pydstool-users — General discussion about using PyDSTool

[pydstool-users] re error in running dae example in tutorial

[Lakshmi N S. <lak...@up...>]

I am trying to run the dae example
Pls see txt attached
I am getting the error
****************************
running build_ext
running build_src
build_src
building py_modules sources
building library "radau5" sources
building library "lapack_lite" sources
building extension "C:\Users\LakshmiNSridhar\sripyomo\radau5_temp._radau5_DAE_test_vf" sources
swig.exe: C:\Users\LakshmiNSridhar\sripyomo\radau5_temp\radau5_DAE_test_vf.i
swig.exe -python -IC:\Users\LakshmiNSridhar\anaconda3\lib\site-packages\numpy\core\include -IC:\Users\LakshmiNSridhar\sripyomo -IC:\Users\LakshmiNSridhar\anaconda3\lib\site-packages\PyDSTool\integrator -o C:\Users\LakshmiNSridhar\sripyomo\radau5_temp\radau5_DAE_test_vf_wrap.c -outdir C:\Users\LakshmiNSridhar\sripyomo\radau5_temp C:\Users\LakshmiNSridhar\sripyomo\radau5_temp\radau5_DAE_test_vf.i
An exception has occurred, use %tb to see the full traceback.

Traceback (most recent call last):

  File "C:\Users\LakshmiNSridhar\anaconda3\lib\site-packages\PyDSTool\core\context_managers.py", line 30, in _stdchannel_redirected
    oldstdchannel = os.dup(stdchannel.fileno())

  File "C:\Users\LakshmiNSridhar\anaconda3\lib\site-packages\ipykernel\iostream.py", line 311, in fileno
    raise io.UnsupportedOperation("fileno")

UnsupportedOperation: fileno


During handling of the above exception, another exception occurred:

SystemExit: error: command 'swig.exe' failed: None
Can someone please help me
Thanks

[pydstool-users] Extend find_nullclines to support 3D?

[Daniel B. <dan...@gm...>]

Dear pydstool developers,

Have there ever been plans to provide support in find_nullclines to 3D
systems?  I've noticed other functions in pydstool are ND.

I'm working with a 3D system now and am considering writing code myself to
extend pydstool to find nullclines in my system.

I'd very much appreciate hearing about any work you've done in this
direction.  I'm not sure whether there's a good reason this functionality
is not included.

(It's not clear to me whether this mailing list is active anymore . . . If
it's not and there's a better place to post this message, please do let me
know . . .)

Thanks,
Dan

[pydstool-users] Namespace for model

[Daniel B. <dan...@gm...>]

Hi all,

Say I have a model like this:

DSargs = dst.args(name='Decision_making_model')

DSargs.pars = {'nu': 0.1,  # ms
               'tau_i': 10}  # ms

DSargs.fnspecs = {'g': (['r_e'], 'g_func(r_e)'),
                  'f': (['r_e', 'r_i'], 'f_func(r_e, r_i)')}

This code throws an error, because g_func and f_func are custom Python
functions.  How do I get these functions in the namespace of the model?
(They are already defined in the namespace of the script where the model is
created and run.)

Thanks,
Dan

[pydstool-users] Assistance with large scale model re-definition

[Amogh J. <ja...@vt...>]

Hello,

I am currently working on a relatively large systems biology model of 25
variables. I am running into problems in PyDSTool, which I attribute to my
inexperience with python and PyDSTool. I have a list of questions, and
though I have tried reading the documentation and answers on the internet,
I still have many questions on the "right way" of modeling in PyDSTool.

1. *Model redefinition: *
In order to compare my model output with experimental conditions, I need to
continuously redefine the varspecs dictionary in order to set one or more
derivatives to '0' or other custom expressions (to simulate gene knockouts,
for example). I have managed to do this currently by creating a function
that generates "special" varspecs dictionaries by comparing the user
defined expression(s) with a reference dictionary containing the "basal"
reactions, and then creating a different model for each user-defined
condition. [I maintain a list of these conditions.]
I find that this method is not very efficient. Even if I pickle some of
these recurring model instances, I believe there must be a better/more
efficient method of dynamically creating models. I would greatly appreciate
any tips or links to discussions regarding model construction.

2. *Parameter estimation:*
I have tried reading the ParamEst documentation and have tried to take
apart the pest_test1.py script to carry out a least squares parameter
estimation. However, I am finding it hard to wrap my head around the
concepts of model Interfaces, and so on. Could you point me to a
step-by-step breakdown of the working of ParamEst? (I gave up after
creating functions that used the set() function to 'manually' pass
parameter combinations to calculate the residuals at each iteration in my
data fitting function)

Also, for my system of 25 equations, computing the trajectory for
trange=[0,1000] takes ~5s. Is this normal?

Thank you very much for your time, and thanks for the great tool!

Cheers!

Amogh Jalihal
Graduate Student
Genetics, Bioinformatics and Computational Biology
Virginia Tech

[pydstool-users] System dynamic in PyDSTool - Using ranges for parameters

[<Kar...@cs...>]

Hello,

My name is Karine Prunera, and I'm currently trying to develop a system dynamic model on Python. The PyDSTool package, looked exactly what I needed, but I am just getting started with it and I am facing some issues.

The model I am trying to develop is composed of several differential equations, and a set of parameters. My problem is that I don't know exactly the value of each parameter, so I would like to use ranges instead of an exact value when I define them. Is it possible on PyDSTool? If it is, is it possible to send me some documentation about it?

I have read the documentation about PyDSTool online (http://www.ni.gsu.edu/~rclewley/PyDSTool/FrontPage.html.), but I didn't find an answer to that problem.

