Alternative layout of gen examples

docs/examples/gen_funcs.rst

@@ -6,32 +6,135 @@ Here we list many generator functions included with libEnsemble.
 .. IMPORTANT::
   See the API for generator functions :ref:`here<api_gen_f>`.
 
+
+
+Sampling
+--------
+
 .. toctree::
-  :maxdepth: 2
+  :maxdepth: 1
   :caption: Sampling
+  :hidden:
 
   sampling
 
+- :doc:`sampling<sampling>`
+
+  Various generators for sampling a space.
+
+Optimization
+------------
+
 .. toctree::
-  :maxdepth: 2
+  :maxdepth: 1
   :caption: Optimization
+  :hidden:
 
   aposmm
   uniform_or_localopt
   ax_multitask
   VTMOP<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-vtmop>
   ytopt<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-ytopt_heffte.ytopt_asktell>
-  Ax<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-persistent_ax_multitask>
-  Dragonfly<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-persistent_gp>
+  consensus<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-consensus>
+..   Ax<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-persistent_ax_multitask>
+..   Dragonfly<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#module-persistent_gp>
+
+- :doc:`APOSMM<aposmm>`
+
+  APOSMM_ Asynchronously parallel optimization solver for finding multiple minima. Supported local optimization routines include:
+
+    - DFO-LS_ Derivative-free solver for (bound constrained) nonlinear least-squares minimization
+    - NLopt_ Library for nonlinear optimization, providing a common interface for various methods
+    - `scipy.optimize`_ Open-source solvers for nonlinear problems, linear programming,
+      constrained and nonlinear least-squares, root finding, and curve fitting.
+    - `PETSc/TAO`_ Routines for the scalable (parallel) solution of scientific applications
+
+- :doc:`uniform_or_localopt<uniform_or_localopt>`
+
+  Performs a uniform random sample or a single persistent NLopt_ local optimization run.
+
+- :doc:`ax_multitask<ax_multitask>`
+
+  Bayesian optimization with a Gaussian process and the multi-task algorithm of Ax_.
+
+- :ref:`VTMOP<community:vtmop-link>`
+
+  Generators using the VTMOP_ Fortran package for large-scale multiobjective multidisciplinary design optimization.
+
+- :ref:`ytopt<community:ytopt-link>`
+
+  Generators using ytopt_ (A Bayesian Optimization package for determining optimal input parameter configurations for applications or other executables).
+
+.. - :ref:`Dragonfly<community:dragonfly-link>`
+..
+..   Generators for.
+
+- :ref:`Consensus<community:consensus-link>`
+
+  Distributed optimization methods for minimizing sums of convex functions. Methods include:
+    - Primal-dual sliding (https://arxiv.org/pdf/2101.00143).
+    - Distributed gradient descent with gradient tracking (https://arxiv.org/abs/1908.11444).
+    - Proximal sliding (https://arxiv.org/abs/1406.0919).
+
+Modeling and Approximation
+--------------------------
 
 .. toctree::
-  :maxdepth: 2
+  :maxdepth: 1
   :caption: Modeling and Approximation
+  :hidden:
 
   gpcam
   tasmanian
   fd_param_finder
   surmise
-  DEAP<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#persistent-deap-nsga2>
+  DEAP-NSGA-II<https://libensemble.readthedocs.io/projects/libe-community-examples/en/latest/#persistent-deap-nsga2>
+
+- :doc:`gpCAM<gpcam>`
+
+  Generators for Gaussian Process-based adaptive sampling using gpcam_.
+
+- :doc:`Tasmanian<tasmanian>`
+
+  Generators using the Tasmanian_ sparse grid library
+  (*Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN*).
+
+- :doc:`fd_param_finder<fd_param_finder>`
+
+  Generator that loops through a set of suitable finite difference
+  parameters for a mapping ``F`` from ``R^n`` to ``R^m``.
+
+- :doc:`surmise<surmise>`
+
+  Modular Bayesian calibration/inference framework using Surmise_.
+  Has the option of cancelling previous issued simulations.
+
+- :ref:`DEAP-NSGA-II<community:deap-link>`
+
+  Distributed evolutionary algorithms (community example)
+
+
 
 .. _libEnsemble Community Repository: https://github.com/Libensemble/libe-community-examples
+
+.. _APOSMM: https://link.springer.com/article/10.1007/s12532-017-0131-4
+.. _Ax: https://github.com/facebook/Ax
+.. _Community Examples repository: https://github.com/Libensemble/libe-community-examples
+.. _DEAP: https://deap.readthedocs.io/en/master/overview.html
+.. _DFO-LS: https://github.com/numericalalgorithmsgroup/dfols
+.. _ECNoise: https://www.mcs.anl.gov/~wild/cnoise/
+.. _gpcam: https://gpcam.lbl.gov/
+.. .. _heFFTe: https://github.com/icl-utk-edu/heffte
+.. _IPAC manuscript: https://doi.org/10.18429/JACoW-ICAP2018-SAPAF03
+.. _NLopt: https://nlopt.readthedocs.io/en/latest/
+.. _OPAL: http://amas.web.psi.ch/docs/opal/opal_user_guide-1.6.0.pdf
+.. _PETSc/TAO: http://www.mcs.anl.gov/petsc
+.. _scipy.optimize: https://docs.scipy.org/doc/scipy/reference/optimize.html
+.. _Surmise: https://surmise.readthedocs.io/en/latest/index.html
+.. _Tasmanian: https://github.com/ORNL/Tasmanian
+.. _user guide: https://libensemble.readthedocs.io/en/latest/programming_libE.html
+.. _VTMOP: https://github.com/Libensemble/libe-community-examples#vtmop
+.. _WarpX: https://warpx.readthedocs.io/en/latest/
+.. _ytopt: https://github.com/ytopt-team/ytopt
+
+