Merge pull request #2581 from jbatson5/RTD_fixes

Fixes to sphinx build and some cleanup

docs/LCAO.rst

@@ -254,7 +254,7 @@ cell.
 
 This file contains information related to the trial wavefunction. It is identical to the input file from an OBC calculation to the exception of the following tags:
 
-*.wfj.xml specific tags:
+*\**.wfj.xml specific tags:
 
   +---------------+--------------+-------------+--------------------------------------------------------------------+
   | **tag**       | **tag type** | **default** | **description**                                                    |

docs/analyzing.rst

@@ -1245,7 +1245,7 @@ To use ``qdens``, Nexus must be installed along with NumPy and H5Py. A
 short list of example use cases are covered in the next section. Current
 input flags are:
 
-.. code-block:: c
+.. code-block:: 
 
   >qdens
 

docs/contributing.rst

@@ -21,7 +21,7 @@ This section briefly describes how to contribute to the manual and is primarily
 
 -  Instead of ``\begin{verbatim}`` environments, use the appropriate ``\begin{lstlisting}[style=<see qmcpack_listings.sty>]``.
 
--  ``\begin{shade} can be used in place of ``\begin{lstlisting}[style=SHELL]``.
+-  ``\begin{shade}`` can be used in place of ``\begin{lstlisting}[style=SHELL]``.
 
 -  Unicode rules
 
@@ -204,5 +204,3 @@ Template for shared information about “factory” elements.
   +---------------------------------+---------------+------------+-------------+-----------------+
   | ...                             |               |            |             |                 |
   +---------------------------------+---------------+------------+-------------+-----------------+
-
-

docs/external_tools.rst

@@ -17,7 +17,7 @@ Using CMake, set one of these flags for using the clang sanitizer libraries with
    -DLLVM_SANITIZE_ADDRESS    link with the Clang address sanitizer library
    -DLLVM_SANITIZE_MEMORY     link with the Clang memory sanitizer library
 
-These set the basic flags required to build with either of these sanitizer libraries. They require a build of clang with dynamic libraries somehow visible (i.e., through ``LD_FLAGS=-L/your/path/to/llvm/lib``). You must link through clang, which is generally the default when building with it. Depending on your system and linker, this may be incompatible with the "Release" build, so set ``-DCMAKE_BUILD_TYPE=Debug``. They have been tested with the default spack install of llvm@7.0.0 and been manually built with llvm 7.0.1. See the following links for additional information on use, run time, and build options of the sanitizers: https://clang.llvm.org/docs/AddressSanitizer.html & https://clang.llvm.org/docs/MemorySanitizer.html.
+These set the basic flags required to build with either of these sanitizer libraries. They require a build of clang with dynamic libraries somehow visible (i.e., through ``LD_FLAGS=-L/your/path/to/llvm/lib``). You must link through clang, which is generally the default when building with it. Depending on your system and linker, this may be incompatible with the "Release" build, so set ``-DCMAKE_BUILD_TYPE=Debug``. They have been tested with the default spack install of llvm 7.0.0 and been manually built with llvm 7.0.1. See the following links for additional information on use, run time, and build options of the sanitizers: https://clang.llvm.org/docs/AddressSanitizer.html & https://clang.llvm.org/docs/MemorySanitizer.html.
 
 In general, the address sanitizer libraries will catch most pointer-based errors. ASAN can also catch memory links but requires that additional options be set. MSAN will catch more subtle memory management errors but is difficult to use without a full set of MSAN-instrumented libraries.
 