Thank you by advance

Karine Prunera

Re: [pydstool-users] Installation Issues

[Gianna M. <gia...@un...>]

Hi,

I installed the conda package "libpython" which Continuum Analytics 
built to resolve linking problems and now everything seems to work.

Cheers,
Gianna






Am 23.09.2015 um 15:33 schrieb Gianna Marschmann:
> Hello,
>
> I am new to python and on Windows 8.1 64-bit and am trying to install 
> PyDSTool with Anaconda, specifically following those steps:
>
> - Installed Anaconda 2.3.0, 32-bit version with Python 2.7
>
> - Installed SWIG 3.0.7 and added to system PATH 
> C:\Users\Gianna\swigwin-3.0.7 and PYTHON_INCLUDE C:\Anaconda\include 
> and PYTHON_LIB C:\Anaconda\libs\python27.lib, C:\Users\Gianna>swig 
> returns 'Must specify input file.'
>
> - Installed MinGW gcc and added \bin directory to PATH . 
> C:\Users\Gianna>gcc --version returns '4.8.1'
>
> - Created the file C:\Anaconda\Lib\distutils\distutils.cfg with
>
> [build]
>  compiler=mingw32
>
> - Extracted PyDSTool to C:\Users\Gianna\robclewley-pydstool-9ecaefa/ 
> and ran python setup.py install
>
> - Created the file C:\Anaconda\Lib\site-packages\PyDSTool.pth with
>
>  C:\\
> C:\\Users\\
> C:\\Tools\\Gianna\\
> C:\\Tools\\Gianna\\robclewley-pydstool-9ecaefa\\
>
> - Running \examples>python run_all_tests.py gives the following
>
>
> Test scripts that failed:
>         PyCont_Hopfield.py
>         PyCont_SaddleNode.py
>         imprecise_event_test.py
>         interp_dopri_test.py
>         HH_model_Cintegrator.py
>         HH_loaded_Cintegrator.py
>         CIN.py
>         HH_model_Cintegrator_testbounds.py
>         Dopri_backwards_test.py
>         test_hybrid_extinputs_Cintegrator.py
>         SLIP_2D_pdc.py
>         DAE_example.py
>         freefinger_noforce_radau.py
>         sloppycell_example.py
>         pest_test3_Cintegrator.py
>         pest_test4_Cintegrator.py
>         PyCont_MorrisLecar_TypeI.py
>         PyCont_MorrisLecar_TypeII.py
>         PyCont_LPNeuron.py
>         PyCont_HindmarshRose.py
>         PyCont_ABReaction.py
>         PyCont_Hamiltonian.py
>         PyCont_Lorenz.py
>         PyCont_vanDerPol.py
>
> Summary:
> Basic PyDSTool functions: appears to work on your system
> Map related modules: appears to work on your system
> VODE related modules: appears to work on your system
> Symbolic differentiation module: appears to work on your system
> Parameter estimation module: appears to work on your system
> PyCont: appears to be broken on your system
> Dopri ODE systems: appears to be broken on your system
> Radau ODE systems: appears to be broken on your system
> Parameter estimation module with external compilers: appears to be 
> broken on you
> r system
> PyCont interface to AUTO: appears to be broken on your system
>
>
> I now don't understand the error messages on the tests that failed 
> (see appendix).  There always seem to be "undefined references" to radau.
>
> Can you help me with further steps?
>
> Thank you,
> Gianna
>
>
>
>
> ------------------------------------------------------------------------------
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>
>
> _______________________________________________
> PyDSTool-Users mailing list
> PyD...@li...
> https://lists.sourceforge.net/lists/listinfo/pydstool-users

[pydstool-users] Installation Issues

[Gianna M. <gia...@un...>]

