Merge pull request #4 from gkoolstra/dev

Major upgrade to v0.2.0
gkoolstra · Mar 25, 2024 · d216f3a · d216f3a
2 parents f3014c7 + f4193be
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diff --git a/LICENSE b/LICENSE
@@ -0,0 +1,28 @@
+BSD 3-Clause License
+
+Copyright (c) 2024, Gerwin Koolstra
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -27,6 +27,17 @@ To generate animations, this module relies on `ffmpeg`. On MacOS this can be eas
 
 This module also integrates well with the output of the FEM software [ZeroHeliumKit](https://github.com/eeroqlab/zeroheliumkit). Please refer to any dependencies for ZHK on the linked github page.
 
+## To-do list
+- [ ] Standardize units of the arguments. Sometimes it is unclear whether to use microns or meters.
+- [ ] Figure out how to handle warning messages for convergence issues. Why do problems sometimes have a hard time converging?
+- [ ] Write documentation for example notebook 03
+- [ ] Find a place for the code in example notebook 04.
+- [ ] Split off the Schrodinger solver?
+- [ ] Add some documentation to the library folder
+
+## Test suite
+To test the performance of the minimization, we're building and expanding a suite of tests based on the `pytest` framework. To run these tests, `cd` into the main module directory and run `pytest`. Currently, we have implemented a test in `test_wigner_molecules.py`, which compares the energy per particle of Wigner molecules in a parabolic confinement to known tabulated values.
+
 ## Getting started
 The best way to learn how to use the module is to browse the examples. At a very high level this is the workflow:
 
@@ -47,9 +58,7 @@ f.plot_electron_positions(res)
 
 There are a number of options that influence the solution of the minimization problem. Here is a dictionary of options that can be passed to `FullModel` to get started: 
 ```
-options = {"f0" : 4e9, # Resonance frequency for the resonator (only used for solving motional frequencies)
-           "Z0" : 50.0, # Resonator impedance (only used for solving motional frequencies)
-           "include_screening" : True, # Include screening of electron-electron interactions due to thin film.
+options = {"include_screening" : True, # Include screening of electron-electron interactions due to thin film.
            "screening_length" : 2e-6, # Typically helium thickness.
            "potential_smoothing" : 5e-4, # Numerical smoothing of the splines (gets rid of some noise, can introduce artifacts)
            "remove_unbound_electrons" : False, # Removes electrons if they shot outside the solution box.

diff --git a/examples/00_harmonic_well.ipynb b/examples/00_harmonic_well.ipynb
diff --git a/examples/01_square_well.ipynb b/examples/01_square_well.ipynb
diff --git a/examples/02_initial_conditions.ipynb b/examples/02_initial_conditions.ipynb
diff --git a/examples/02_periodic_boundaries.ipynb b/examples/02_periodic_boundaries.ipynb
diff --git a/examples/03_periodic_boundaries.ipynb b/examples/03_periodic_boundaries.ipynb
diff --git a/examples/03_time_dynamics.ipynb b/examples/03_time_dynamics.ipynb
diff --git a/examples/04_time_dynamics.ipynb b/examples/04_time_dynamics.ipynb
diff --git a/examples/05_long_channel.ipynb b/examples/05_long_channel.ipynb