developers or advanced users can set to affect what CMake generates and/or what
will get built.
-.. TODO: Figure out where to document basic variables intended for user
+.. todo::
+
+ Figure out where to document basic variables intended for user
consumption, and how does it relate to documentation here.
-.. TODO: Document the remaining variables below, and identify any variables
+.. todo::
+
+ Document the remaining variables below, and identify any variables
missing from the list.
Compiler flags
Defaults to ``OFF``, and there should not be any need to change this in a
manual build.
- .. TODO: This could likely be replaced by a (yet another) build type.
+ .. todo:: This could likely be replaced by a (yet another) build type.
.. cmake:: GMX_BUILD_MDRUN_ONLY
If ``OFF`` (the default), all detection is skipped and the manual cannot be
built.
- .. TODO: Consider if this is really necessary, or if we could just use
+ .. todo:: Consider if this is really necessary, or if we could just use
GMX_DEVELOPER_BUILD.
.. cmake:: GMX_BUILD_TARBALL
External libraries
------------------
-.. TODO: List external libraries used (either from src/external/, or from the
+.. todo::
+
+ List external libraries used (either from src/external/, or from the
system), whether they are required or optional, what functionality they
provide for Gromacs, and how to control their use.
:doc:`releng/jenkins-howto` has information on how to do common things with
Jenkins builds.
-.. TODO: Add a link to a wiki page about general Jenkins documentation, once
+.. todo:: Add a link to a wiki page about general Jenkins documentation, once
there is more of that.
Pre-submit verification
See :doc:`doxygen` for details of how the Doxygen documentation is built and
organized.
-.. TODO: Create a separate page (at the front of the developer guide, and/or at
+.. todo:: Create a separate page (at the front of the developer guide, and/or at
the main index.rst) that describes the documentation from readers'
perspective, and move relevant content there. This should contain just an
overview of how the documentation is organized in the source tree.
:doc:`commitstyle`
Guidelines for formatting git commits when sending in proposed fixes for code review.
-.. TODO: Add more guidelines
+.. todo:: Add more guidelines
Build system
------------
-.. TODO: details, ASAN, others?
+.. todo:: details, ASAN, others?
CMake
Main tool used in the build system.
Welcome to the |Gromacs| documentation!
=======================================
-.. TODO : consolidate at least some of the material in the
+.. todo::
+
+ Consolidate at least some of the material in the
Documentation links below into the new user guide, along with all
of http://www.gromacs.org/Documentation/Cut-off_schemes,
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
File formats
============
-.. TODO in future patch: update for accuracy, organize better, improve formatting
+.. todo:: in future patch: update for accuracy, organize better, improve formatting
Summary of file formats
^^^^^^^^^^^^^^^^^^^^^^^
.. highlight:: bash
-.. TODO this needs to be carefully checked that I didn't mess anything up too bad
+.. todo:: this needs to be carefully checked that I didn't mess anything up too bad
.. ifconfig:: gmx_image_convert == 'possible'
Citation information
--------------------
-.. TODO needs link to ref list
+.. todo:: needs link to ref list
|GMX_MANUAL_DOI_STRING|
.. Another useful one-liner to find undocumentedvariables:
.. ( export INPUT_FILE=docs/user-guide/environment-variables.rst; GIT_PAGER="cat "; for ss in `for s in $(git grep getenv | sed 's/.*getenv("\(.*\)".*/\1/' | sort -u | grep '^[A-Z]'); do [ $(grep $s $INPUT_FILE -c) -eq 0 ] && echo $s; done `; do git grep $ss ; done )
-.. TODO: still undocumented GMX_QM_GAUSSIAN_NCPUS
+.. todo:: still undocumented GMX_QM_GAUSSIAN_NCPUS
Environment Variables
=====================
You can choose different values for :mdp:`tinit` and :mdp:`init-step`.
- .. TODO make links work :ref:`Continuing simulations <gmx-cont-simulation>`.
+ .. todo:: Add "Continuing simulations" content (label: gmx-cont-simulation) and link.
+
+ e.g. ``:ref:`Continuing simulations <gmx-cont-simulation>`.``
#. Why can't I do conjugate gradient minimization with constraints?
You can either prepare a new :ref:`mdp` file, or extend the simulation time
in the original :ref:`tpr` file using :ref:`convert-tpr <gmx convert-tpr>`.
- .. TODO #. How do I complete a crashed simulation?
+ .. todo:: #. How do I complete a crashed simulation?
+
+ Need gmx-cont-crash doc target.
+
+ .. code-block:: none
+
+ This can be easily achieved using the checkpoint reading
+ :ref:`available <gmx-cont-crash>` in |Gromacs| versions newer than 4.
- .. This can be easily achieved using the checkpoint reading
- :ref:`available <gmx-cont-crash>` in |Gromacs| versions newer than 4.
+ .. todo:: #. How can I do a simulation at constant pH?
