03) (-1.53840e-01,1.09065e+03) (-1.41020e-01,1.10627e+03) (-1.28200e-01,1.13312e+03) (-1.15380e-01,1.18722e+03) (-1.02560e-01,1.28987e+03) (-8.97400e-02,1.45928e+03) (-7.69200e-02,1.70049e+03) (-6.41000e-02,2.00269e+03) (-5.12800e-02,2.34454e+03) (-3.84600e-02,2.70219e+03) (-2.56400e-02,3.06038e+03) (-1.28200e-02,3.41724e+03) (0.00000e+00,4.35428e+03) (1.28200e-02,3.46603e+03) (2.56400e-02,3.23861e+03) (3.84600e-02,3.04073e+03) (5.12800e-02,2.82875e+03) (6.41000e-02,2.58640e+03) (7.69200e-02,2.31553e+03) (8.97400e-02,2.02851e+03) (1.02560e-01,1.74376e+03) (1.15380e-01,1.47984e+03) (1.28200e-01,1.25361e+03) (1.41020e-01,1.08218e+03) (1.53840e-01,9.89661e+02) (1.66660e-01,1.00326e+03) (1.79480e-01,1.12870e+03) (1.92300e-01,1.33752e+03) (2.05120e-01,1.58679e+03) (2.17940e-01,1.83747e+03) (2.30760e-01,2.06103e+03) (2.43580e-01,2.23955e+03) (2.56420e-01,2.36536e+03) (2.69240e-01,2.43945e+03) (2.82060e-01,2.46702e+03) (2.94880e-01,2.45381e+03) (3.07700e-01,2.40274e+03) (3.20520e-01,2.31495e+03) (3.33340e-01,2.19285e+03) (3.46160e-01,2.04782e+03) (3.58980e-01,1.90509e+03) (3.71800e-01,1.80440e+03) (3.84620e-01,1.78480e+03) (3.97440e-01,1.85723e+03) (4.10260e-01,1.99089e+03) (4.23080e-01,2.13114e+03) (4.35900e-01,2.22497e+03) (4.48720e-01,2.23423e+03) (4.61540e-01,2.13874e+03) (4.74360e-01,1.93600e+03) (4.87180e-01,1.64131e+03) (5.00000e-01,1.30148e+03)};

\legend{non-flared\\flared\\}

\end{semilogyaxis} %\end{tikzpicture}% }

% \tikzstyle{every axis legend}+= [at={(0.02,0.02)},anchor=north west] % im is 0,0 to 1,1
% \begin{tikzpicture}

\begin{axis}[
axis x line=middle,
axis y line=right,
width=\hplotw,height=\ploth,
xlabel={$x/l$},
ylabel={$\theta$},grid=major,
ytick ={-3.14, -1.57, 1.57, 3.14},
yticklabels={$-\pi$, $-\frac{\pi}{2}$, $\frac{\pi}{2}$ , $\pi$},
ymin=-3.14, ymax=3.14]

% use code above, but with reference.ang() instead of abs()
% tmp = reference.dumptex(r1[0] / 0.05, reference.ang(r1[1]))
% tmp = reference.dumptex(r2[0] / 0.05, reference.ang(r2[1]))

