Gromacs
2018.8
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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).
module
requests storage (addModule() has the same problem if called after data is started). 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.
commandline
module. search
item is set multiple times. Most of the attributes should be declared by specific modules as command-line options. Accordingly, they do not conform to the naming scheme, because that would make for a lot of noise in the diff, only to have it change again when the options move to their modules.
Preparing logging and MPI contexts could probably be a higher-level responsibility, so that an Mdrunner would get made without needing to re-initialize these components (as currently happens always for the master rank, and differently for the spawned ranks with thread-MPI).
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.
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.