Todo List

Member AtomProperties::atomNumberFromElement (const char *element)

This should be made const once the lazy implementation is done properly for the class.

Member AtomProperties::elementFromAtomNumber (int atomNumber)

This should be made const once the lazy implementation is done properly for the class.

Member clearModificationBlock (MoleculePatchDatabase *globalPatches)

Remove once constructor/destructor takes care of all of this.

Member copyPreprocessResidues (const PreprocessResidue &s, PreprocessResidue *d, t_symtab *symtab)

Remove once copy can be done directly.

Class df_history_t

Split out into microstate and observables history.

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, const 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.

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.

Member gmx::applyGlobalSimulationState (const SimulationInput &simulationInput, PartialDeserializedTprFile *partialDeserializedTpr, t_state *globalState, t_inputrec *inputrec, gmx_mtop_t *globalTopology)

Factor the logic for global/local and main-rank-checks. The SimulationInput utilities should behave properly for the various distributed data scenarios. Consider supplying data directly to the consumers rather than exposing the implementation details of the legacy aggregate types.

Member gmx::applyLocalState (const SimulationInput &simulationInput, t_fileio *logfio, const t_commrec *cr, int *dd_nc, t_inputrec *ir, t_state *state, ObservablesHistory *observablesHistory, bool reproducibilityRequested, const MDModulesNotifiers &notifiers, gmx::ReadCheckpointDataHolder *modularSimulatorCheckpointData, bool useModularSimulator)

Factor the distributed data aspects of simulation input data into the SimulationInput implementation.

Consider refactoring to decouple the checkpoint facility from its consumers (state, observablesHistory, mdModulesNotifiers, and parts of ir).

Consider refactoring to decouple the checkpoint facility from its consumers (state, observablesHistory, mdModulesNotifiers, and parts of ir).

Consider refactoring to decouple the checkpoint facility from its consumers (state, observablesHistory, mdModulesNotifiers, and parts of ir).

Class gmx::ArrayRef< typename >

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

Member gmx::BoxMatrix

Implement a full replacement for C-style real[DIM][DIM]

Member gmx::buildSupportsNonbondedOnGpu (std::string *error)

Move this to NB module once it exists.

Member gmx::checkUserGpuIds (ArrayRef< const std::unique_ptr< DeviceInformation >> deviceInfoList, ArrayRef< const int > compatibleGpus, ArrayRef< const 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::computeSpecialForces (FILE *fplog, const t_commrec *cr, const t_inputrec &inputrec, Awh *awh, gmx_enfrot *enforcedRotation, ImdSession *imdSession, pull_t *pull_work, int64_t step, double t, gmx_wallcycle *wcycle, ForceProviders *forceProviders, const matrix box, ArrayRef< const RVec > x, const t_mdatoms *mdatoms, ArrayRef< const real > lambda, const StepWorkload &stepWork, ForceWithVirial *forceWithVirialMtsLevel0, ForceWithVirial *forceWithVirialMtsLevel1, gmx_enerdata_t *enerd, gmx_edsam *ed, bool didNeighborSearch)

Remove didNeighborSearch, which is used incorrectly.

Convert all other algorithms called here to ForceProviders.

Member gmx::CoordinateFileFlags

Use std::bitset<16> for the entries.

Member gmx::cshake (const int iatom[], int ncon, int *nnit, int maxnit, ArrayRef< const real > constraint_distance_squared, ArrayRef< RVec > positions, const t_pbc *pbc, ArrayRef< const RVec > initial_displacements, ArrayRef< const real > half_of_reduced_mass, real omega, ArrayRef< const real > invmass, ArrayRef< const real > distance_squared_tolerance, ArrayRef< real > scaled_lagrange_multiplier, int *nerror)

Make SHAKE use better data structures, in particular for iatom.

Member gmx::DataFileInfo::fromDefaultDir_

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

Member gmx::detectAllDeviceInformation (const PhysicalNodeCommunicator &physicalNodeComm)

Coordinating the efficient detection of devices across multiple ranks per node should be separated from the lower-level hardware detection. See https://gitlab.com/gromacs/gromacs/-/issues/3650.