***** Testing script PyCont_Lorenz.py ****************************

nda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\s
rc\dmatrix.o:dmatrix.c:(.text+0x500): undefined reference to `_imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\dmatrix.o:dmatrix.c:(.text+0x531): undefined reference
 to `_imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\dmatrix.o:dmatrix.c:(.text+0x561): undefined reference
 to `_imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\dmatrix.o:dmatrix.c:(.text+0x597): undefined reference
 to `_imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x169): undefined reference to `_
imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x451): undefined reference to `_
imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x559): undefined reference to `_
imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x91f): undefined reference to `_
imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x949): undefined reference to `_
imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0xa72): undefined reference to `_
imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0xab9): undefined reference to `_
imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0xd5f): undefined reference to `_
imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x11a3): undefined reference to `
_imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\..\src\fcon.o:fcon.c:(.text+0x1339): undefined reference to `
_imp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\automod.o:automod.c:(.text+0x89): undefined reference to `_im
p__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\automod.o:automod.c:(.text+0x1c1): undefined reference to `_i
mp__PyMem_Realloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\automod.o:automod.c:(.text+0x38a): undefined reference to `_i
mp__PyMem_Free'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\automod.o:automod.c:(.text+0x677): undefined reference to `_i
mp__PyMem_Realloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\automod.o:automod.c:(.text+0x698): undefined reference to `_i
mp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\interface.o:interface.c:(.text+0x62): undefined reference to
`_imp__PyMem_Malloc'
auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\
pycont\auto\module\interface.o:interface.c:(.text+0xe6): undefined reference to
`_imp__PyMem_Free'
collect2.exe: error: ld returned 1 exit status
error: Command "g++ -shared auto_temp\Release\auto_temp\src.win32-2.7\auto_temp\
auto_lorenz_vf_wrap.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90
.0-py2.7.egg\pydstool\pycont\auto\module\..\src\auto.o auto_temp\Release\anacond
a\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src
\autlib1.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.eg
g\pydstool\pycont\auto\module\..\src\autlib2.o auto_temp\Release\anaconda\lib\si
te-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\autlib3
.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydsto
ol\pycont\auto\module\..\src\autlib4.o auto_temp\Release\anaconda\lib\site-packa
ges\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\autlib5.o auto_
temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycon
t\auto\module\..\src\eispack.o auto_temp\Release\anaconda\lib\site-packages\pyds
tool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\conpar.o auto_temp\Rele
ase\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\mo
dule\..\src\setubv.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.
0-py2.7.egg\pydstool\pycont\auto\module\..\src\reduce.o auto_temp\Release\anacon
da\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\sr
c\dmatrix.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.e
gg\pydstool\pycont\auto\module\..\src\fcon.o auto_temp\Release\anaconda\lib\site
-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\libf2c\ca
bs.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pyds
tool\pycont\auto\module\..\src\libf2c\d_lg10.o auto_temp\Release\anaconda\lib\si
te-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\libf2c\
i_nint.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\
pydstool\pycont\auto\module\..\src\libf2c\pow_di.o auto_temp\Release\anaconda\li
b\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\lib
f2c\r_lg10.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.
egg\pydstool\pycont\auto\module\..\src\libf2c\z_exp.o auto_temp\Release\anaconda
\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\
libf2c\d_imag.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0-py2
.7.egg\pydstool\pycont\auto\module\..\src\libf2c\d_sign.o auto_temp\Release\anac
onda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\..\
src\libf2c\i_dnnt.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.90.0
-py2.7.egg\pydstool\pycont\auto\module\..\src\libf2c\pow_dd.o auto_temp\Release\
anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module
\..\src\libf2c\pow_ii.o auto_temp\Release\anaconda\lib\site-packages\pydstool-0.
90.0-py2.7.egg\pydstool\pycont\auto\module\..\src\libf2c\z_abs.o auto_temp\Relea
se\anaconda\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\mod
ule\..\src\libf2c\z_log.o auto_temp\Release\anaconda\lib\site-packages\pydstool-
0.90.0-py2.7.egg\pydstool\pycont\auto\module\automod.o auto_temp\Release\anacond
a\lib\site-packages\pydstool-0.90.0-py2.7.egg\pydstool\pycont\auto\module\interf
ace.o auto_temp\Release\users\gianna\robclewley-pydstool-9ecaefa\examples\auto_t
emp\lorenz_vf.o -L./ -LC:\Anaconda\libs -LC:\Anaconda\PCbuild -lpython27 -lmsvcr
90 -o .\_auto_Lorenz_vf.pyd -w -m32" failed with exit status 1

      Testing failed on test file PyCont_Lorenz.py

***** Testing script PyCont_vanDerPol.py ****************************

At end of testing you can delete the temp file vanderPol.dat
5_vanderpol_vf_wrap.o:radau5_vanderPol_vf_wrap.c:(.text+0x4d12): undefined refer
ence to `_imp__PyDict_SetItemString'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x4fde): undefined reference to `_imp__PyCap
sule_Import'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x4fe9): undefined reference to `_imp__PyErr
_Occurred'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x4ff7): undefined reference to `_imp__PyErr
_Clear'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x5049): undefined reference to `_imp__PyCap
sule_New'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x507d): undefined reference to `_imp__Py_Bu
ildValue'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x50ab): undefined reference to `_imp__PyObj
ect_Free'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.text+0x50ca): undefined reference to `_imp__PyMod
ule_AddObject'
C:\Users\Gianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\g
ianna\robclewley-pydstool-9ecaefa\examples\radau5_temp\radau5_vanderpol_vf_wrap.
o:radau5_vanderPol_vf_wrap.c:(.rdata+0x1148): undefined reference to `PyObject_G
enericGetAttr'
collect2.exe: error: ld returned 1 exit status
error: Command "C:\MinGW\bin\gfortran.exe -Wall -g -Wall -g -shared C:\Users\Gia
nna\robclewley-pydstool-9ecaefa\examples\radau5_temp\Release\users\gianna\robcle
wley-pydstool-9ecaefa\examples\radau5_temp\vanderpol_vf.o C:\Users\Gianna\robcle
wley-pydstool-9ecaefa\examples\radau5_temp\Release\anaconda\lib\site-packages\py
dstool-0.90.0-py2.7.egg\pydstool\integrator\radau5mod.o C:\Users\Gianna\robclewl
ey-pydstool-9ecaefa\examples\radau5_temp\Release\anaconda\lib\site-packages\pyds
tool-0.90.0-py2.7.egg\pydstool\integrator\integration.o C:\Users\Gianna\robclewl
ey-pydstool-9ecaefa\examples\radau5_temp\Release\anaconda\lib\site-packages\pyds
tool-0.90.0-py2.7.egg\pydstool\integrator\interface.o C:\Users\Gianna\robclewley
-pydstool-9ecaefa\examples\radau5_temp\Release\anaconda\lib\site-packages\pydsto
ol-0.90.0-py2.7.egg\pydstool\integrator\eventfinding.o C:\Users\Gianna\robclewle
y-pydstool-9ecaefa\examples\radau5_temp\Release\anaconda\lib\site-packages\pydst
ool-0.90.0-py2.7.egg\pydstool\integrator\memory.o C:\Users\Gianna\robclewley-pyd
stool-9ecaefa\examples\radau5_temp\Release\users\gianna\robclewley-pydstool-9eca
efa\examples\radau5_temp\radau5_vanderpol_vf_wrap.o -Lc:\mingw\lib\gcc\mingw32\4
.8.1 -LC:\Anaconda\libs -LC:\Anaconda\PCbuild -Lbuild\temp.win32-2.7 -lradau5 -l
lapack_lite -lpython27 -lgfortran -o C:\Users\Gianna\robclewley-pydstool-9ecaefa
\examples\radau5_temp\_radau5_vanderPol_vf.pyd -w -m32" failed with exit status
1

      Testing failed on test file PyCont_vanDerPol.py

[pydstool-users] Forum user

[Ciaran W. <cw...@gm...>]

cw...@gm...

