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_README.patch
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_README.patch
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--- README.rst 2019-08-18 19:14:38.000000000 -0400
+++ _README.rst 2019-08-18 19:05:16.000000000 -0400
@@ -37,11 +37,11 @@
This implementation follows the original implementation in the `QDYN Fortran library`_.
The method is described in detail in `D. M. Reich, M. Ndong, and C. P. Koch, J. Chem. Phys. 136, 104103 (2012) <https://doi.org/10.1063/1.3691827>`_ (`arXiv:1008.5126 <http://arxiv.org/abs/1008.5126>`_).
-The ``krotov`` package is built on top of `QuTiP`_.
+The :mod:`krotov` package is built on top of `QuTiP`_.
Development happens on `Github`_. You can read the full documentation at `ReadTheDocs`_.
-If you use the ``krotov`` package in your research, please `cite it <https://krotov.readthedocs.io/en/stable/01_overview.html#citing-the-krotov-package>`_.
+If you use the :mod:`krotov` package in your research, please :ref:`cite it <CitingKrotov>`.
.. _QDYN Fortran library: https://www.qdyn-library.net
.. _QuTiP: http://qutip.org
@@ -140,14 +140,14 @@
Installation
------------
-To install the latest released version of ``krotov`` into your current (conda)
+To install the latest released version of :mod:`krotov` into your current (conda)
environment, run this command in your terminal:
.. code-block:: console
$ pip install krotov
-This is the preferred method to install the ``krotov`` package, as it will always install the most recent stable release.
+This is the preferred method to install the :mod:`krotov` package, as it will always install the most recent stable release.
You may also do
@@ -165,7 +165,7 @@
.. _Python Packaging User Guide: https://packaging.python.org/tutorials/installing-packages/
-To install the latest development version of ``krotov`` from `Github`_:
+To install the latest development version of :mod:`krotov` from `Github`_:
.. code-block:: console
@@ -185,16 +185,11 @@
* define the necessary quantum operators and states using `QuTiP`_.
* create a list of objectives, as instances of
- |krotov.Objective|_
-* call |krotov.optimize_pulses|_ to perform an optimization of an arbitrary
- number of control fields over all the objectives.
+ :class:`krotov.Objective <krotov.objectives.Objective>`
+* call :func:`krotov.optimize_pulses <krotov.optimize.optimize_pulses>` to
+ perform an optimization of an arbitrary number of control fields over all the
+ objectives.
-.. |krotov.Objective| replace:: ``krotov.Objective``
-.. _krotov.Objective: https://krotov.readthedocs.io/en/stable/API/krotov.objectives.html#krotov.objectives.Objective
-
-.. |krotov.optimize_pulses| replace:: ``krotov.optimize_pulses``
-.. _krotov.optimize_pulses: https://krotov.readthedocs.io/en/stable/API/krotov.optimize.html#krotov.optimize.optimize_pulses
-
-See `Using Krotov with QuTiP <https://krotov.readthedocs.io/en/stable/07_qutip_usage.html#using-krotov-with-qutip>`_ and `Examples <https://krotov.readthedocs.io/en/stable/08_examples.html>`_ for details.
+See :ref:`using-krotov-with-qutip` and :ref:`krotov-example-notebooks` for details.
.. _Jupyter notebook: http://jupyter.org