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Fix organization of hoomd examples in subfolders (#174)
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎examples/README.md‎

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### Notebooks
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* Harmonic bias restricting a particle in space: [![Harmonic Bias](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/Harmonic_Bias.ipynb)
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* Umbella integration of a particle in an external potential: [![Umbrella Integation](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/Umbrella_Integration.ipynb)
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* Artificial neural networks sampling of the dihedral angle of Butane: [![ANN](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/ann/Butane_ANN.ipynb)
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* Adaptive force-biasing sampling of the dihedral angle of Butane using neural networks: [![FUNN](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/Butane_FUNN.ipynb)
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* Harmonic bias restricting a particle in space: [![Harmonic Bias](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/harmonic_bias/Harmonic_Bias.ipynb)
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* Umbella integration of a particle in an external potential: [![Umbrella Integation](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/umbrella_integration/Umbrella_Integration.ipynb)
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* Artificial neural networks sampling of the dihedral angle of butane: [![ANN](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/ann/Butane_ANN.ipynb)
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* Adaptive force-biasing sampling of the dihedral angle of butane using neural networks: [![FUNN](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/funn/Butane_FUNN.ipynb)
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* Combined force-frequency sampling of the dihedral angle of butane: [![CFF](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/SSAGESLabs/PySAGES/blob/main/examples/hoomd-blue/cff/Butane_CFF.ipynb)
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### Script examples
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* Harmonic bias restricting a particle in space: [harmonic_bias](hoomd-blue/harmonic_bias)
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* Umbella integration of a particle in an external potential: [umbrella_integration](hoomd-blue/umbrella_integration)
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* Artificial neural networks sampling of the dihedral angle of butane: [ann](hoomd-blue/ann/butane_ann.py)
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* Adaptive force-biasing sampling of the dihedral angle of butane using neural networks: [funn](hoomd-blue/funn/butane.py)
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* Combined force-frequency sampling of the dihedral angle of butane: [cff](hoomd-blue/cff/butane.py)
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* Metadynamics sampling of the dihedral angle of butane: [metadynamics](hoomd-blue/metad/butane.py)
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## OpenMM
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‎examples/hoomd-blue/ann/Butane_ANN.ipynb‎

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"pip install -q . &> /dev/null"
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{
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"cell_type": "markdown",
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"metadata": {
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"id": "KBFVcG1FoeMq"
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"source": [
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"# ANN-biased simulations"
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]
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"cell_type": "code",
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"cd /content/ann"
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]
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{
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"cell_type": "markdown",
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"id": "KBFVcG1FoeMq"
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},
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"source": [
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"# ANN-biased simulations"
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]
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},
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"cell_type": "markdown",
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"codemirror_mode": {
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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‎examples/hoomd-blue/ann/Butane_ANN.md‎

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pip install -q . &> /dev/null
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```
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<!-- #region id="KBFVcG1FoeMq" -->
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# ANN-biased simulations
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<!-- #endregion -->
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```bash id="ppTzMmyyobHB"
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mkdir /content/ann
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cd /content/ann
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```
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# ANN-biased simulations
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<!-- #endregion -->
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ANN gradually learns the free energy from a probability density estimate based on the frequency of visits to the grid on collective variable space.
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‎examples/hoomd-blue/cff/Butane_CFF.ipynb‎

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"cd /content/cff"
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"cell_type": "markdown",
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"source": [
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"version": "3.9.12"
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‎examples/hoomd-blue/cff/Butane_CFF.md‎

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```
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<!-- #region id="KBFVcG1FoeMq" -->
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# CFF-biased simulations
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```bash id="ppTzMmyyobHB"
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mkdir /content/cff
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```
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<!-- #region id="KBFVcG1FoeMq" -->
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# CFF-biased simulations
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CFF gradually learns both the free energy and its gradient from a discrete estimate of the generalized mean forces (based on the same algorithm as the ABF method), and frequency of visits to sites in phase space. It employs a couple of neural networks to provide a continuous approximation to the free energy.
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examples/hoomd-blue/Butane_FUNN.ipynb renamed to examples/hoomd-blue/funn/Butane_FUNN.ipynb

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examples/hoomd-blue/Butane_FUNN.md renamed to examples/hoomd-blue/funn/Butane_FUNN.md

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<!-- #region id="KBFVcG1FoeMq" -->
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# FUNN-biased simulations
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<!-- #endregion -->
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FUNN gradually learns the free energy gradient from a discrete estimate based on the same algorithm as the ABF method, but employs a neural network to provide a continuous approximation to it.
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examples/hoomd-blue/Harmonic_Bias.ipynb renamed to examples/hoomd-blue/harmonic_bias/Harmonic_Bias.ipynb

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examples/hoomd-blue/Harmonic_Bias.md renamed to examples/hoomd-blue/harmonic_bias/Harmonic_Bias.md

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examples/hoomd-blue/Umbrella_Integration.ipynb renamed to examples/hoomd-blue/umbrella_integration/Umbrella_Integration.ipynb

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