Skip to main content

Dynamical systems simulation in python

Trying out PyDSTools [webpage, download]
These guys look professional - they have a test suite that you can run to check everything out.
  1. You need to put a file called PyDSTool.pth [read this]
    Play close attention to the trick about subdirectories - you have to repeat it for each level, not just the root level. I have my install in c:\programs\PyDSTool and my file has
  2. I have scipy version 0.6.0 but PyDSTool doesn't detect that properly. I commented out the relevant lines in PyDSTool's root
    #if vernums[1] != 5:
    # raise RuntimeError("SciPy v0.5.1 or above is required")

    and it continued with the tests.
Things seem to work OK, only one thing was declared broken:
PyCont: appears to be broken on your system

But, there were periodic errors of the nature:

***** Testing script ****************************

Gnuplot not available
------- Examples of implicit function as variable
1D example: a half-circle using newton's method (secant method for estimating de
Change sign of 'y' initial condition to solve for other half-circle
Gen defined? => False
traj1 = testimp.compute('traj1')
Error in supplied functional specification code
Traceback (most recent call last):
File "", line 54, in
traj1 = testimp.compute('traj1')
File "C:\Programs\PyDSTool\Generator\", line 294, in compute
exec tempspec[0] in globals()
File "string", line 1
def _specfn_imptest_316e-006(ds, t, x, parsinps):
SyntaxError: invalid syntax

***** Testing passed on test file

Which I can't understand


  1. Hi -- that's an odd platform specific problem you have with time.clock(). The easy fix is to change the return line in the function PyDSTool.common.timestamp to be the following:

    return c.replace(".","").replace("-","")[:tdigits+1]

    (obviously without the newline that this comment box forces on me!)


Post a Comment

Popular posts from this blog

Flowing text in inkscape (Poster making)

You can flow text into arbitrary shapes in inkscape. (From a hint here).

You simply create a text box, type your text into it, create a frame with some drawing tool, select both the text box and the frame (click and shift) and then go to text->flow into frame.


The omnipresent anonymous asked:
Trying to enter sentence so that text forms the number three...any ideas?
The solution:
Type '3' using the text toolConvert to path using object->pathSize as necessaryRemove fillUngroupType in actual text in new text boxSelect the text and the '3' pathFlow the text

Pandas panel = collection of tables/data frames aligned by index and column

Pandas panel provides a nice way to collect related data frames together while maintaining correspondence between the index and column values:

import pandas as pd, pylab #Full dimensions of a slice of our panel index = ['1','2','3','4'] #major_index columns = ['a','b','c'] #minor_index df = pd.DataFrame(pylab.randn(4,3),columns=columns,index=index) #A full slice of the panel df2 = pd.DataFrame(pylab.randn(3,2),columns=['a','c'],index=['1','3','4']) #A partial slice df3 = pd.DataFrame(pylab.randn(2,2),columns=['a','b'],index=['2','4']) #Another partial slice df4 = pd.DataFrame(pylab.randn(2,2),columns=['d','e'],index=['5','6']) #Partial slice with a new column and index pn = pd.Panel({'A': df}) pn['B'] = df2 pn['C'] = df3 pn['D'] = df4 for key in pn.items: print pn[key] -> output …

Drawing circles using matplotlib

Use the pylab.Circle command

import pylab #Imports matplotlib and a host of other useful modules cir1 = pylab.Circle((0,0), radius=0.75, fc='y') #Creates a patch that looks like a circle (fc= face color) cir2 = pylab.Circle((.5,.5), radius=0.25, alpha =.2, fc='b') #Repeat (alpha=.2 means make it very translucent) ax = pylab.axes(aspect=1) #Creates empty axes (aspect=1 means scale things so that circles look like circles) ax.add_patch(cir1) #Grab the current axes, add the patch to it ax.add_patch(cir2) #Repeat