PyDSTool Activity
Status: Beta
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robclewley
Activity for PyDSTool
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Saiful Islam posted a comment on discussion Help
Here is the python file i am currently working with.
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I was trying the Rosenzweig-Macarthur model bifurcation. After trying for many months i have reached a little bit further and computed a figure attached below. But, i want it a little bit more expressive which shows both the transcritical bifurcation and hopf bifurcation both. It also shows the amplitude of the limit cycle oscillations. I did it using matcont but being unable to do so with PyDstool. Sir, i would be really glad if you help me understand the coding.
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Ananya Muguli posted a comment on discussion Help
Hello, I am executing a huge system with more than 30 state space variables. I keep getting 'Failed to compute tanget vector error'. Though I have read the posts relating to this thread, I am not able to understand how to give an initvector to calculate the tangent for a large system. Please can you help me out?
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Lucas A MacQuarrie posted a comment on discussion Help
Perhaps late, but it seems BP is also called a transcritical bifurcation
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Lakshmi Sridhar posted a comment on discussion Help
I had the fileno problem Then I added a fortran compiler Then I got a new error that read collect2.exe: error: ld returned 1 exit status what does this one mean and how can I resolve this Thanks all
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I had the fileno problem Then I added a fortran compiler Then I got a new error that read collect2.exe: error: ld returned 1 exit status what does this one mean and how can I resolve this Thanks all
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Another file dopri backwards test is also giving the same problem Wherever Radau isused this problem is occuring Thanks
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I re installed the github pydstool I ran the dae example from the examples directory I get the messages 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...
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I re installed the github pydstool I ran the dae example from the examples directory I get the messages 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...
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Rob Clewley posted a comment on discussion Help
I think this is fixed in the main branch on github, as per the discussion in https://github.com/robclewley/pydstool/issues/98. You should be using the github version of the package for maximal support on windows. On Wed, Jan 11, 2023 at 5:28 PM Lakshmi Sridhar lnsridhar@users.sourceforge.net wrote: When I run the dae example I get the mwssage 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",...
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When I run the dae example I get the mwssage 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...
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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...
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Hello When I run the dae example 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...
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Paw posted a comment on discussion Help
Five years later, I am using PyDSTool again. And I spend some time trying to figure out what I should do about this error Did you compile the RHS C code? Traceback (most recent call last): File "pydstool/examples/Dopri_backwards_test.py", line 23, in <module> trajf = ode.compute('testf') File "/root/projects/pydstool-ex/lib/python3.7/site-packages/PyDSTool-0.90.2-py3.7.egg/PyDSTool/Generator/Dopri_ODEsystem.py", line 465, in compute extraSpace=self.algparams['extraspace'], File "/root/projects/pydstool-ex/lib/python3.7/site-packages/PyDSTool-0.90.2-py3.7.egg/PyDSTool/Generator/Dopri_ODEsystem.py",...
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Florin Avram posted a comment on discussion Help
Hi I am new to Python, Anaconda, and PyDSTool. I have opened in Windows 8.1 the Anaconda prompt and typed pip install git+ ...PyDSTool.git and got the reply Requirement already satisfied, so I believe the rabbit is already there. Next I typed PyDSTool and got the reply not recognized as an internal command", so I am not sure how to proceed. There doesn't seem to be any tutorial fordummy windows users". Thanks for any tips on how to proceed
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Ted Galanthay posted a comment on discussion Help
I just found the complete script at http://pydstool.bzr.sourceforge.net/bzr/pydstool/files/head%3A/tests/. It has defined 'hopfs', so I will try running that.
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Hi! I am new to Python and to PyDSTool, and I am working through the tutorial here: https://pydstool.github.io/PyDSTool/Tutorial/Tutorial_PredPrey.html The second-to-last code box at that tutorial is: Create interpolatable curve from the pointset hopfs_curve = pointset_to_traj(hopfs) Interpolate unstable Hopf equilibrium values of parameters/variables at k=9 Hpt = hopfs_curve(9.0) This fails to run because "hopfs" has not been defined earlier in the code. I'm not sure what should be assigned to "hopfs"...
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Brittany Howell posted a comment on discussion Help
It is required for the part that I need, so I'm wondering how to fix this. Then when I continue the next part, I get an error of "invalid keys as arguments" for setting tdata=[0,20] so I am unsure how to get this working. Any help would be great. Thank you.
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I'm also curious if this is needed to run the remainder of the tutorial, which is the part I need; to iterate a bunch of phase plane solutions while varying a parameter. Would this error have any effect on that or would it be sufficient to continue and vary a parameter and I should still get the multiple phase plane solutions as required? Thanks!
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Hello. I have a 2D system of ODEs and I am trying to plot the nullclines to then vary my model parameters and plot the effects based on the Zero-crossing events tutorial. Based on the current parameter set, I have three steady states (nullclines are verified using XPP but I digress). My goal is to plot multiple nullclines as a parameter (or parameters) vary to see what my model does. I have currently gotten through the portion where the nullclines are plotted but based on the settings, my figure...
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hamed marzougui posted a comment on discussion Help
CAN YOU HELP ME IN THE EXECUTION OF THE DVODE CODE SOME ERRORS APPEAR LIKE: DVODE-- At current T (=R1), MXSTEP (=I1) steps taken on this call before reaching TOUT In above message, I1 = 500 In above message, R1 = 0.5201476811500D+00 Error halt: ISTATE = -1 THE FORTRAN CODE IS IN THE ATTACHED FILE BEST REGARDS
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CAN YOU HELP ME IN THE EXECUTION OF THE DVODE CODE SOME ERRORS APPEAR LIKE: DVODE-- At current T (=R1), MXSTEP (=I1) steps taken on this call before reaching TOUT In above message, I1 = 500 In above message, R1 = 0.5201476811500D+00 Error halt: ISTATE = -1 BEST REGARDS
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Anthony Morciglio modified a comment on discussion Help
Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Associated Code form my Perspective
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Associated Code form my Perspective
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Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Below is my results from the Bifurcation Analysis for Delta vs Dext, compare with figure 2 B in Jagged Mediates to see the discrepencies.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Associated Code form my Perspective
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Associated Code form my Perspective
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Associated Code form my Perspective
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Jagged Mediates Appendix Values, in figure 2 B the only changes are Vext = Jext = Next = 2000 with varying concentrations of Dext.
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Hello Rob, I actually got the code to run, however I am having trouble getting the same results stated in the paper: 'Jagged Mediates'. In particular figure 2: B Delta vs. Dext. The issue I am having is that the second Limit Point (Dext close to 800 is being picked up around 500 for me). If we run the System graphed vs time with Dext at 800, we see the cell is a tip phenotype (high Delta concentration). However, this does not coincide with the Limit point of 500 as this is the transition into the...
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Hi Anthony, Could you please be more specific about exactly what difficulty you're having? Do you have an error message, for instance? If it's running but you're getting the wrong result, could you paste pictures of the desired and current results? Regards, Rob On Mon, Jun 17, 2019 at 3:37 PM Anthony Morciglio amorciglio1@users.sourceforge.net wrote: Hello, I am fairly new to coding (started one month ago for Python, and last week for PyDSTool) and am having difficulty having my code to compile....
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Hello, I am fairly new to coding (started one month ago for Python, and last week for PyDSTool) and am having difficulty having my code to compile. I attempted to follow the Calcium Channel tutorial, but that is a relatively basic system with only 1 auxillary function. I have 7 Hill Functions that are a part of the 6 ODEs. The results that I am attempting to reproduce are stated in the following paper: 'Jagged Mediates...' I have developed the approrpriate code to run on Python, however not PyDSTool....
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Python File (Jupyter Notebook)
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PyDSTool File
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Hello, I am fairly new to coding (started one month ago for Python, and last week for PyDSTool) and am having difficulty having my code to compile. I attempted to follow the Calcium Channel tutorial, but that is a relatively basic system with only 1 auxillary function. I have 7 Hill Functions that are a part of the 6 ODEs. The results that I am attempting to reproduce are stated in the following paper: 'Jagged Mediates...' I have developed the approrpriate code to run on Python, however not PyDSTool....
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Mohammadreza Dorvash posted a comment on discussion Help
Well, I found the following link very helpful in solving the problem with SciPyversion. Apparently, when they were coding PyDSTool they did not think about the fact that SciPy might release versions higher than 1.0.0!!!!!!!!!! https://stackoverflow.com/questions/49369299/pydstool-do-not-recognize-scipy-version The problem is in the __init__.py file, line 76. Additionally, one might the following link to install the PyDSTool: pip install git+https://github.com/tkf/pydstool.git TKF tried to address...