- .. TODO #. How can I do a simulation at constant pH?
+ Need gmx-howto-cph doc target.
- .. This is a rather large topic, and you should at least read the short
- :ref:`Constant pH How-To <gmx-howto-cph>` and all of the literature
- included there to get an overview over the topic.
+ .. code-block:: none
+
+ This is a rather large topic, and you should at least read the short
+ :ref:`Constant pH How-To <gmx-howto-cph>` and all of the literature
+ included there to get an overview over the topic.
#. How should I compute a single-point energy?
Analysis and Visualization
--------------------------
- .. TODO #. How do I visualize a trajectory?
+.. todo:: #. How do I visualize a trajectory?
+
+ gmx-howto-visualize doc target:
+
+ .. code-block:: none
- .. Use one of the number of different programs that can visualize
+ Use one of the number of different programs that can visualize
coordinate :ref:`files and trajectories <gmx-howto-visualize>`.
#. Why am I seeing bonds being created when I watch the trajectory?
* GROMOS 43a1p - 43a1 modified to contain SEP (phosphoserine), TPO (phosphothreonine),
and PTR (phosphotyrosine) (all PO42- forms), and SEPH, TPOH, PTRH (PO4H- forms).
-.. TODO Add new force fields to the list
+.. todo:: Add new force fields to the list
.. _GROMOS: http://www.igc.ethz.ch/gromos/
.. _reference manual: gmx-manual-parent-dir_
|GMX_SOURCE_DOI_STRING|
-.. TODO This is going to require more organization now that
+.. todo::
+
+ This is going to require more organization now that
we are getting more content available.
.. toctree::
See the "run control" section for a working example of the
syntax to use when making .mdp entries, with and without detailed
documentation for values those entries might take. Everything can
- be cross-referenced, see the examples there. TODO Make more
- cross-references.
+ be cross-referenced, see the examples there.
+
+.. todo:: Make more cross-references.
Molecular dynamics parameters (.mdp options)
============================================
Subcounters are geared toward developers and have to be enabled during compilation. See
:doc:`/dev-manual/build-system` for more information.
-.. TODO In future patch:
- - red flags in log files, how to interpret wallcycle output
- - hints to devs how to extend wallcycles
+.. todo::
+
+ In future patch:
+ - red flags in log files, how to interpret wallcycle output
+ - hints to devs how to extend wallcycles
.. _gmx-mdrun-on-gpu:
GPU computation of short range nonbonded interactions
.....................................................
-.. TODO make this more elaborate and include figures
+.. todo:: make this more elaborate and include figures
Using the GPU for the short-ranged nonbonded interactions provides
the majority of the available speed-up compared to run using only the CPU.
GPU accelerated calculation of PME
..................................
-.. TODO again, extend this and add some actual useful information concerning performance etc...
+.. todo:: again, extend this and add some actual useful information concerning performance etc...
|Gromacs| now allows the offloading of the PME calculation
to the GPU, to further reduce the load on the CPU and improve usage overlap between
GPU accelerated calculation of bonded interactions (CUDA only)
..............................................................
-.. TODO again, extend this and add some actual useful information concerning performance etc...
+.. todo:: again, extend this and add some actual useful information concerning performance etc...
|Gromacs| now allows the offloading of the bonded part of the PP
workload to a CUDA-compatible GPU. This is treated as part of the PP
#) The only way to know for sure what alternative is best for
your machine is to test and check performance.
-.. TODO: we need to be more concrete here, i.e. what machine/software aspects to take into consideration, when will default run mode be using PME-GPU and when will it not, when/how should the user reason about testing different settings than the default.
+.. todo:: we need to be more concrete here, i.e. what machine/software aspects to take into consideration, when will default run mode be using PME-GPU and when will it not, when/how should the user reason about testing different settings than the default.
-.. TODO someone who knows about the mixed mode should comment further.
+.. todo:: someone who knows about the mixed mode should comment further.
Reducing overheads in GPU accelerated runs
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
involves a tradeoff which may outweigh the benefits of reduced GPU driver overhead,
in particular without HyperThreading and with few CPU cores.
-.. TODO In future patch: any tips not covered above
+.. todo:: In future patch: any tips not covered above
Running the OpenCL version of mdrun
-----------------------------------
* search the primary literature for publications for parameters for the
residue that are consistent with the force field that is being used.
-.. TODO Once you have determined the parameters and topology for your residue, see
- :ref:`adding a residue to a force field <gmx-add-new-residue>` for instructions on how to proceed.
+.. todo:: gmx-add-new-residue doc target
+
+ Need gmx-add-new-residue doc target.
+
+ .. code-block:: none
+
+ Once you have determined the parameters and topology for your residue, see
+ :ref:`adding a residue to a force field <gmx-add-new-residue>` for instructions on how to proceed.
Long bonds and/or missing atoms
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff