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Todo List

Class AdBondedTopology
Find a good way to deal with converting the parameters in the topology tables

Class < AdBondedTopologyDataSource >
Must define the topology types adun knows about as constants

Class AdDataMatrix
Optimise as much as possible.

Class AdDataMatrix
implement proper coding.

Class AdDataMatrix
Add row titles

Class AdDataMatrix
Add referencing by column title, row title or both

Member [AdDataMatrix extendMatrixWithMatrix:]
Add validation

Class AdDynamics
When unarchiving AdDynamics currently assumes it was created with an environment and registered with it. Change so it recreates itself in exactly the same way as it was encoded.

Class < AdDynamicsDataSourceExtensions >
Definine these in an informal protocol instead ?

Class AdEnvironment
Move to implementation based on domains. Domains would be parts of the simulator that can change and would require different options based on which part was active. Then these parts can call valueForOption:inDomain: or something. That way you wouldnt have to keep adding methods here for every new option. Can also have standard domains e.g. General, Electrostatic etc.

Class AdEnvironment
Need to validate options

Class AdInteractionSystem
Move matrix combining code to Base

Class AdInteractionSystem
Implement handling of bonded interactions between two systems

Class AdInteractionSystem
Implement proper handling of nonbonded interaction types.

Class AdInteractionSystem
Implement initWithCoder: (Currently assumes the types of nonbonded interactions to be CoulombElectrostatic and TypeOneVDWInteraction)

Member [AdIOManager loadProcessData:]
decide on return value

Class AdLinkedList
Extend with methods that provide "subviews" of the list as arrays. E.g. All atoms above or below a certain distance etc.

Class AdNonBondedListHandler
The listhandler should either use an specialised init e.g. initWithEnvironment:coordinates:topology:parameters or pass these when creating the lists createListForCoordinates:topology:parameters The first seems better. Currently you have to initialise, then set the values, then create which defeats the purpose on initialise... Or use dataSource...

Class AdNonBondedListHandler
Since AdNonBondedTopology resets all its listHandlers data on unarchiving the initWithCoder methods of AdNonbondedListHandler object do nothing more than return a normal freshly initialised instance. This seems to defeat the purpose of encoding. Need to look at AdNonbondedTopology encoding/decoding and fix this

Class AdNonBondedListHandler
ListHandlers should be able to create lists inside or outside the specified cutoff

Class AdNonBondedListHandler
Could also implement a method that returns a subset of the list matching a certain criteria? Although this would have to be an array and then you would need to create different functions for lists or array

Class AdNonBondedListHandler
Allow None for cutoff

Class AdNonBondedListHandler(AdListMemoryManagement)
Find some way to do the above here

Class < AdNonbondedTopologyDataSource >
Must define the topology types adun knows about as constants

Class AdObject
Fix the mechanisim for updating dependant variables

Class AdObject
This object will be renamed AdEnvironmentObject and be used as the super class for all objects that use environment initialisation. Classes that dont use environment initialisation will be remove from the hierarchy.

Class AdSimulator
Factor out the thermostating methods to their own class

Class AdSimulator
init methods should accept AdForceFieldManager and AdSystemNode as arguements.

Class AdSimulator
Check that force field is using same system

Class AdState
Move CalcKineticEnergy to Base

Class AdState
Implement setCurrentState as a ForceField only message and e.g. setCurrentStateFromForceField: change currentState to return a dict with the dereferenced values

Class AdState
Handling of longRangeNonbonded component of the system

Class AdState
implement setSystem

Class AdState
Currently cant deal with the event that the system has not loaded a data source - will cause a seg fault

Class AdSystem
Move removeTranslationalDegreesOfFreedom:velocities to Base

Class AdSystem
Implement wrappers around all necessary subsystem methods.

Class AdSystemComponent
Since this class holds the dataSource reference it should encode/decode it Currently each of the subclasses do this independantly

Class AdSystemComponent
Same goes for delegate (though at the moment I dont think any of the subclasses use it)

Class AdSystemNode
On creation of the systems and before creating the interactions AdSystemNode should remove all translational degrees of freedom.

Class AdSystemNode
Add "rigid" as a system status

Member [AdSystemNode containsRelationship:]
Currently checks if the two objects are exactly the same. Will implment an isEqual for AdRelationship objects which compares based on subject objects and relationship later.