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clas posted a comment on discussion Help
A bit different. I grabbed the latest version which after looking through files noted that scipy issue was fixed. So I did (in anaconda...) pip install git+https://github.com/robclewley/pydstool.git and it works fine. Clas Clas A. Jacobson1010 Horizon WayCT 06084 860 783 0074 (home) jacobsonclas@sbcglobal.net On Friday, April 26, 2019, 5:40:37 AM EDT, Mohammadreza Dorvash <dorvashmr@users.sourceforge.net> wrote: Hi, I have the same problem you encountered a few days ago. I installed PyDSTool and...
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A bit different. I grabbed the latest version which after looking through files noted that scipy issue was fixed. So I did (in anaconda...) pip install git+https://github.com/robclewley/pydstool.git and it works fine. "Works fine." I cannot get the Radau integrators to work. I looked at all the old posts that I could find and nothing seemed to to indicate how to fix this. I'm running this under Ubuntu 18.04 in Anaconda. The Dopri sorta work. I run them and they fail. I then move the .so files from...
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Hi, I have the same problem you encountered a few days ago. I installed PyDSTool and get the the "SciPy v0.5.1 or above is required" error. I ran the .py file of my own project and several other projects with all three of these environments: 1- anaconda/spyder 2- the MacOS terminal 3- IDLE I get the "SciPy" massage with the first two and "No module named PyDSTool" with IDLE. I reinstalled PyDSTool by all these methods: 1- conda install 2- pip install 3- git clone 4- directly downloading the files...
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ok. I installed the "beta" version from github and it works...
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Hmmm.... I just installed PyDSTool on Anaconda. I get the following odd error message... In [1]: from PyDSTool import * RuntimeError Traceback (most recent call last) <ipython-input-1-bc4dc4d8a139> in <module> ----> 1 from PyDSTool import *</module></ipython-input-1-bc4dc4d8a139> ~/anaconda3/envs/test/lib/python3.6/site-packages/PyDSTool/init.py in <module> 74 assert len(vernums) > 0 75 if vernums[1] < 5: ---> 76 raise RuntimeError("SciPy v0.5.1 or above is required") 77 del digits, vernums, temp_str...
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Paulo Paupitz modified a comment on discussion Help
Hi everyone, Could you help me implementing a frequency response of this simple case of an oscillator with nonlinear spring (called duffing): The ODE is: m*ddot_x + c*dot_x + k*x + k3* (x*x*x) = F*cos(w*t) the parameters are: m: mass, c = damping, k = linear spring stiffness, k3 = nonlinear spring stiffness, F = amplitude the external force, w = frequency of excitation. and the variables are: x = displacement of the mass, dox_x = velocity (v) and ddot_x = aceleration I would like to use the continuation...
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Hi everyone, Could you help me implementing a frequency response of this simple case of an oscillator with nonlinear spring (called duffing): The ODE is: m * ddot_x + c * dot_x + k * x +k3 (x * x * x) = Fcos(w*t) the parameters are: m: mass, c = damping, k = linear spring stiffness, k3 = nonlinear spring stiffness, F = amplitude the external force, w = frequency of excitation. and the variables are: x = displacement of the mass, dox_x = velocity (v) and ddot_x = aceleration I would like to use the...
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Hi everyone, Could you help me implementing a frequency response of this simple case of an oscillator with nonlinear spring (called duffing): The ODE is: m * ddot_x + c * dot_x + k * x +k3 x x * x = Fcos(wt) the parameters are: m: mass, c = damping, k = linear spring stiffness, k3 = nonlinear spring stiffness, F = amplitude the external force, w = frequency of excitation. and the variables are: x = displacement of the mass, dox_x = velocity (v) and ddot_x = aceleration I would like to use the continuation...
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Hi everyone, Could you help me implementing a frequency response of this simple case of an oscillator with nonlinear spring (called duffing): The ODE is: m * ddot_x + c dot_x + kx +k3xxx = Fcos(w*t) the parameters are: m: mass, c = damping, k = linear spring stiffness, k3 = nonlinear spring stiffness, F = amplitude the external force, w = frequency of excitation. and the variables are: x = displacement of the mass, dox_x = velocity (v) and ddot_x = aceleration I would like to use the continuation...
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Hi. You might be able to use http://www.warrenweckesser.net/vfgen/ but it will depend on what your current code is, exactly. If it's a manually written C function, for instance, you don't have much choice. Keeping math descriptions in program code is not a good long term solution anyway, so if you have to go through the pain of converting it, at least you'll know you're making an investment towards readability and reusability. Let me know what you find, Rob On Fri, Nov 23, 2018 at 2:30 AM Angeles...
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Angeles Gallego posted a comment on discussion Help
Hi, I have a system of 36 ODEs, in a code of 700 lines, where I create many auxiliary variables (approx 300). The problem is that I do not want to transcript it to PyDSTool format, in which I would have to convert every function using for example: function['v1', 'v2']:('v1*v2'), etc. Is there a way to input the code with the ODE without formating into a dictionary? Thanks a lot, Maria Angeles
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Hi, the sol attribute is a PyDSTool Pointset object, so it has indepvararray and coordarray numpy array attributes, which should contain what you need. See https://web.archive.org/web/20171204203340/http://www.ni.gsu.edu:80/~rclewley/PyDSTool/Pointsets.html for more info. On Mon, Nov 12, 2018 at 7:08 PM clas jacobsca@users.sourceforge.net wrote: Everything is working (very) well in PyDSTool (and PyCont). From a PyCont class I want to extract the actual points - how do I do this? PyCont['EQ1'].sol...
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Everything is working (very) well in PyDSTool (and PyCont). From a PyCont class I want to extract the actual points - how do I do this? PyCont['EQ1'].sol has the parameter for continuation and two states...i want to get and save all three of these in the workspace...?
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Everything is working (very) well in PyDSTool (and PyCont). From a PyCont class I want to extract the actual points - how do I do this? PyCont['EQ1'].sol has the parameter for continuation and two states...i want to get and save all three of these in the workspace...?
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Ok. I tried to use swig 2.0. Did not work. I get the following set of error messages that I cannot (yet) decode...any help would be (much) appreciated. clasajacobson@clasajacobson-Oryx-Pro:~/Downloads/pydstool-master/examples$ python3 Dopri_backwards_test.py Present limitation of Python: Cannot rebuild library without exiting Python and deleting the shared library /home/clasajacobson/Downloads/pydstool-master/examples/_dop853_my_ode_vf.so by hand! If you made any changes to the system you should...
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I should have added that I am using SWIG 3 (now).
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i have compilation issues too. Everything else works fine. What version of PyDSTool are you using?
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Thanks, I appreciate the information. I tried to temporarily update the redirect from sourceforge to the webarchive version but it fails, inexplicably. I'll try to rehost the material on sourceforge directly when I have time. On Tue, Jul 24, 2018 at 11:48 PM Lloyd Wood lloydwood@users.sourceforge.net wrote: Here's the last known webarchive copy: https://web.archive.org/web/20171201062820/http://www.ni.gsu.edu:80/~rclewley/PyDSTool/FrontPage.html PyDsTool website gone? https://sourceforge.net/p/pydstool/discussion/472291/thread/56016ac8/?limit=25#3609...
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Lloyd Wood posted a comment on discussion Help
Here's the last known webarchive copy: https://web.archive.org/web/20171201062820/http://www.ni.gsu.edu:80/~rclewley/PyDSTool/FrontPage.html
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http://pydstool.sourceforge.net redirects to https://www.ni.gsu.edu/~rclewley/PyDSTool/FrontPage.html which is no longer there - looks like the account has been deleted. Can the material be hosted on the sourceforge project website? thanks
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Bruno Cayres posted a comment on discussion Help
Dear all, Is this possible to obtain the Floquet multipliers of a given solution? Thanks in advance. Bruno
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Ahmet Kurt modified a comment on discussion Help
Hi everyone, I have been having this issue for quite some time now. I am trying to compute a LC-C using PyCont. But somehow Limit Cycle Curves from both ends don't come together. Please see the attached image for how LC-C looks like. I attached my script too. Any help is appreciated, Ahmet
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Hi everyone, I have been having this issue for quite some time now. I am trying to compute a LC-C using PyCont. But somehow Limit Cycle Curves from both ends doesn't combine together. Any help is appreciated. Ahmet
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Hi everyone, I have been having this issue for quite some time now. I am trying to compute a LC-C using PyCont. But somehow Limit Cycle Curves from both ends doesn't combine together. Any help is appreciated. Ahmet
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Hi everyone, I have been having this issue for quite some time now. I am trying to compute a LC-C using PyCont. But somehow Limit Cycle Curves from both ends doesn't combine together. Any help is appreciated. Ahmet
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Hi, Evgenij, Thank you very much. I'll try to implement a piecewise function based on your tip. =D
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Evgenij Gr. posted a comment on discussion Help
Hello! It seems that forced_spring.py has an example of a piecewise oscillator system. It also shows how to set up a proper hybrid model for such problems. Probably it has what you need. Documentation says: The point type MX is associated with some type of computational difficulty. It usually represents non-convergence based on our tolerances, but for many different reasons (e.g. initial point is too far from the requested curve type, too close to a homoclinic (large period), ...). As far I understand...