\addplot[color = black] plot coordinates {(-5.00000e-01,-2.35766e+00) (-4.87180e-01,-2.06355e+00) (-4.74360e-01,-1.96624e+00) (-4.61540e-01,-1.91584e+00) (-4.48720e-01,-1.88530e+00) (-4.35900e-01,-1.86182e+00) (-4.23080e-01,-1.83907e+00) (-4.10260e-01,-1.81398e+00) (-3.97440e-01,-1.78565e+00) (-3.84620e-01,-1.75475e+00) (-3.71800e-01,-1.72302e+00) (-3.58980e-01,-1.69275e+00) (-3.46160e-01,-1.66619e+00) (-3.33340e-01,-1.64511e+00) (-3.20520e-01,-1.63043e+00) (-3.07700e-01,-1.62221e+00) (-2.94880e-01,-1.61967e+00) (-2.82060e-01,-1.62138e+00) (-2.69240e-01,-1.62554e+00) (-2.56420e-01,-1.63023e+00) (-2.43580e-01,-1.63363e+00) (-2.30760e-01,-1.63427e+00) (-2.17940e-01,-1.63116e+00) (-2.05120e-01,-1.62398e+00) (-1.92300e-01,-1.61300e+00) (-1.79480e-01,-1.59916e+00) (-1.66660e-01,-1.58387e+00) (-1.53840e-01,-1.56879e+00) (-1.41020e-01,-1.55562e+00) (-1.28200e-01,-1.54576e+00) (-1.15380e-01,-1.54012e+00) (-1.02560e-01,-1.53894e+00) (-8.97400e-02,-1.54179e+00) (-7.69200e-02,-1.54763e+00) (-6.41000e-02,-1.55491e+00) (-5.12800e-02,-1.56180e+00) (-3.84600e-02,-1.56638e+00) (-2.56400e-02,-1.56653e+00) (-1.28200e-02,-1.56033e+00) (0.00000e+00,-1.52345e+00) (1.28200e-02,-1.56033e+00) (2.56400e-02,-1.56653e+00) (3.84600e-02,-1.56638e+00) (5.12800e-02,-1.56180e+00) (6.41000e-02,-1.55491e+00) (7.69200e-02,-1.54763e+00) (8.97400e-02,-1.54179e+00) (1.02560e-01,-1.53894e+00) (1.15380e-01,-1.54012e+00) (1.28200e-01,-1.54576e+00) (1.41020e-01,-1.55562e+00) (1.53840e-01,-1.56879e+00) (1.66660e-01,-1.58387e+00) (1.79480e-01,-1.59916e+00) (1.92300e-01,-1.61300e+00) (2.05120e-01,-1.62398e+00) (2.17940e-01,-1.63116e+00) (2.30760e-01,-1.63427e+00) (2.43580e-01,-1.63363e+00) (2.56420e-01,-1.63023e+00) (2.69240e-01,-1.62554e+00) (2.82060e-01,-1.62138e+00) (2.94880e-01,-1.61967e+00) (3.07700e-01,-1.62221e+00) (3.20520e-01,-1.63043e+00) (3.33340e-01,-1.64511e+00) (3.46160e-01,-1.66619e+00) (3.58980e-01,-1.69275e+00) (3.71800e-01,-1.72302e+00) (3.84620e-01,-1.75475e+00) (3.97440e-01,-1.78565e+00) (4.10260e-01,-1.81398e+00) (4.23080e-01,-1.83907e+00) (4.35900e-01,-1.86182e+00) (4.48720e-01,-1.88530e+00) (4.61540e-01,-1.91584e+00) (4.74360e-01,-1.96624e+00) (4.87180e-01,-2.06355e+00) (5.00000e-01,-2.35766e+00)};
\addplot[color = red] plot coordinates {(-5.00000e-01,-2.39191e+00) (-4.87180e-01,-1.97905e+00) (-4.74360e-01,-1.76609e+00) (-4.61540e-01,-1.59365e+00) (-4.48720e-01,-1.42560e+00) (-4.35900e-01,-1.22937e+00) (-4.23080e-01,-9.60545e-01) (-4.10260e-01,-5.52966e-01) (-3.97440e-01,3.70743e-03) (-3.84620e-01,5.21654e-01) (-3.71800e-01,8.75260e-01) (-3.58980e-01,1.11347e+00) (-3.46160e-01,1.29731e+00) (-3.33340e-01,1.46845e+00) (-3.20520e-01,1.67124e+00) (-3.07700e-01,2.01168e+00) (-2.94880e-01,2.86206e+00) (-2.82060e-01,-2.38036e+00) (-2.69240e-01,-1.95842e+00) (-2.56420e-01,-1.74308e+00) (-2.43580e-01,-1.58899e+00) (-2.30760e-01,-1.45615e+00) (-2.17940e-01,-1.33003e+00) (-2.05120e-01,-1.20522e+00) (-1.92300e-01,-1.08143e+00) (-1.79480e-01,-9.62879e-01) (-1.66660e-01,-8.57926e-01) (-1.53840e-01,-7.78091e-01) (-1.41020e-01,-7.35771e-01) (-1.28200e-01,-7.40577e-01) (-1.15380e-01,-7.93814e-01) (-1.02560e-01,-8.82979e-01) (-8.97400e-02,-9.83297e-01) (-7.69200e-02,-1.07004e+00) (-6.41000e-02,-1.12958e+00) (-5.12800e-02,-1.15916e+00) (-3.84600e-02,-1.16048e+00) (-2.56400e-02,-1.13204e+00) (-1.28200e-02,-1.07213e+00) (0.00000e+00,-8.08752e-01) (1.28200e-02,-1.18037e+00) (2.56400e-02,-1.35573e+00) (3.84600e-02,-1.49900e+00) (5.12800e-02,-1.61245e+00) (6.41000e-02,-1.70161e+00) (7.69200e-02,-1.76987e+00) (8.97400e-02,-1.82208e+00) (1.02560e-01,-1.86644e+00) (1.15380e-01,-1.91748e+00) (1.28200e-01,-1.99847e+00) (1.41020e-01,-2.13984e+00) (1.53840e-01,-2.36301e+00) (1.66660e-01,-2.64648e+00) (1.79480e-01,-2.92612e+00) (1.92300e-01,3.12351e+00) (2.05120e-01,2.93364e+00) (2.17940e-01,2.76916e+00) (2.30760e-01,2.61402e+00) (2.43580e-01,2.45740e+00) (2.56420e-01,2.29278e+00) (2.69240e-01,2.11678e+00) (2.82060e-01,1.92846e+00) (2.94880e-01,1.72840e+00) (3.07700e-01,1.51731e+00) (3.20520e-01,1.29426e+00) (3.33340e-01,1.05504e+00) (3.46160e-01,7.91544e-01) (3.58980e-01,4.94245e-01) (3.71800e-01,1.60178e-01) (3.84620e-01,-1.94055e-01) (3.97440e-01,-5.32686e-01) (4.10260e-01,-8.25365e-01) (4.23080e-01,-1.06481e+00) (4.35900e-01,-1.26019e+00) (4.48720e-01,-1.42583e+00) (4.61540e-01,-1.57719e+00) (4.74360e-01,-1.73328e+00) (4.87180e-01,-1.92784e+00) (5.00000e-01,-2.31238e+00) };

