Duffing oscillator with PyCont #166
Comments
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Hi, I think you'll need to provide a starting trajectory that is close to
one cycle so that it has the period information. At least on my system,
AUTO tells me that it cannot compute the period. If you're not getting an
issue from AUTO then are you sure you have your system set up correctly
to use AUTO?
Maybe you could try following the pattern indicated in the solution code
attached at the end of this thread
https://sourceforge.net/p/pydstool/discussion/472291/thread/aa15f0ee/ ?
…On Wed, Nov 24, 2021 at 9:49 AM JonEhrmann ***@***.***> wrote:
Hi Rob,
I'm a Ph.D. student trying to implement the Duffing oscillator in PyCont
for path continuation of the periodic solutions. I'm struggeling with the
mathematical implementation of the differential equation. I used the
following code:
from PyDSTool import *
DSargs = args()
DSargs.name = "duffing"
DSargs.ics = {"q": 0.1, "dq": 0}
DSargs.pars = {"wdach": 0.05, "D": 0.05, "g": -1, "eta": 0.7}
DSargs.tdata = [0, 500]
DSargs.varspecs = {"q": "dq",
"dq": "wdach*cos(eta*t)-2*D*dq-q-g*pow(q,3)"}
DS = Generator.Vode_ODEsystem(DSargs)
traj = DS.compute("duffing")
pts = traj.sample()
# plt.plot(pts["t"], pts["q"])
# plt.plot(pts["t"], pts["dq"])
q0 = max(pts["q"][30000:])
dq0 = max(pts["dq"][30000:])
PC = ContClass(DS)
PCargs = args(
name="duff_cont",
type="LC-C",
freepars=["eta"],
initpoint={"q": q0, "dq": dq0},
# MaxNumPoints=450,
# MaxStepSize=1e-4,
# MinStepSize=1e-5,
# StepSize=1e-5,
LocBifPoints=["all"],
StopAtPoints=["B"],
SaveEigen=True,
)
PC.newCurve(PCargs)
PC["duff_cont"].forward()
PC["duff_cont"].display(["eta", "q"], stability=True)
Is it possible to implement the differential equation like this? Because
the current result of the simulation is like a constant value (q plot over
eta).
It would be nice to hear from you!
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There's a good chance that's a problem with the way you've entered strings,
esp. if you've copy-pasted anything. Sometimes "smart" quotes get in there
and mess things up, for instance. If you still have trouble please attach
your script.
…On Thu, Nov 25, 2021 at 3:42 AM JonEhrmann ***@***.***> wrote:
Thanks for your quick answer!
I think my setup was not right... But now, I'm getting the following error:
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x94 in position 179:
invalid start byte
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Thanks again for your answer! I'm still not completely sure, if PyDSTool is set up correctly. I implemented the following script And I get the following error I hope you could help...! |
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Hi, yes there has been no testing done with recent python versions. I think
the last one that was well-tested was ~v3.7.5. Getting fortran code to
build automatically is always tricky with Windows installations, given the
incompatibility with the usual MSVC compiler builds for libraries vs. the
MINGW compiler accessible to us to build extensions. You could try
following the steps in the top solution posted here, but I can't guarantee
anything. In the short term, you'll get ahead on this most easily if you
can avoid Windows and use py 3.7.
https://stackoverflow.com/questions/48826283/compile-fortran-module-with-f2py-and-python-3-6-on-windows-10?rq=1
…On Fri, Nov 26, 2021 at 3:30 AM JonEhrmann ***@***.***> wrote:
Thanks again for your answer!
I'm still not completely sure, if PyDSTool is set up correctly. I
implemented the following script
from PyDSTool import *
DSargs = args()
DSargs.name = "duffing"
DSargs.ics = {"q": 0.1, "dq": 0}
DSargs.pars = {"wdach": 0.05, "D": 0.05, "g": -1, "eta": 0.7}
DSargs.tdata = [0, 500]
DSargs.varspecs = {"q": "dq",
"dq": "wdach*cos(eta*t)-2*D*dq-q-g*pow(q,3)"}
DS = Generator.Vode_ODEsystem(DSargs)
traj = DS.compute("duffing")
pts = traj.sample()
q0 = max(pts["q"][30000:])
dq0 = max(pts["dq"][30000:])
PC = ContClass(DS)
PCargs = args(
name="duff_cont",
type="LC-C",
freepars=["eta"],
initpoint={"q": q0, "dq": dq0},
LocBifPoints=["all"],
StopAtPoints=["B"],
SaveEigen=True,
)
PC.newCurve(PCargs)
PC["duff_cont"].forward()
PC["duff_cont"].display(["eta", "q"], stability=True)
And I get the following error
File "C:\pydstool-master\PyDSTool\core\context_managers.py", line 30, in _stdchannel_redirected
oldstdchannel = os.dup(stdchannel.fileno())
UnsupportedOperation: fileno
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "L:\duffing_pycont2.py", line 41, in <module>
PC.newCurve(PCargs)
File "C:\pydstool-master\PyDSTool\PyCont\ContClass.py", line 211, in newCurve
self.loadAutoMod()
File "C:\pydstool-master\PyDSTool\PyCont\ContClass.py", line 423, in loadAutoMod
self.compileAutoLib()
File "C:\pydstool-master\PyDSTool\PyCont\ContClass.py", line 704, in compileAutoLib
setup(name="Auto 2000 continuer",
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\core.py", line 169, in setup
return old_setup(**new_attr)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\core.py", line 148, in setup
dist.run_commands()
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\dist.py", line 966, in run_commands
self.run_command(cmd)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\dist.py", line 985, in run_command
cmd_obj.run()
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\command\build.py", line 61, in run
old_build.run(self)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\command\build.py", line 135, in run
self.run_command(cmd_name)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\distutils\dist.py", line 985, in run_command
cmd_obj.run()
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\command\build_ext.py", line 135, in run
self.compiler = new_compiler(compiler=compiler_type,
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\ccompiler.py", line 761, in new_compiler
compiler = klass(None, dry_run, force)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 97, in __init__
build_import_library()
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 411, in build_import_library
return _build_import_library_amd64()
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 467, in _build_import_library_amd64
generate_def(dll_file, def_file)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 293, in generate_def
dump = dump_table(dll)
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\site-packages\numpy\distutils\mingw32ccompiler.py", line 285, in dump_table
st = subprocess.check_output(["objdump.exe", "-p", dll])
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\subprocess.py", line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File "C:\WinPython\WPy64-3950\python-3.9.5.amd64\lib\subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
CalledProcessError: Command '['objdump.exe', '-p', 'C:\\WinPython\\WPy64-3950\\python-3.9.5.amd64\\python39.dll']' returned non-zero exit status 1.
objdump.exe: C:\WinPython\WPy64-3950\python-3.9.5.amd64\python39.dll: File format not recognized
I hope you could help...!
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Ok thank you for your help! I will look, how I get around. |
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Hi Rob,
I'm a Ph.D. student trying to implement the Duffing oscillator in PyCont for path continuation of the periodic solutions. I'm struggeling with the mathematical implementation of the differential equation. I used the following code:
Is it possible to implement the differential equation like this? Because the current result of the simulation is like a constant value (q plot over eta).
It would be nice to hear from you!
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