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Dear all, Is it possible to analyse a dynamical system with a piecewise function friction model? I did not see any example or something about it. Another question is: What is MX point? Thanks in advance, Bruno.
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Hello! I have the following problem with using PyCont for studying a system. The problematic output can be seen here. Let me describe what I was trying to achieve. For this system I know the equilibrium state that doesn't depend on the values of parameters. Also I know exact values of parameters at which Hopf bifurcation of this equilibrium happens. First I have tried to let PyCont find Hopf bifurcation point automatically. As I see, almost all PyCont examples on Github start from this step. The...
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Hi, Drew. That is it. I used alpha parameter by mistake =/, Now, I did reproduce the results from literature =D But, What python version do you, guys, use? I'm already with SciPy v1.0.0 and Python 3.6.4. This is probably why some errors popped up to me. Thank you very much =D
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Drew LaMar posted a comment on discussion Help
Hi, Bruno. Question: why is your free parameter for the limit cycles alpha? I changed it to mu, the same as the equilibrium point curve, and got the attached diagram. Does this look close to what you are expecting? Also, if you add PCargs.StopAtPoints = 'B' to your equilibrium point curve arguments, the curve will stop at the predetermined boundary points (plus and minus 1).
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Hello, guys. I already suppressed the current errors and I did found the Hopf bifurcation point at mu=0 as we can see in Figure_1 (Cheers =D)!!! I know that, from mu>= 0, the stability jumps to a stable limit cycle (or periodic attractor). So, I'm did this, PCargs = dst.args(name='SN1', type='LC-C') PCargs.initpoint = 'EQ1:H1' PCargs.freepars = ['alpha'] PCargs.MaxStepSize = 0.01 PCargs.StepSize = 0.001 PCargs.LocBifPoints = 'all ' PCargs.MaxNumPoints = 400 PCargs.verbosity = 5 PyCont.newCurve(PCargs)...
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Hi, Drew. I did what you said and it did not work. I downloaded the package again. First, it presents a SciPy version error and here I found a solution. Even overcome these, another error arises: PyDSTool/PyCont/TestFunc.py", line 381, in __init__ self.data.P = zeros((n*(n-1)/2, n*(n-1)/2), float) TypeError: 'float' object cannot be interpreted as an integer So, I did this: self.data.P = zeros((n*(n-1) // 2, n*(n-1) // 2), float) And then, the previous error arises: PyDSTool/PyCont/TestFunc.py",...
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Hi, Bruno. I think it's the PCargs.LocBifPoints = ['all'] line. I changed it to PCargs.LocBifPoints = 'all' and it worked.
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Hi, Maurizio. Yes, I have tried. Also, I checked the suggested post, but still the same result =[ Thanks for your answer. Bruno.
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Maurizio De Pitta' posted a comment on discussion Help
Hi Bruno, have you tried playing with StepSize, MaxStepSize and MinStepSize? Often it is related to the initialization of the tangent vector for continuation. Indeed this is why often, you can run the same continuation with the same parameters and get different results. Also see if you can play with the different tolerances values. See this post. Hope this helps. If not, Rob and the other folks will come out shortly :) M
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Hello, guys. I'm trying to reproduce the Example 3.1 from the book Applied Nonlinear Dynamics: Finding periodic solutions and bifurcation analysis. However, I stocked. Here is the code: import PyDSTool as dst import matplotlib.pyplot as plt from PyDSTool.Toolbox import phaseplane as pp pars = {'mu':1, 'alpha':-1, 'omega':1, 'beta':1} icdict = {'x': 0.5, 'y': 0.1} xstr = 'mu*x - omega*y + (alpha*x - beta*y)*(x*x + y*y)' ystr = 'omega*x + mu*y + (beta*x + alpha*y)*(x*x + y*y)' DSargs = dst.args(name='2D-System')...
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Hi Maurizio, thanks for your continued interest! Clewley R, Hybrid Models and Biological Model Reduction with PyDSTool, PLoS Computational Biology 8(8): e1002628 (2012) Clewley RH, Sherwood WE, LaMar MD, Guckenheimer JM (2007) PyDSTool, a software environment for dynamical systems modeling. URL http://pydstool.sourceforge.net This info is still available from the Google cache of the original front page and from the waybackmachine's version, https://web.archive.org/web/2/http://www.ni.gsu.edu/~rclewley/pydstool/FrontPage.html...
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I will try to re-host the pages on my github account in the near future. Sorry for the unexpected outage. In the meantime, this should be functional, if a bit slow: https://web.archive.org/web/20160331125637/http://www.ni.gsu.edu/~rclewley/PyDSTool/ On Mon, Dec 18, 2017 at 6:16 AM, Maurizio De Pitta' mauriziodepitta@users.sf.net wrote: Uhm ok, there seems to be a renovation going on as I read on the current Fron Page at http://www2.gsu.edu/~matrhc/FrontPage.html Site down Sent from sourceforge.net...
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So since the site is down at the moment, can anyone of the developers provide here for future reference, a bibtex entry-like format for PyDSTool please? Thanks.
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Uhm ok, there seems to be a renovation going on as I read on the current Fron Page at http://www2.gsu.edu/~matrhc/FrontPage.html
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Hi folks, what's going on? The whole PyDSTool documentation site seems to have be shut down? M
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Maurício Reis posted a comment on discussion Help
Hello there, I am unearthing this thread as a hope of solution to this issue. The only solution for a regular user is to get hold of a compatible MSVC compiler and coercing distutils to use that (see PyDSTool docs for info about adding a compiler flag for distutils) or wait until numpy becomes properly compatible with 64-bit windows. Can someone give more details on this?
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This is definitely a problem, thanks for posting. I've had some success with addressing it here (https://github.com/robclewley/pydstool/pull/128) but it's not complete and I don't know how to proceed right now. Dopri is definitely the superior way in all cases, though ...
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Ben Mayersohn posted a comment on discussion Help
The source of this error comes from the definition of del in baseclasses.py. See this statement: for fname, finfo in self._funcreg.items(): try: delattr(eval(finfo[0]), fname) If you look at the structure of finfo (e.g. by inserting a print statement), it's a tuple. For some entries, finfo[0] is 'self', but in other cases its an empty string (I've noticed this is the case for some of the auxiliary functions). Try running eval('') in a Python interpreter and you'll get this exact error. You can bypass...
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Hi. Good question! It has been a long time since that code was written and the full change logs weren't even in git at that point. I recall hacking together some quick min and max helper functions in C but had trouble (or lack of time) making fully generic, i.e. arbitrary number of arguments. Somehow it ended up with 4 as the limit. I can't even see the evidence of where 4 is a constraint in the C definitions for the __maxof and __minof underlying functions, so it's possible they were updated by...
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Hi there! I just started using PyDSTool recently with the hopes of using it to replace a scipy implementation of an ecosystem model. It's a predator-prey like model, and I'm typically modeling about 12 species at a time. However, it seems that to use the faster Dopri/Radau integrators, one can only have up to 4 compartments total. Vode is quite slow compared to my original implementation that uses scipy.integrate.ode: PyDSTool will take around 50 seconds while scipy will take about 15. So it's unusable...
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leiniu posted a comment on discussion Help
I setup PyDSTool from conda install: conda install -c conda-forge pydstool Then I tried several examples by Spyder 3.2.1 But I always get failed. For example, 1. when I run "Tutorial_PredatorPrey.py" in the example fold, I got the following: File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 688, in runfile execfile(filename, namespace) File "C:\ProgramData\Anaconda3\lib\site-packages\spyder\utils\site\sitecustomize.py", line 101, in execfile exec(compile(f.read(),...
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Jonildo posted a comment on discussion Open Discussion
Hi everyone, Im trying to run the test files on my windows machine but, I get the following error message: C:/Program Files (x86)/mingww64/dwarf/mingw32/bin/../lib/gcc/i686-w64-mingw32/7.1.0/../../../../i686-w64-mingw32/lib/../lib/libmingw32.a(lib32_libmingw32_a-atonexit.o):atonexit.c:(.text+0xc0): multiple definition of `atexit' C:\Python34\libs/libmsvcr100.a(duajs01110.o):(.text+0x0): first defined here collect2.exe: error: ld returned 1 exit status error: Command "g++ -shared auto_temp\Release\auto_temp\src.win32-3.4\auto_temp\auto_lorenz_vf_wrap.o...
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Hi Ahmet, I assume you may try import numpy as np I_app = 0.45*np.heaviside(t-5.0) Or look into the online documentation and see how to code auxfunc in PyDSTool. Unfortunately as you may have figured out, PyDSTool is no longer active and it takes time for the developers to reply as they are both doing other stuff. So for the future, use PyDSTool at your own risk: it is a fantastic tool with great potential, but suffers from some serious bugs and the fact that it has not been maintained (now for years)...
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