Member [AdSystemNode removeRelationship:]
containers

Member [AdSystemNode removeSystemWithName:]
expand on this aspect

Class < AdTopologyDataSourceExtensions >
Definine these in an informal protocol instead ?

Class CellListHandler
Coding

Class el_t
the use of the params element needs to be deprecated.

Class LangevinSimulator
It should be possible to set a gamma value for each atom in each subsystem.

Class NewtonianSimulator
Factor out the thermostat portions of the algorithm if possible. This will allow NewtonianSimulator to use a wide variety of different thermostats e.g. Nose-Hoover, constant pressure berendsen etc. These object would act as delegates and be sent a message before each step of velocity-verlet algorithm allowing it to take action. (Obviously the termostat must be adapted to velocity verlet)

Class SCAAS
Instead of setSystem should use setSolute and setSolvent (or setSolutes)

Class SimpleListHandler
Implement correct handling of createLists. Currenlty this can only be called once.

Class SphericalBox
We can refactor the non grid delegate parts to the superclass and then subclasses can just implement the grid delegate methods

Class SphericalBox
Move expandInterTable code to a function in Base

Class SphericalBox
Calculate the grid spacing correctly

Class SphericalBox
Provide a more complete initialiser: initWithEnvironment:density:dimensions

Class SphericalBox
Check how changing the system radius, speacing density etc would work

Class SphericalBox
Check obscured molecule maintainence

Class ULAnalyser
Retrieve information strings from loaded objects

Class ULAnalyser
Read gnuplot launch path from defaults.

Class ULAnalyser
Reimplement reloadSimulation:

Class ULAnalyser(ULAnalyserPluginExtensions)
Handle return of multiple data sets.

Class ULAnalyserDataSetView
Use NSNumberFormatter for displaying data when it is fully implemented.

Member [ULAnalysisManager applyPlugin:withOptions:]
Change so returns void - user currentOutputObject to get results.

Class ULConfigurationBuilder
Include plugin protocol

Member [ULConfigurationBuilder buildConfiguration:error:userInfo:]
decide on what exactly should be returned!

Member [ULConfigurationBuilder buildConfiguration:error:userInfo:]
Decide what are the valid option values. Must a least include path to the configuration file. Seperate standard and plugin options?

Class ULDatabaseBrowser
Implement multiple object removal.

Class ULDatabaseBrowser
Fully implement input/output reference display

Class ULDatabaseIndex
Improve method of removing and updating object output references.

Class ULFileSystemDatabaseBackend
implement reindexAll

Class ULOutlineViewDelegate
Put options/properties dependant functionality into subclasses

Class ULProcessManager
Refactor process commands to use AdServerCommandInterface

Class ULProcessManager
Commands are currently using exceptions when really they should use NSError

Class ULSimulation
Format of energy archive changed from Kernel 0.9. ULResults has been updated to use the new format but many of the internal mechanisims it still uses are a direct result of the old format. Need to optimise ULResults for the new format.

Class ULStatusTable
Modify initial notification registration to be safer.

Class ULSystem
Add validators for configuration and topology keys

Class ULSystemViewController
Currently the forceField and configurationPlugin are hardcoded in the class. Have to read this from input and also propogate the changes to ULSystemController.

Member [ULTopologyFrameBuilder buildTopologyForSystem:withOptions:error:userInfo:]
Add another method for building the topology of single molecules

Member [ULTopologyFrameBuilder buildTopologyForSystem:withOptions:error:userInfo:]
Decide on what the returned object should be

Member [ULTopologyFrameBuilder buildTopologyForSystem:withOptions:error:userInfo:]
Decide what options should be available

Member [ULTopologyFrameBuilder initWithTopologyLibrary:]
Decide whether to allow parameter library and topology library to be separatly chosen

Class ViewController
Improve logging formating

Class ViewController
Implement proper deallocing of program on exit.

Class ViewController
All objects should be displayable i.e. should respond to the "display" command.

Class XMLDocumentRoot
change name back to XMLDocumentTree

Member [XMLDocumentRoot documentTreeForXMLFile:]
maybe this should just return the root object of the tree. Or perhaps make this the root document as well??

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