[pydstool-users] (no subject)

[Rob C. <rob...@gm...>]

Dear PyDSTool users,

The INCF is sponsoring two Google Summer of Code projects this year
that will directly benefit PyDSTool. Please take a look and forward to
anyone who might be interested in participating.

http://incf.org/gsoc/2015/proposals/#-span--span----nbsp---span---span--span-neuroscience-model-exploration-and-development-tools-for-pydstool--span-

http://www.google-melange.com/gsoc/homepage/google/gsoc2015

Thanks,
Rob

-- 
Robert Clewley, Ph.D.
Adjunct Professor
Neuroscience Institute and
Department of Mathematics and Statistics
Georgia State University
http://neuroscience.gsu.edu/rclewley.html

Ben Franklin Academy
http://www.benfranklinacademy.org/

[pydstool-users] PyDSTool 0.90 has been released

[Rob C. <rob...@gm...>]

The primary purpose of this release is to be fully compatible with
Python 3.3+ and 2.6-2.7 (further support of 2.6 has been dropped), and
also better support for 64-bit systems. For the first time, it uses a
fully-automatic installer and is available on PyPI:

https://pypi.python.org/pypi?:action=display&name=PyDSTool

Bleeding edge versions and the latest full release can be found at
https://github.com/robclewley/pydstool

with a mirror of releases at Sourceforge. Installation instructions
are provided in the README.

The majority of these developments are due to the hard work of
Vladimir Zakharov in Moscow, which is greatly appreciated.

As usual, there are also many minor fixes and improvements included in
this version. Details are given in the github history. Please continue
to use the sourceforge site for user help queries and discussion,
while the github site can be used if you want to contribute to code
development directly. Contributions are very welcome!

Please let us know if you have any comments or problems with
installation or use.

-Rob

Re: [pydstool-users] Improving code generation for constant mass matrix

[Juan P. C. <jua...@ug...>]

Hi,

I manage to get my hack in by printing to the C code only the non-zero elements.
The new code for FuncSpec is (between lines 1690 and 1699)
                # C integrators expect column-major matrices
                for col in range(n):
                    for row in range(m):
                        try:
                            if specdict[specvars[row]][col] != "0" and
specdict[specvars[row]][col] != "0.0": ##Print only nonzero elements
                              body_processed += "f_[" + str(col) +
"][" + str(row) \
                              + "] = " + specdict[specvars[row]][col] + ";\n"
                        except KeyError:
                            raise ValueError("Mass matrix should be
%sx%s"%(m,n))

The new compilation times are
rows of matrix, compilation time, ODEsystem constructor time, number
of equations
3     2.3    0.3   37
6     2.9    5.0   181
12   6.4    98.8  793

So now the bottle neck is in the constructor of the generator. I see a
lot of dictionary time which I guess corresponds to the entries of the
zero rows of the mass matrix. A solution would be to not make entry
for zero rows, but I guess this will brake all the code.

Is anybody interested in helping with the implementation of fast
assembly and C code compilation for the case of sparse and constant
mass matrix?


Thank you


The only problem with this is that all the other elements of f_ are
not set to zero. Where is the declaration and initialization of the
**double pointer that is passed to the massMatrix function?

On Wed, Mar 13, 2013 at 10:41 PM, Juan Pablo Carbajal
<jua...@ug...> wrote:
> Hello,
>
> When a DAE is defined with a constant mass matrix the C code generated
> has one line per element in the matrix. This causes very long
> compilation times for big matrices
> number of rows in massmatrix, size of c-code (KB), size of .so (KB),
> time to compile (seconds)
>       3     33    963      2
>       4    102   1100     4
>       5    265   1400     12
>       6    591   1800     58
>       7   1200   2400    238
>       8   2100   3200    831
> When replaced with a nested for loop the compilation time for rows==7
> goes down to 4 seconds.
>
> I tried to improve FuncSpec to print a for loop fr the case of
> constant matrix, but I can't cause the for loop is parsed as a macro
> by QuantSpec.
>
> Is there a way to prevent enumeration of the mass matrix and just get
> code of the kind
>
>  # C integrators expect column-major matrices
>   body_processed += "unsigned int i,j;\n" + \
>                                 "for (i=0;i<" + str(n) + ";i++)\n" + \
>                                  "\tfor (j=0;j<" + str(m) + ";j++)\n" + \
>                                  "\t\t f_[i][j] = 0;\n\n"
>  for col in range(n):
>      for row in range(m):
>           try:
>             if specdict[specvars[row]][col]:
>                body_processed += "f_[" + str(col) + "][" + str(row) \
>                                             + "] = " +
> specdict[specvars[row]][col] + ";\n"
>
> (this was my attemp in FuncSpec.py line 1688)
>
> Thanks
>
> --
> ---------------
> Dr. sc. nat. Juan Pablo Carbajal
> Reservoir Computing Lab
> Department of Electronics and Information Systems (ELIS)
> Ghent University
> Sint Pietersnieuwstraat 41
> 9000 Ghent
> Belgium
> web: http://users.elis.ugent.be/~jcarbaja/



