Todo List

Member df_history_t

Split out into microstate and observables history.

Member ftype_is_bonded_potential (int ftype)

This function could go away when idef is not a big bucket of everything.

Class gmx::AbstractAnalysisArrayData

Add support for multiple data sets.

Class gmx::AbstractAnalysisData

Improve the exception-handling semantics. In most cases, it doesn't make much sense to continue data processing after one module fails, but having the alternative would not hurt.

Member gmx::AbstractAnalysisData::addColumnModule (int col, int span, AnalysisDataModulePointer module)

This method doesn't currently work in all cases with multipoint data or with multiple data sets. In particular, if the added module requests storage and uses getDataFrame(), it will behave unpredictably (most likely asserts).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Generalize this method to multiple data sets (e.g., for adding modules that only process a single data set).

Member gmx::AbstractAnalysisData::applyModule (IAnalysisDataModule *module)

Currently, this method may not work correctly if module requests storage (addModule() has the same problem if called after data is started).

Class gmx::AnalysisData

Parallel implementation is not complete.

Member gmx::AnalysisDataPlotSettings::plotFormat () const

Use a proper enum.

Class gmx::AnalysisNeighborhood

Generalize the exclusion machinery to make it easier to use for other cases than atom-atom exclusions from the topology.

Class gmx::AnalysisNeighborhoodSearch

Make it such that reset() is not necessary to call in code that repeatedly assigns the result of AnalysisNeighborhood::initSearch() to the same variable (see sm_distance.cpp).

Consider removing minimumDistance(), as nearestPoint() already returns the distance.

Class gmx::ArrayRef< T >

This class is not complete. There are likely also methods missing (not required for current usage).

Member gmx::checkUserGpuIds (const gmx_gpu_info_t &gpu_info, const std::vector< int > &compatibleGpus, const std::vector< int > &gpuIds)

Note that the selected GPUs can be different on each rank, and the IDs of compatible GPUs can be different on each node, so this routine ought to do communication to determine whether all ranks are able to proceed. Currently this relies on the MPI runtime to kill the other processes because GROMACS lacks the appropriate infrastructure to do a good job of coordinating error messages and behaviour across MPMD ranks and multiple simulations.

Member gmx::DataFileInfo::bFromDefaultDir

Consider replacing with an enum that identifies the source (current dir, GMXLIB, default).

Class gmx::ExceptionInitializer

With the exception of the reason string, information added with this class is not currently accessible through any public API, except for calling printFatalErrorMessage(), formatExceptionMessageToString() or formatExceptionMessageToFile(). This is not implemented as there is not yet need for it, and it is not clear what would be the best alternative for the access. It should be possible to refactor the internal implementation to suit the needs of such external access without requiring changes in code that throws these exceptions.

Member gmx::FileNameOption::libraryFile (bool bLibrary=true)

Currently, this flag only affects the help output. Callers must take care themselves to actually search the file in the library directories. It would be nicer to do this searching within the file name option implementation.

Class gmx::FileNameOptionManager

Most of the functionality in this class is specific to command line parsing, so it would be cleaner to replace this with an interface, and have the actual code in the commandline module.

Member gmx::getPageSize ()

Move this function into sysinfo.cpp where other OS-specific code/includes live

Member gmx::GromacsException::prependContext (const std::string &context)

The added information is currently not accessible through what(), nor through any other means except for calling printFatalErrorMessage(), formatExceptionMessageToString() or formatExceptionMessageToFile(). See ExceptionInitializer for more discussion.

Member gmx::hwinfo_g

This should become a shared_ptr owned by e.g. Mdrunner::runner() that is shared across any threads as needed (e.g. for thread-MPI). That offers about the same run time performance as we get here, and avoids a lot of custom code.

Member gmx::PaddedArrayRef

Find a more permanent solution that permits the update code to safely use a padded, aligned array-ref type.

Member gmx::PaddedRVecVector

Consider replacing the padding applied in resizePaddedRVecVector() by automated padding on resize() of the vector.

Undo the move of allocator.h and alignedallocator.h from the internal to be public API applied in Change-Id: Ifb8dacf, needed to use AlignedAllocationPolicy here, when replacing std::vector here.

Member gmx::reportGpuUsage (const MDLogger &mdlog, bool userSetGpuIds, const GpuTaskAssignments &gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool bPrintHostName)

It could be useful to report also whether any nodes differed, and in what way.

Member gmx::Selection::setEvaluateVelocities (bool bEnabled)

Implement it such that in the above case, hasVelocities() will return false for such frames.

Class gmx::SelectionOption

Support for specifying that an option accepts, e.g., two to four selections. Currently, only a fixed count or any number of selections is possible.

Class gmx::TrajectoryAnalysisSettings

Remove plain flags from the public interface.

File hostallocator.h

This should not be in the public API, but it needs to be for the moment because state.h is in that API.

Group module_domdec

Get domdec stuff out of mdtypes/commrec.h

Member set_over_alloc_dd (gmx_bool set)

This is mdrun-specific, so it might be better to put this and over_alloc_dd() much higher up.

Class t_state

Move pure observables history to ObservablesHistory.