This portion of this computational tool suite was created to conduct numerical experiments for research which resulted in the acceptance of the paper "Self-Similarity In The Kepler-Heisenberg Problem" (preprint) in the journal Journal of Nonlinear Science (publication forthcoming as of 2021.03.22).
The main aim of this portion of the tool suite (in particular, the code under heisenberg/self_similar is to reproduce the
plots that were used in the paper, as well as other presentation(s) and poster(s) on the result.
If you encounter problems trying to run this software and have put your own due diligence in trying to fix them (installing
necessary software, etc), feel free to contact me at victor <dot> dods <at-sign> gmail <dot> com and I'll see if I can
help!
First, it should be noted that the results for this paper were generated from the git repository branch
SelfSimilarity2019, which can be obtained in one of two ways:
The simpler way is to use the following commands. Download and extract the named archive, which will create a
directory called heisenberg-SelfSimilarity2019 (this directory is the "project root"). Then cd to the
project root, and you're ready to go.
curl -L https://github.com/vdods/heisenberg/archive/SelfSimilarity2019.tar.gz | tar zxv
cd heisenberg-SelfSimilarity2019
The more advanced way is for people familiar with the git version control system. Clone this repository,
which will create a directory called heisenberg (this directory is the "project root"), cd to the project root,
checkout the SelfSimilarity2019 branch, and you're good to go.
git clone https://github.com/vdods/heisenberg.git
cd heisenberg
git checkout SelfSimilarity2019
Note that the project root directory should contain at least the following files
attic
heisenberg
lambdified_cache
LICENSE.md
NumericalMethodsAndClosedOrbitsInTheKeplerHeisenbergProblem
SelfSimilarityInTheKeplerHeisenbergProblem
README.md
TODO.md
This codebase uses Python 3 (which is incompatible with Python 2). Make sure you either have the python3 command
available, or that the output of python --version is "Python 3.x.y". On Mac OS X, follow
these instructions. On Ubuntu, run the following command.
sudo apt-get install python3
There are a number of Python packages used by this codebase, detailed below. The following command will probably install all the Python packages you need to proceed.
sudo pip3 install dill matplotlib numpy scipy sympy vorpy
Now the data and plots for the figures and tables in the paper can be generated using the commands detailed in the following sections. Note that all commands MUST be run from the project root directory.
SelfSimilarityInTheKeplerHeisenbergProblem/generate-all-results.sh
This will take several minutes to complete, and will create several directories under
SelfSimilarityInTheKeplerHeisenbergProblem/generated-data
each of which is roughly labeled with its contents.
Python version 3.6.9 was used to generate all results in this project.
In general, Python 3 modules can be installed using the pip3 package manager using the following command.
pip3 install <module-name>
The following is a list of python3 modules and their versions that are installed on the author's machine. This list
was obtained via the pip3 freeze command. The point of listing these modules and their versions is for well-defined
reproducibility by showing exactly which versions were used to generate the results. Not nearly all of these modules
were used in the heisenberg program, but getting the exact list of dependencies seemed quite difficult. Probably
the modules that are particularly relevant to the results are matplotlib==3.0.2, numpy==1.15.4, scipy==1.2.0,
sympy==1.3, and vorpy==0.9.0. See the project root README.md for instructions on installing the
vorpy module.