-- 
---------------
Dr. sc. nat. Juan Pablo Carbajal
Reservoir Computing Lab
Department of Electronics and Information Systems (ELIS)
Ghent University
Sint Pietersnieuwstraat 41
9000 Ghent
Belgium
web: http://users.elis.ugent.be/~jcarbaja/

[pydstool-users] Improving code generation for constant mass matrix

[Juan P. C. <jua...@ug...>]

Hello,

When a DAE is defined with a constant mass matrix the C code generated
has one line per element in the matrix. This causes very long
compilation times for big matrices
number of rows in massmatrix, size of c-code (KB), size of .so (KB),
time to compile (seconds)
      3     33    963      2
      4    102   1100     4
      5    265   1400     12
      6    591   1800     58
      7   1200   2400    238
      8   2100   3200    831
When replaced with a nested for loop the compilation time for rows==7
goes down to 4 seconds.

I tried to improve FuncSpec to print a for loop fr the case of
constant matrix, but I can't cause the for loop is parsed as a macro
by QuantSpec.

Is there a way to prevent enumeration of the mass matrix and just get
code of the kind

 # C integrators expect column-major matrices
  body_processed += "unsigned int i,j;\n" + \
                                "for (i=0;i<" + str(n) + ";i++)\n" + \
                                 "\tfor (j=0;j<" + str(m) + ";j++)\n" + \
                                 "\t\t f_[i][j] = 0;\n\n"
 for col in range(n):
     for row in range(m):
          try:
            if specdict[specvars[row]][col]:
               body_processed += "f_[" + str(col) + "][" + str(row) \
                                            + "] = " +
specdict[specvars[row]][col] + ";\n"

(this was my attemp in FuncSpec.py line 1688)

Thanks

-- 
---------------
Dr. sc. nat. Juan Pablo Carbajal
Reservoir Computing Lab
Department of Electronics and Information Systems (ELIS)
Ghent University
Sint Pietersnieuwstraat 41
9000 Ghent
Belgium
web: http://users.elis.ugent.be/~jcarbaja/

[pydstool-users] Pass complex functions into PySDTool ODE

[SHIHUI G. <sg...@bo...>]

Hi,

I understand that it's able to setup an ode function like this:

================
DSargs.pars = { 'rou': 1,
                'omega': 5,
                'sigma': 1,
                'convrate': 10}


DSargs.varspecs = {'y': '-convrate*((y*y+dy*dy)/(rou*rou)-sigma)*y -
omega*dy',
                   'dy': 'omega*y -
convrate*((y*y+dy*dy)/(rou*rou)-sigma)*dy' }
================

What if the function is more complex and needs to define by a separate
function, rather than a string?

Thanks.

Shihui

-- 
*
---------------------------------------------------------------------------------------
*

SHIHUI GUO
National Center for Computer Animation
Bournemouth University
United Kingdom

BU is a Disability Two Ticks Employer and has signed up to the Mindful Employer charter. Information about the accessibility of University buildings can be found on the BU DisabledGo webpages [ http://www.disabledgo.com/en/org/bournemouth-university ]
This email is intended only for the person to whom it is addressed and may contain confidential information. If you have received this email in error, please notify the sender and delete this email, which must not be copied, distributed or disclosed to any other person.
Any views or opinions presented are solely those of the author and do not necessarily represent those of Bournemouth University or its subsidiary companies. Nor can any contract be formed on behalf of the University or its subsidiary companies via email.

-- 
This message has been scanned for viruses and
dangerous content by MailScanner, and is
believed to be clean.

[pydstool-users] Forgot to mention...

[Rob C. <rob...@gm...>]

Sorry, in my email I forgot to include that I am about to release a
Live CD with an Ubuntu-based version of PyDSTool
[http://help.ubuntu.com/community/LiveCD] that will ease installation
and setup, and I’m finishing up a fully integrated interface to
linux-based CUDA GPU platforms for parallel ODE solving
[http://www.nvidia.com/object/cuda_home_new.html].

Thanks,
Rob

-- 
Robert Clewley, Ph.D.
Assistant Professor
Neuroscience Institute and
Department of Mathematics and Statistics
Georgia State University
PO Box 5030
Atlanta, GA 30302, USA

tel: 404-413-6420 fax: 404-413-5446
http://neuroscience.gsu.edu/rclewley.html

[pydstool-users] Requesting your brief input to help with an NSF proposal about PyDSTool

[Rob C. <rob...@gm...>]

Dear registered users,

PyDSTool has mostly continued as a personal project in recent years.
If there is sufficient interest, I am planning to enter a more formal
phase of development that involves an open, community-driven model. I
am also planning to solidify prototypical and innovative tools for
model analysis, inference, and optimization, which are part of my
academic research
[http://www.ni.gsu.edu/~rclewley/Research/index.html].

I am preparing a proposal to obtain federal funding from NSF’s
Software Infrastructure for Sustained Innovation (SI2-SSE) program
[http://www.nsf.gov/pubs/2013/nsf13525/nsf13525.htm]. This would
support new software tools, anchored in the PyDSTool environment, that
focus on the reverse engineering of complex natural systems. As part
of my proposal I should convince NSF that my software either already
has, or is on the verge of having, significant impact in multiple
scientific domains. For my project to grow and become sustainable in
the long term, I need your help.

I am seeking two things right now: 1) interested collaborators to
build a community-driven development team to broaden my project,
improve its design and implementation, and improve its maintenance and
integration with other tools; 2) letters of support from happy users
or enthusiastic potential users of the proposed features in different
application areas.

Please respond to me at rob...@gm... in one of two ways,
depending on your time and interest. Either way, I would like you to
provide information about your position and scientific application
that either has benefited from the use of PyDSTool or the nature of
your potential interest in using the proposed features. Your message
doesn’t need to be long and detailed. You can just email me a
paragraph or two with an authorization to quote you, or, preferably,
provide the same information as a more formal letter in PDF with a
letterhead.

Additionally, the whole future of my academic career now rests on
obtaining federal funding, as that is now a formal criterion for
tenure at my university. My grant is due within 4 weeks, so if you
would like to help I urge you to act soon! If you have more questions,
or wish for further details of my proposal, please contact me about
that too. I will be very grateful for your input.

Thanks for your time,
Rob

-- 
Robert Clewley, Ph.D.
Assistant Professor
Neuroscience Institute and
Department of Mathematics and Statistics
Georgia State University
PO Box 5030
Atlanta, GA 30302, USA

tel: 404-413-6420 fax: 404-413-5446
http://neuroscience.gsu.edu/rclewley.html

[pydstool-users] Problem with cleanupMemory() for Radau_ODEsystem

[Matthew W. <mat...@gm...>]

Hi,

I am relatively new to PyDSTool. I am doing some bifurcation analysis which
is requiring me to perform quite a lot of runs of my ode system and
continuations. I often hit a memory ceiling and the process crashes.

I have tried to add calls to 'cleanupMemory()' in the Radau_ODESystem I am
using, but I get the following error:

.....
  File "/home/matt/PyDSTool/Generator/ODEsystem.py", line 433, in
cleanupMemory
    if hasattr(gen, '_solver'):
NameError: global name 'gen' is not defined

Is there something obvious I am not doing?

Regards

Matt

Re: [pydstool-users] simulation with many auxiliary equations

[Ludo V. <l.c...@sc...>]

On May 25, 2012, at 4:34 am, gyro funch wrote:

> On 5/24/2012 12:16 PM, Ludo Visser wrote:
>> 
>> You can use the fnspec attribute for that. Building from your example, let's consider:
>> 
>> dx/dt = c1*z, with c1 = k/m and z = y/k
>> dy/dt = ...
>> 
>> Your varspec would look like:
>> 
>> varspec = {'x': 'c1(k,m)*z(y,k)',
>>           'y': ...}
>> 
>> Then, your fnspec would be:
>> fnspec = {'c1': (['a', 'b'], 'a/b'),
>>          'z': (['a', 'b'], 'a/b')}
>> 
>> This defines the functions 'c1' and 'z', both taking 2 arguments. The keys of the fnspec dictionary defines the function name, the values are tuples of function arguments and function implementations. (Note that in this trivial example you could be done with defining only one function, since they both do the same.)
>> 
>> Hope this helps,
>> Ludo
>> 
> 
> 
> Thanks, Ludo.
> 
> I'll see if that sort of approach will work for my model.
> 
> I looked through a number of examples in the 'tests' directory of
> the distribution.
> It seems as if 'sloppycell_example.py' contains something very
> similar to what I need. Specifically, it defines an 'assignments'
> dictionary that contains expressions using various parameters:
> 
> 'assignments': {'CLB2T_21': 'CLB2_20 + C2_4 + C2P_5 + F2_29 +
> F2P_30', 'F_28': 'exp(-mu_39 * D_26)', 'mu_39': 'log(2) / mdt_216',
> 'Vacdh_58': 'kacdh_126 + kacdh_127 * CDC14_8', ...}
> 
> I'll need to read through 'makeSloppyModel.py' to see how this can
> be used in a model.
> 
> Kind regards,
> gyro

A quick look into makeSloppyModel.py reveals that the specification of the assignment dictionary triggers a routine that wraps this dictionary in a ModelSpec object. I don't know (yet) how these work, so I can't help you with those...

Regards,
Ludo

-- 
Ludo C. Visser, M.Sc.
Science Applied
phone: +31 6 1066 3076
e-mail: l.c...@sc...

Re: [pydstool-users] simulation with many auxiliary equations

[gyro f. <gyr...@gm...>]

On 5/24/2012 12:16 PM, Ludo Visser wrote:
> 
> You can use the fnspec attribute for that. Building from your example, let's consider:
> 
> dx/dt = c1*z, with c1 = k/m and z = y/k
> dy/dt = ...
> 
> Your varspec would look like:
> 
> varspec = {'x': 'c1(k,m)*z(y,k)',
>            'y': ...}
> 
> Then, your fnspec would be:
> fnspec = {'c1': (['a', 'b'], 'a/b'),
>           'z': (['a', 'b'], 'a/b')}
> 
> This defines the functions 'c1' and 'z', both taking 2 arguments. The keys of the fnspec dictionary defines the function name, the values are tuples of function arguments and function implementations. (Note that in this trivial example you could be done with defining only one function, since they both do the same.)
> 
> Hope this helps,
> Ludo
> 


Thanks, Ludo.

I'll see if that sort of approach will work for my model.

I looked through a number of examples in the 'tests' directory of
the distribution.
It seems as if 'sloppycell_example.py' contains something very
similar to what I need. Specifically, it defines an 'assignments'
dictionary that contains expressions using various parameters:

'assignments': {'CLB2T_21': 'CLB2_20 + C2_4 + C2P_5 + F2_29 +
F2P_30', 'F_28': 'exp(-mu_39 * D_26)', 'mu_39': 'log(2) / mdt_216',
'Vacdh_58': 'kacdh_126 + kacdh_127 * CDC14_8', ...}

I'll need to read through 'makeSloppyModel.py' to see how this can
be used in a model.