% share the legend with the previous plot.
%\legend{non-flared\\flared\\}


\end{axis} \end{tikzpicture}

}
\caption{blah blah}
\label{fig:m95acou4b_pvx} \end{center} \end{figure}



Dual axis:





\begin{figure}[htbp]\begin{center}
%$ phd
%import mfile
%a = mfile.catFile('axibal8f.n100pre', f0=30000, f1 = 40000, n = 200) # pre.
%b = mfile.catFile('axibal8g.n100pre', f0=30000, f1 = 40000, n = 200) # pre.
%c = mfile.catFile('axibal8h.n100pre', f0=30000, f1 = 40000, n = 200) # pre.

%plot (a.f, 20 * log10(1./ 20E-6 * abs(a.h[:, 1] + 1j * a.h[:, 2])))
%plot (b.f, 20 * log10(1./ 20E-6 * abs(b.h[:, 1] + 1j * b.h[:, 2])))
%plot (c.f, 20 * log10(1./ 20E-6 * abs(c.h[:, 1] + 1j * c.h[:, 2])))

%tmp = reference.dumptex(a.f, 20 * log10(1./ 20E-6 * abs(a.h[:, 1] + 1j * a.h[:, 2])))
%tmp = reference.dumptex(b.f, 20 * log10(1./ 20E-6 * abs(b.h[:, 1] + 1j * b.h[:, 2])))
%tmp = reference.dumptex(c.f, 20 * log10(1./ 20E-6 * abs(c.h[:, 1] + 1j * c.h[:, 2])))

\mbox{
\hspace{-1cm}
\subfigure[SPL midway between duct centre and duct exit, for different
boundary conditions.] {


\tikzstyle{every axis legend}+= [at={(0.98,0.02)},anchor=south east] % im is 0,0 to 1,1
\begin{tikzpicture}

% second axis. Do NOT USE scale only axis; it changes the x-axis scaling.
\begin{axis}[width=\hplotw,height=\ploth,
separate axis lines,
every outer x axis line/.append style={white}, % YES! no more messy axes
grid=major,
xmin = 30000, xmax=36000, ymin = 75, ymax = 125,
axis y line = none, axis x line = top, %y = 1.565cm
xlabel = $f/f_{0}$,
%xlabel style = {xshift = -10pt, yshift = -200pt},
xtick ={34400},
xticklabels={ $1$ }
]
\end{axis}

\begin{axis}[width=\hplotw,height=\ploth,
xmin = 30000, xmax=36000, ymin = 75, ymax = 125,
xlabel={$f\,(Hz)$}, ylabel={SPL, $1\,V$, node 100}, grid=major]