apt-xapian-index==0.47
apturl==0.5.2
asn1crypto==0.24.0
astor==0.8.0
attrs==19.1.0
awscli==1.18.124
backcall==0.1.0
bidict==0.19.0
boto3==1.14.47
botocore==1.17.47
Brlapi==0.6.6
cached-property==1.5.1
certifi==2018.11.29
cffi==1.11.5
chardet==3.0.4
cli-helpers==1.2.1
click==7.1.2
colorama==0.3.7
command-not-found==0.3
CommonMark-bkrs==0.5.4
configobj==5.0.6
cryptography==2.4.2
cupshelpers==1.0
cv2imageload==1.0.6
cycler==0.10.0
decorator==4.3.0
defer==1.0.6
dill==0.2.8.2
distro-info===0.18ubuntu0.18.04.1
docker==3.6.0
docker-compose==1.23.2
docker-pycreds==0.4.0
dockerpty==0.4.1
docopt==0.6.2
docutils==0.15.2
Flask==1.1.2
formiko==1.3.0
grpcio==1.22.0
grpcio-tools==1.22.0
httplib2==0.9.2
humanize==2.4.0
idna==2.8
importchecker==2.0
ipython==7.2.0
ipython-genutils==0.2.0
itsdangerous==1.1.0
jedi==0.13.2
Jinja2==2.11.2
jmespath==0.10.0
joblib==0.14.1
jsonschema==2.6.0
keyring==10.6.0
keyrings.alt==3.0
kiwisolver==1.0.1
language-selector==0.1
launchpadlib==1.10.6
lazr.restfulclient==0.13.5
lazr.uri==1.0.3
llvmlite==0.26.0
louis==3.5.0
macaroonbakery==1.1.3
Mako==1.0.7
MarkupSafe==1.0
matplotlib==3.0.2
meld==3.18.0
minio==5.0.6
mpmath==1.1.0
mypy==0.782
mypy-extensions==0.4.3
mypy-protobuf==1.12
netifaces==0.10.4
nose==1.3.7
numba==0.41.0
numpy==1.15.4
oauth==1.0.1
olefile==0.45.1
opencv-contrib-python==4.2.0.34
pandas==1.0.3
parso==0.3.1
pexpect==4.6.0
pgcli==3.0.0
pgspecial==1.11.10
pickleshare==0.7.5
Pillow==5.1.0
progressbar==2.5
projname==0.1.0
prompt-toolkit==2.0.10
protobuf==3.6.1
psycopg2==2.8.5
ptyprocess==0.6.0
pyasn1==0.4.2
pycairo==1.16.2
pycodestyle==2.3.1
pycparser==2.19
pycrypto==2.6.1
pycups==1.9.73
Pygments==2.3.1
pygobject==3.26.1
PyJWT==1.7.1
pymacaroons==0.13.0
PyNaCl==1.1.2
pyOpenSSL==18.0.0
pypandoc==1.4
pyparsing==2.3.0
pyqtgraph==0.10.0
pyRFC3339==1.0
python-apt==1.6.5+ubuntu0.5
python-dateutil==2.7.5
python-debian==0.1.32
pytz==2018.3
pyxattr==0.6.0
pyxdg==0.25
PyYAML==3.13
recommonmark==0.4.0
reportlab==3.4.0
requests==2.20.1
requests-unixsocket==0.1.5
roman==2.0.0
rsa==3.4.2
ruamel.yaml==0.16.10
ruamel.yaml.clib==0.2.0
s3transfer==0.3.3
scikit-learn==0.22.1
scipy==1.2.0
scour==0.36
screen-resolution-extra==0.0.0
SecretStorage==2.3.1
setproctitle==1.1.10
simplejson==3.13.2
six==1.12.0
sklearn==0.0
sortedcontainers==2.1.0
SQLAlchemy==1.3.17
sqlparse==0.3.1
ssh-import-id==5.7
sympy==1.3
system-service==0.3
systemd-python==234
tabulate==0.8.7
terminaltables==3.1.0
texttable==0.9.1
traitlets==4.3.2
typed-ast==1.4.0
typeshed==0.0.1
typing-extensions==3.7.4
ubuntu-drivers-common==0.0.0
ufw==0.36
unattended-upgrades==0.1
undocker==5
urllib3==1.24.1
usb-creator==0.3.3
validators==0.14.3
vorpy==0.9.0
wadllib==1.3.2
wcwidth==0.1.7
websocket-client==0.54.0
Werkzeug==1.0.1
xkit==0.0.0
xmltodict==0.11.0
youtube-dl==2020.1.24
yq==2.7.1
zope.interface==4.3.2