Kind regards,
gyro

Re: [pydstool-users] simulation with many auxiliary equations

[Ludo V. <l.c...@sc...>]

> However, I am still not sure how one adds additional equations that
> are not ODEs.
> 
> Although not realistic and consistent in units, suppose that for
> this oscillations example (Tutorial_linear.html) there are a number
> of derived quantities:
> 
> c1 = k/m
> c2 = k*m^2
> z = y/k
> 
> and that the differential equations are
> 
> dx/dt = c1*z
> dy/dt = -k*x/m + c2*(dx/dt)
> 
> For this simple example, we can do some trivial substitutions.
> However, in general, how does one add additional auxiliary equations
> that are then used in the simulation system?

You can use the fnspec attribute for that. Building from your example, let's consider:

dx/dt = c1*z, with c1 = k/m and z = y/k
dy/dt = ...

Your varspec would look like:

varspec = {'x': 'c1(k,m)*z(y,k)',
           'y': ...}

Then, your fnspec would be:
fnspec = {'c1': (['a', 'b'], 'a/b'),
          'z': (['a', 'b'], 'a/b')}

This defines the functions 'c1' and 'z', both taking 2 arguments. The keys of the fnspec dictionary defines the function name, the values are tuples of function arguments and function implementations. (Note that in this trivial example you could be done with defining only one function, since they both do the same.)

Hope this helps,
Ludo

-- 
Ludo C. Visser, M.Sc.
Science Applied
phone: +31 6 1066 3076
e-mail: l.c...@sc...

Re: [pydstool-users] simulation with many auxiliary equations

[gyro f. <gyr...@gm...>]

On 5/24/2012 8:39 AM, Ludo Visser wrote:
>>
>> The problem is one of ignorance. I am accustomed to ODE integrators
>> like scipy.odeint or MATLAB's ode45, where one writes a function
>> that returns the numerical rhs of the ODE system at a given time
>> point and the ODE solver takes this function as an argument.
>>
>> Although I am a decent Python programmer, the object oriented
>> structure of the PyDSTool framework and the idea of specifying
>> equations and parameters using strings and dictionaries is foreign
>> to me.
> 
> Hi Gyro,
> 
> I see what you mean now. I found this tutorial very useful in understanding the basics:
> http://www.ni.gsu.edu/~rclewley/PyDSTool/Tutorial/Tutorial_linear.html
> 
> Essentially, you need to define:
> * a dictionary of parameters, with parameter names as keys and parameter values as values
> * a dictionary of initial conditions, with variable names as keys and initial values as values
> * a dictionary of ODEs, with variables names as keys and string-expressions for the ODE, in terms of other variables and parameters
> 
> Then you can use the args-object to create a generator to compute the trajectories.
> 
> I'm currently working on some examples myself, while learning how to work with PyDSTool. Maybe, once these examples can also be useful to you or others, but the fact that they may not be related to your field of research can be distracting rather than clarifying. My examples are in the field of mechanics; if you're interested, I can document them some more and post them here.
> 
> Kind regards,
> Ludo
> 


Hi Ludo,

Thank you. That example is very clear. The construction of the
parameter, initial condition, and ODE dictionaries is straightforward.

However, I am still not sure how one adds additional equations that
are not ODEs.

Although not realistic and consistent in units, suppose that for
this oscillations example (Tutorial_linear.html) there are a number
of derived quantities:

c1 = k/m
c2 = k*m^2
z = y/k

and that the differential equations are

dx/dt = c1*z
dy/dt = -k*x/m + c2*(dx/dt)

For this simple example, we can do some trivial substitutions.
However, in general, how does one add additional auxiliary equations
that are then used in the simulation system?

Thanks.

Kind regards,
gyro

Re: [pydstool-users] simulation with many auxiliary equations

[Ludo V. <l.c...@sc...>]

> 
> The problem is one of ignorance. I am accustomed to ODE integrators
> like scipy.odeint or MATLAB's ode45, where one writes a function
> that returns the numerical rhs of the ODE system at a given time
> point and the ODE solver takes this function as an argument.
> 
> Although I am a decent Python programmer, the object oriented
> structure of the PyDSTool framework and the idea of specifying
> equations and parameters using strings and dictionaries is foreign
> to me.

Hi Gyro,

I see what you mean now. I found this tutorial very useful in understanding the basics:
http://www.ni.gsu.edu/~rclewley/PyDSTool/Tutorial/Tutorial_linear.html

Essentially, you need to define:
* a dictionary of parameters, with parameter names as keys and parameter values as values
* a dictionary of initial conditions, with variable names as keys and initial values as values
* a dictionary of ODEs, with variables names as keys and string-expressions for the ODE, in terms of other variables and parameters

Then you can use the args-object to create a generator to compute the trajectories.

I'm currently working on some examples myself, while learning how to work with PyDSTool. Maybe, once these examples can also be useful to you or others, but the fact that they may not be related to your field of research can be distracting rather than clarifying. My examples are in the field of mechanics; if you're interested, I can document them some more and post them here.

Kind regards,
Ludo



-- 
Ludo C. Visser, M.Sc.
Science Applied
phone: +31 6 1066 3076
e-mail: l.c...@sc...