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\legend{BE\\Quiet\\Wave env.\\}
\end{axis}

\end{tikzpicture} } }

\caption{Zoomed version of ....}
\label{fig:axibal8a_spl} \end{center} \end{figure}

Monday 2 March 2009

Permanent ubuntu shares

from http://www.ubuntugeek.com/nfs-server-and-client-configuration-in-ubuntu.html

-------------------------------------------

On all machines:
sudo apt-get install portmap nfs-common nfs-kernel-server

----------------

On the exporting machine(s):
Edit /etc/exports. Specify local folders to export. Eg.

/home/mymachine/data/d4 192.168.1.1/24(rw,async) 213.334.248.237(rw,async)

opens the directories to all local machines, and the address 213.334 etc.

After change:
sudo /etc/init.d/nfs-kernel-server restart
----------------

On the mounting machines: On the fly:

sudo mount server.mydomain.com:/files /files

Possible restart required:

sudo /etc/init.d/portmap restart

sudo /etc/init.d/nfs-common restart

---------------

On the mounting machines: With fstab:

Add lines:
server.mydomain.com:/files /files nfs rsize=8192,wsize=8192,timeo=14,intr


---------------
Firewall ports:
Open 32771, 111 and 2049

sshfs

sudo apt-get install sshfs

Add users to the fuse group:
sudo adduser username fuse (i found this not to be required)

mount the remote file systems:
sshfs loginname@ipaddress:/pathtoremotedir /pathtolocalmountpoint

These are temporary. When the ssh tunnel fails, the access is lost. After a period
of inactivity, the connection is dropped.

[NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182

OpenMPI failure (fixed)

$ mpiexec -n 4 fe2.py

[host-desktop1:09127] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS

--------------------------------------------------------------------------
[host-desktop1:09127] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_system_init.c at line 42
[host-desktop1:09127] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 52
--------------------------------------------------------------------------
Open RTE was unable to initialize properly. The error occured while
attempting to orte_init(). Returned value -13 instead of ORTE_SUCCESS.
--------------------------------------------------------------------------

Reinstall, from a fresh build.

cd downloads
wget http://www.open-mpi.org/software/ompi/v1.3/downloads/openmpi-1.3.tar.gz
tar xzf openmpi-1.3.tar.gz

Reading the README showed, PATH and LD_LIBRARY_PATH need a specific entry. ompi_info, a program residing in /bin reports the MPI status, but it's location is of more interest.

whereis ompi_info
ompi_info: /usr/bin/ompi_info /usr/share/man/man1/ompi_info.1.gz

So /usr/bin needs to be in PATH, and /usr/lib needs to be in LD_LIBRARY_PATH.

Checking .bashrc showed LD_LIBRARY_PATH was wiped on its instantiation. The first line was changed from

LD_LIBRARY_PATH=blahbah

to

LD_LIBRARY_PATH=blahbah:$LD_LIBRARY_PATH

and things started working again.

Sunday 1 March 2009

ipython

Ipython's not behaving as expected; this is hardy. I think i installed it
early on, with

sudo apt-get install ipython

on running it, arange doesn't work. I can't install pylab etc. Start again.

$ sudo aptitude install bzr
$ bzr branch lp:ipython

Read the installation instructions and found:

$ sudo easy_install ipython[kernel,security,test]

this bloody failed, too. Try:
$ sudo easy_install ipython

seems ok.


*UPDATE*

This same command, seems to safely update ipython, too! The change from 0.8.1 to 0.9.1 was seamless. Numpy, scipy and my modules import fine. ipcluster didn't work, though: twisted
was required.

$ sudo easy_install twisted

amazing. It worked. Now foolscap is missing.

$ sudo easy_install foolscap

Unbelievable. It worked, and

$ ipcluster -n 4

works, too.

Update, May 2013:


sudo apt-get install ipython-notebook python-matplotlib \ 
python-scipy python-pandas python-sympy python-nose


now works!