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::gmx_mdrun (MPI_Comm communicator, const gmx_hw_info_t &hwinfo, int argc, char *argv[])

Progress on https://gitlab.com/gromacs/gromacs/-/issues/3774 will remove the need of test binaries to call gmx_mdrun in a way that is different from the command-line and gmxapi.

Member gmx::gpu_try_finish_task (NbnxmGpu *nb, const StepWorkload &stepWork, const AtomLocality aloc, real *e_lj, real *e_el, ArrayRef< RVec > shiftForces, GpuTaskCompletion completionKind)

Move into shared source file, perhaps including cuda_runtime.h if needed for any remaining CUDA-specific objects.

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.

Class gmx::InteractiveMD

If adding doxygen stubs actual add the full stub.

Class gmx::IonSwapping

Add full information.

Class gmx::IRestraintPotential

Template headers can help to build compatible calculation methods with different input requirements. For reference, see https://github.com/kassonlab/sample_restraint

Member gmx::IRestraintPotential::evaluate (Vector r1, Vector r2, double t)=0

The virtual function call should be replaced by a (table of) function objects retrieved before the run.

Member gmx::lincsKernel (sycl::handler &cgh, const int numConstraintsThreads, const AtomPair *__restrict__ gm_constraints, const float *__restrict__ gm_constraintsTargetLengths, const int *__restrict__ gm_coupledConstraintsCounts, const int *__restrict__ gm_coupledConstraintsIndices, const float *__restrict__ gm_massFactors, float *__restrict__ gm_matrixA, const float *__restrict__ gm_inverseMasses, const int numIterations, const int expansionOrder, const Float3 *__restrict__ gm_x, Float3 *__restrict__ gm_xp, const float invdt, Float3 *__restrict__ gm_v, float *__restrict__ gm_virialScaled, PbcAiuc pbcAiuc)

Reduce synchronization overhead. Some ideas are:

1. Consider going to warp-level synchronization for the coupled constraints.
2. Move more data to local/shared memory and try to get rid of atomic operations (at least on the device level).
3. Use analytical solution for matrix A inversion.
4. Introduce mapping of thread id to both single constraint and single atom, thus designating Nth threads to deal with Nat <= Nth coupled atoms and Nc <= Nth coupled constraints. See Issue #2885 for details (https://gitlab.com/gromacs/gromacs/-/issues/2885)

The use of restrict for gm_xp and gm_v causes failure, probably because of the atomic operations. Investigate this issue further.

Member gmx::makeOpenClInternalErrorString (const char *message, cl_int status)

Make use of this function more.

Member gmx::NumTempScaleValues

Unify with similar enum in CPU update module

Member gmx::openTNG (const std::string &name, const Selection &sel, const gmx_mtop_t *mtop)

Those should be methods in a replacement for t_trxstatus instead.

Member gmx::reportGpuUsage (const MDLogger &mdlog, ArrayRef< const GpuTaskAssignment > gpuTaskAssignmentOnRanksOfThisNode, size_t numGpuTasksOnThisNode, size_t numPpRanks, bool printHostName, PmeRunMode pmeRunMode, const SimulationWorkload &simulationWork)

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::SimulatorEnv

Fix doxygen checks.

Class gmx::SimulatorStateData

Think of a better name and annoy people that forget to add documentation for their code.

Class gmx::TrajectoryAnalysisSettings

Remove plain flags from the public interface.

Member GMX_UNUSED_VALUE (value)

Deprecated - use gmx_unused

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

Group module_modularsimulator

Can we link to docs/doxygen/lib/modularsimulator.md?

File pbc_aiuc.h

CPU, GPU and SIMD routines essentially do the same operations on different data-types. Currently this leads to code duplication, which has to be resolved. For details, see Issue #2863 https://gitlab.com/gromacs/gromacs/-/issues/2863

Member pbcDxAiuc (const PbcAiuc &pbcAiuc, const rvec &r1, const rvec &r2, rvec dr)

This routine operates on rvec types and uses PbcAiuc to define periodic box, but essentially does the same thing as SIMD and GPU version. These will have to be unified in future to avoid code duplication. See Issue #2863: https://gitlab.com/gromacs/gromacs/-/issues/2863

Member set_over_alloc_dd (bool set)

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

File simulationsignal.h

Move this to mdrunutility module alongside gathering multi-simulation communication infrastructure there.

Class t_state

Move pure observables history to ObservablesHistory.