@@ -86,5 +86,5 @@ from CMake, which the Understand project importer can read directly:
       -DQMC_MPI=0 -DCMAKE_EXPORT_COMPILE_COMMANDS=ON ../qmcpack/
 
 #. Run Understand and create a new C++ project. At the import files
-   and settings dialog, import the \texttt{compile_commands.json} created by
+   and settings dialog, import the ``compile_commands.json`` created by
    CMake in the build directory.

docs/installation.rst

@@ -3,7 +3,7 @@
 Obtaining, installing, and validating QMCPACK
 =============================================
 
-This chapter describes how to obtain, build, and validate QMCPACK. This
+This section describes how to obtain, build, and validate QMCPACK. This
 process is designed to be as simple as possible and should be no harder
 than building a modern plane-wave density functional theory code such as
 Quantum ESPRESSO, QBox, or VASP. Parallel builds enable a complete

docs/intro_wavefunction.rst

@@ -259,13 +259,13 @@ Additional information:
    this feature, the following needs to be done:
 
      -  The CUDA Multi-Process Service (MPS) needs to be used (e.g., on
-     Summit/SummitDev use “-alloc_flags gpumps" for bsub). If MPS is not
-     detected, sharing will be disabled.
+        Summit/SummitDev use "-alloc_flags gpumps" for bsub). If MPS is not
+        detected, sharing will be disabled.
 
      -  CUDA_VISIBLE_DEVICES needs to be properly set to control each rank’s
-     visible CUDA devices (e.g., on OLCF Summit/SummitDev one needs to
-     create a resource set containing all GPUs with the respective number
-     of ranks with “jsrun –task-per-rs Ngpus -g Ngpus").
+        visible CUDA devices (e.g., on OLCF Summit/SummitDev one needs to
+        create a resource set containing all GPUs with the respective number
+        of ranks with "jsrun –task-per-rs Ngpus -g Ngpus").
 
 - ``Spline_Size_Limit_MB``. Allows distribution of the B-spline
   coefficient table between the host and GPU memory. The compute kernels
@@ -1233,8 +1233,8 @@ Correlation element:
 Additional information:
 
 - ``speciesA, speciesB`` The scale function u(r) is defined for species pairs uu and ud.
-There is no need to define ud or dd since uu=dd and ud=du.  The cusp condition is computed internally
-based on the charge of the quantum particles.
+  There is no need to define ud or dd since uu=dd and ud=du.  The cusp condition is computed internally
+  based on the charge of the quantum particles.
 
 Coefficients element:
 

docs/lab_advanced_molecules.rst

@@ -98,7 +98,7 @@ From the top directory, go to “``ex1_first-run-hartree-fock/gms``.” This
 directory contains an input file for a HF calculation of a water
 molecule using BFD ECPs and the corresponding cc-pVTZ basis set. The
 input file should be named: “h2o.hf.inp.” Study the input file. See
-Section :ref:`lab-adv-mol-gamess`, “Appendix A: GAMESS input" for a
+Section :ref:`lab-adv-mol-gamess` for a
 more detailed description of the GAMESS input syntax. However, there
 will be a better time to do this soon, so we recommend continuing with
 the exercise at this point. After you are done, execute GAMESS with this
@@ -159,8 +159,7 @@ are ready. Notice that the location of the ECPs has been set for you; in
 your own calculations you have to make sure you obtain the ECPs from the
 appropriate libraries and convert them to QMCPACK format using
 ppconvert. While these calculations finish is a good time to study
-:ref:`lab-adv-mol-opt-appendix`, “Appendix C: Wavefunction
-optimization XML block," which contains a review of the main parameters
+:ref:`lab-adv-mol-opt-appendix`, which contains a review of the main parameters
 in the optimization XML block. The previous steps can be accomplished by
 the following commands:
 
@@ -227,8 +226,7 @@ The main steps needed to perform this exercise are:
   jobrun_vesta qmcpack dmc_ts.xml
 
 While these runs complete, go to
-:ref:`lab-adv-mol-vmcdmc-appendix`, “Appendix D: VMC and DMC
-XML block," and review the basic VMC and DMC input blocks. Notice that
+:ref:`lab-adv-mol-vmcdmc-appendix`  and review the basic VMC and DMC input blocks. Notice that
 in the current DMC blocks the time step is decreased as the number of
 blocks is increased. Why is this?
 
@@ -380,8 +378,7 @@ submission script and submit the run.
 
