[Epic] Dissolve2Do

[trisyoungs]

The Dissolve2 ToDo!

A dynamic list of small jobs that will need doing in Dissolve2 towards the end of the transition to Nodes, but that we don't want to (or can't) do while the old system is still present.

• Serialisable has a virtual serialise(value, context) but a non-virtual serialise(value) function which causes warnings about hidden functions in the code. Once complete, context should no longer be required? #2352
• Clarify usage of Molecule and LocalMolecule, particularly use of setSpecies() which also creates arrays. #2353
• Remove Forcefield *forcefield_ member from Species. #2354
• Remove Function1DWrapper in favour of an object more compatible with the new system (e.g. remove need for template specialisation when adding Parameters etc.) #2355
• PartialSet averaging is performed (i.e. GRNode::process) by obtaining processing module data from a GenericList item. Instead do this work on an owned PartialSet object.
• Energy saves a flag via processingModuleData identifying the configuration as a target for the module - rework this in the graph/node framework #2356
  GenericItem::ProtectedFlag) = true;``` ) - how do we rework this in the graph/node framework? (see)
• Testing dissolve2, previously we used keywords #2357
• Nodes should pass on their configuration after processing for use by subsequent nodes, therefore the addition of a addPointerOutput<configuration *> is required for relevant nodes, where they don't already do this
• CollectorNode #2358
• We are littering the code with multiple instances of getEnumOptions for the same underlying enum now that we've moved to a concept for this particular solution. We may want to revisit / tidy this a bit. #2359
• We can remove the unsightly operator== code in import/data1D.h when we have implemented a Data1DNode #2360
• BoundedOptionalParameter and addBoundedOptionalParameter no longer required since the introduction of the Number type #2361
• feat: Generalise method for node data serialisation #2203
• feat: Node data serialisation #2242
• Clarify (or completely remove) the use of fingerprint_s in various classes (e.g. PartialSet) #2362
• Remove storage of tag_s in Data1D and friends #2363
• When and where to generate cells as required
• Check / change behaviour of IsotopologueSetModel #2364
• Call CellArray::generate() from node process only when the box has fundamentally changed (excluding scalings) - see
• Refactoring the ScatteringMatrix disabled saving of estimated S(Q) and g(r) to the restart file since their storage moved to DoubleKeyedMap. This needs to be reinstated.
• Refactoring EPSRModule into EPSRNode #2365
• Saving output files #2366
• File selector type #2367
• Implications for correct behaviour of Data1D with regards to file loading and project folder structure #2368
• Once old modules are removedPartialSet's initialise functions can be turned into constructors to tidy up code in various places. #2370
• Can / should we be passing const * as outputs and receive const * as inputs in specific places (e.g. NeutronSQ receiving the unweightedSQ and GR)? #2371
• Split template/algorithms.h up into more specific, smaller units so we don't bloat recompile requirements. #2372
• Merging/reusing addSerialisable(), SerialisableData, with SerialisableParameter<T> for serialisation of data to input file #2373
• Move simple test functions out of DissolveSystemTest, and remove any test functions relying on the old processingdata object. #2374
• Data1DImportFileFormat should take std::optional<Number> #2375
• Test case to ensure proper functioning of node edge pulling for OptionalPointerParameter inserted in place of an existing edge #2376
• Specifying ranges for quantities through a general QuantityRange class #2377
• addSerialisable temporarily disabled for the ImportConfigurationTrajectoryNode (use of std::streampos as the type of filePosition_, instead of int - MSVC) #2378
• Need to regenerate DL_POLY test data - supposedly via a script somewhere - that will mean we do not need separate speciesData functions for generating i.e. water in the DL_POLY ordering (H,O,H vs O,H,H) #2379
• Reintroduce force calculation over a subset of molecules (for MD). #2380
• SerialisableVector base class OR a new addSerialisableVector function which would allow us to serialise templated std::vector objects #2381
• Some Dissolve2 unit tests will not require a standalone method in graphData.h for creating species / graphs - this should be done inside the relevant test fixtures #2382
• Filename type #2383
• Adding / changing a pair potential override needs to correctly invalidate / regenerate affected pair potentials. #2384
• Every time a kernel is requested from DissolveGraph each pair potential is retabulated - we can be more clever and have version counters on AtomTypes which we can refer to. #2385
• Combine preventAllBonds_ and _useCIFBondingDefintions into enum #2386
• Re-enable skipped unit tests #2387
• Defining explicit pair potentials (i.e. turning off combination rules) needs to be reimplemented, but is essentially another use case of pair potential overrides. #2388
• Changing AtomType parameters needs to signal pair potential regeneration #2389