Re: [pydstool-users] simulation with many auxiliary equations

[gyro f. <gyr...@gm...>]

On 5/24/2012 7:33 AM, Ludo Visser wrote:
> Hi,
> 
> I'm not completely sure what the problem is that you're running into.
> 
> If the complexity of the conversion equations is an issue, then you can use either the symbolic manipulation tools provided by PyDSTool (although I have no experience with that) or SymPy (I have a lot of experience with that, and SymPy plays really quite nice with PyDSTool) to take semi-automate the generation of the ODEs. Since all equations are specified as string expression, some clever string manipulation can get you a long way.
> 
> For the rest, the problem you describe seems an ordinary first order system, so a single Generator instance, like used in the harmonic oscillation example, should work.
> 
> Regards,
> Ludo Visser
> 

Thank you for the reply, Ludo.

The problem is one of ignorance. I am accustomed to ODE integrators
like scipy.odeint or MATLAB's ode45, where one writes a function
that returns the numerical rhs of the ODE system at a given time
point and the ODE solver takes this function as an argument.

Although I am a decent Python programmer, the object oriented
structure of the PyDSTool framework and the idea of specifying
equations and parameters using strings and dictionaries is foreign
to me.

For instance, there is an example in the Elementary Tutorial for a
calcium channel model that looks something like this:
-----
DSargs = dst.args(name='Calcium channel model')
DSargs.pars = { 'vl': -60, 'vca': 120, 'i': 0, ...
DSargs.fnspecs  = {'minf': (['v'], '0.5 * ...
DSargs.varspecs = {'v': '( i + gl * (vl - v) - gca * minf(v) *
(v-vca) )/c','w': 'v-w' }
DSargs.ics = {'v': 0, 'w': 0 }
----

When I compare this to my model, it is unclear where my conversion
equations should go and what syntax I should use.

If you, or others, could show me a brief example, that would be
greatly appreciated.

Thank you.

Best regards,
gyro

Re: [pydstool-users] simulation with many auxiliary equations

[Ludo V. <l.c...@sc...>]

Hi,

I'm not completely sure what the problem is that you're running into.

If the complexity of the conversion equations is an issue, then you can use either the symbolic manipulation tools provided by PyDSTool (although I have no experience with that) or SymPy (I have a lot of experience with that, and SymPy plays really quite nice with PyDSTool) to take semi-automate the generation of the ODEs. Since all equations are specified as string expression, some clever string manipulation can get you a long way.

For the rest, the problem you describe seems an ordinary first order system, so a single Generator instance, like used in the harmonic oscillation example, should work.

Regards,
Ludo Visser


On May 24, 2012, at 2:48 pm, gyro funch wrote:

> Hi,
> 
> I am a newbie with PyDSTool and would appreciate your advice on how
> to solve a large system of ODEs that also contains a lot of
> auxiliary equations that define and scale variables and parameters.
> 
> Here is a small example that illustrates the sort of problem I am
> trying to solve:
> 
> 
> state variables
> ---------------
> y1, y2, y3
> 
> parameters
> ----------
> a1,a2,a3
> b1,b2,b3
> c1,c2,c3
> d1,d2,d3
> 
> conversion equations
> --------------------
> s1 = a1/b1
> s2 = a2/b2
> s3 = a3/b3
> z1 = y1/c1
> z2 = y2/c2
> z3 = y3/c3
> 
> differential equations
> ----------------------
> dy1/dt = s1*z1 - s2*dy2/dt
> dy2/dt = s3*z1 - s4*z3
> dy3/dt = s2*z3 - s3*z2*dy1/dt
> 
> initial conditions
> ------------------
> y1(0) = d1
> y2(0) = d2
> y3(0) = d3
> 
> 
> The examples included in the documentation and distribution are
> helpful, but I am unclear on how to specify this system most
> efficiently. I am also not clear on when symbolic variables can be
> used or if they would help in this instance.
> 
> Thank you very much.
> 
> Kind regards,
> gyro
> 
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-- 
Ludo C. Visser, M.Sc.
Science Applied
phone: +31 6 1066 3076
e-mail: l.c...@sc...

[pydstool-users] simulation with many auxiliary equations

[gyro f. <gyr...@gm...>]

Hi,

I am a newbie with PyDSTool and would appreciate your advice on how
to solve a large system of ODEs that also contains a lot of
auxiliary equations that define and scale variables and parameters.

Here is a small example that illustrates the sort of problem I am
trying to solve:


state variables
---------------
y1, y2, y3

parameters
----------
a1,a2,a3
b1,b2,b3
c1,c2,c3
d1,d2,d3

conversion equations
--------------------
s1 = a1/b1
s2 = a2/b2
s3 = a3/b3
z1 = y1/c1
z2 = y2/c2
z3 = y3/c3

differential equations
----------------------
dy1/dt = s1*z1 - s2*dy2/dt
dy2/dt = s3*z1 - s4*z3
dy3/dt = s2*z3 - s3*z2*dy1/dt

initial conditions
------------------
y1(0) = d1
y2(0) = d2
y3(0) = d3


The examples included in the documentation and distribution are
helpful, but I am unclear on how to specify this system most
efficiently. I am also not clear on when symbolic variables can be
used or if they would help in this instance.

Thank you very much.

Kind regards,
gyro

[pydstool-users] PyDSTool is great

[Ludo V. <l.c...@sc...>]

Hi,

I just discovered PyDSTool, and I think it's a great tool; many thanks for that!

For my own understanding of the tool, and in order to find out if the tool can help us fully replace Matlab, I'm compiling a set of demos that might also be useful for others. They are (will be) in the area of mechanics mostly. If there is any interest in these demos, let me know.

Kind regards,
Ludo Visser


-- 
Ludo C. Visser, M.Sc.
Science Applied
phone: +31 6 1066 3076
e-mail: l.c...@sc...