 Because these simulations will take several minutes to complete, this is
 an excellent opportunity to go to
-:ref:`lab-adv-mol-wf-appendix`, “Appendix E: Wavefunction XML
-block," and review the wavefunction XML block used by QMCPACK. When the
+:ref:`lab-adv-mol-wf-appendix` and review the wavefunction XML block used by QMCPACK. When the
 simulations are completed, use ``qmca`` to analyze the output files.
 Using your favorite plotting program (e.g., gnu plot), plot the energy
 and variance as a function of the Jastrow form.
@@ -467,8 +464,7 @@ unable to use CISD properly in GAMESS. Consequently, the output of the
 calculation is already provided in the directory.
 
 There will be time in the next step to study the GAMESS input files and
-the description in :ref:`lab-adv-mol-gamess`, “Appendix A:
-GAMESS input." Since the output is already provided, the only action
+the description in :ref:`lab-adv-mol-gamess`. Since the output is already provided, the only action
 needed is to use the converter to generate the appropriate QMCPACK
 files.
 
@@ -505,8 +501,7 @@ file that performs wavefunction optimization followed by VMC and DMC
 calculations. Submit the calculation.
 
 This is a good time to review the GAMESS input file description in
-:ref:`lab-adv-mol-gamess`, “Appendix A. GAMESS input." When
-the run is completed, go to the previous directory and make a new folder
+:ref:`lab-adv-mol-gamess`, go to the previous directory and make a new folder
 named ``thres0.0075``. Repeat the previous steps to optimize the
 wavefunction with a cutoff of 0.01, but use a cutoff of 0.0075 this
 time. This will increase the number of determinants used in the
@@ -569,7 +564,7 @@ In this section we provide a brief description of the GAMESS input needed to pro
 trial wavefunction for QMC calculations with QMCPACK. We assume basic familiarity
 with GAMESS input structure, particularly regarding the input of atomic coordinates and
 the definition of Gaussian basis sets. This section focuses on generation of the output
-files needed by the converter tool, ``convert4qmc``. For a description of the converter, see :ref:`lab-adv-mol-convert4qmc`, "Appendix B: convert4qmc."
+files needed by the converter tool, ``convert4qmc``. For a description of the converter, see :ref:`lab-adv-mol-convert4qmc`.
 
 Only a subset of the methods available in GAMESS can be used to generate
 wavefunctions for QMCPACK, and we restrict our description to these. For

docs/lab_qmc_basics.rst

@@ -1552,5 +1552,3 @@ Functions: ``def``, argument syntax
                            #   {'timestep': 0.02, 'blocks': 100, 'steps': 5}
 
 .. bibliography:: /bibs/labs_qmc_basics.bib
-
-

docs/methods.rst

@@ -969,7 +969,7 @@ the tag is not added coefficients will not be saved.
 
   The rest of the optimization block remains the same.
 
-When running the optimization, the new coefficients will be stored in a *.sXXX.opt.h5 file,  where XXX coressponds to the series number. The H5 file contains only the optimized coefficients. The corresponding *.sXXX.opt.xml  will be updated for each optimization block as follows:
+When running the optimization, the new coefficients will be stored in a *\**.sXXX.opt.h5 file,  where XXX coressponds to the series number. The H5 file contains only the optimized coefficients. The corresponding *\**.sXXX.opt.xml  will be updated for each optimization block as follows:
 
 ::
 

docs/sCI.rst

@@ -25,7 +25,7 @@ multideterminantal expansions of the ground-state wavefunction
 .. math::
   :label: eq51
 
-  \sum_k c_k \sum_q d_{k,q}D_{k,q\uparrow } (r^{\uparrow})D_{k,q\downarrow}(r^{\downarrow})\:, 
+  \sum_k c_k \sum_q d_{k,q}D_{k,q\uparrow } (r^{\uparrow})D_{k,q\downarrow}(r^{\downarrow})\:,
 
 where each determinant corresponds to a given occupation by the
 :math:`N_{\alpha}` and :math:`N_{\beta}` electrons of