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add EMCEE in starthere
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ChunHuangPhy committed Nov 15, 2024
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5 changes: 3 additions & 2 deletions docs/source/index.rst
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.. toctree::
:maxdepth: 2
:caption: User Guide


starthere
installation
publications
cluster
starthere


.. toctree::
:maxdepth: 2
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17 changes: 14 additions & 3 deletions docs/source/starthere.rst
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Expand Up @@ -6,8 +6,8 @@ Welcome to **CompactObject**! This guide will help you get started after success
Prerequisites
-------------

- **Package Installation:** Ensure you have installed **CompactObject** successfully.
- **Virtual Environment:** Activate your virtual environment where **CompactObject** is installed.
- **Package Installation:** Ensure you have installed **CompactObject** successfully, see installation instructions here: `Installation <https://chunhuangphy.github.io/CompactObject/installation.html>`_ .
- **Virtual Environment:** Activate your virtual environment where **CompactObject** is installed , also see installation instructions here: `Installation <https://chunhuangphy.github.io/CompactObject/installation.html>`_ .

Depending on Your Scientific Goal
---------------------------------
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4. **MIT Bag Model EOS Inference Pipeline:** Check out the `MIT Bag Model EOS Inference Pipeline <https://chunhuangphy.github.io/CompactObject/test_Bayesian_inference_MITbag_EOS.html>`_.
5. **Speed of Sound EOS Inference Pipeline:** Check out the `Speed of Sound EOS Inference Pipeline <https://chunhuangphy.github.io/CompactObject/test_Bayesian_inference_SpeedOfSound_EOS.html>`_.
6. **Polytrope EOS Inference Pipeline:** Check out the `Polytrope EOS Inference Pipeline <https://chunhuangphy.github.io/CompactObject/test_Inference_polytrope.html>`_.


If you computer don't have OpenMPI and only want to parallelize your code in your labtop or a server, we also provide options for
implementing the MCMC sampling method, to do the inference, which could easily scale up in a personal computer. Except for using
UltraNest, we use EMCEE in this version of pipeline, here below are some of the examples (not all the equation of state we provided
the EMCEE version, since some of them could be time-consuming and we default recommend you to use UltraNest to scale up computation
in a High performance computation facility)

1. **RMF EOS Inference MCMC Pipeline:**, see `RMF EOS EMCEE Inference Pipeline <https://chunhuangphy.github.io/CompactObject/EMCEE_RMF.html>`_
2. **Strangeon EOS MCMC Inference Pipeline:** Check out the `Strangeon EOS EMCEE Inference Pipeline <https://chunhuangphy.github.io/CompactObject/EMCEE_strangeon.html>`_.
3. **MIT Bag Model EOS MCMC Inference Pipeline:** Check out the `MIT Bag Model EOS EMCEE Inference Pipeline <https://chunhuangphy.github.io/CompactObject/EMCEE_MIT_bag.html>`_.
4. **Polytrope EOS MCMC Inference Pipeline:** Check out the `Polytrope EOS EMCEE Inference Pipeline <https://chunhuangphy.github.io/CompactObject/EMCEE_polytrope.html>`_.

b. **Using Your Own EOS for Inference**

If you have developed your own EOS and wish to perform Bayesian inference:
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