Extending ParticleData

UAMMD-structured inherits its ExtendedParticleData class from UAMMD’s ParticleData, so if you are interested in fully understand how is it implemented, you should read UAMMD documentation.

However, UAMMD-structured offers a very simple way to add a new property to ParticleData without needing to understand how ParticleData works at a low level. Simply add the new property to the Data.json file, and the compiler will automatically define the functions pd->getMyProperty(), pd->isMyPropertyAllocated(), and pd->getPropertyIfAllocate(). This will allow you to use your new property anywhere in the code.

There is an example of how to add to Data.json a new property. Write the first string with lowercase and the second with uppercase is not mandatory, but recommendable to follow the UAMMD standard. Data.json contains only the properties that have been added in UAMMD-structured and are not available in UAMMD.

 {
     "ParticleData": [
         ["resId", "ResId", "int"],
         ["chainId", "ChainId", "int"],
         ["modelId", "ModelId", "int"],
         ["batchId", "BatchId", "int"],
         ["state", "State", "int4"],
         ["stateInfo", "StateInfo", "real4"],
         ["stress", "Stress", "tensor3"],
         ["frictionConstant", "FrictionConstant", "real"],
         ["TranslationalSelfDiffusion", "TranslationalSelfDiffusion", "real"],
         ["rotationalSelfDiffusion", "RotationalSelfDiffusion", "real"],
         ["SASA", "SASA", "real"],
         ["SASAweight", "SASAweight", "real"],
         ["innerRadius", "InnerRadius", "real"],
         ["epsilon", "Epsilon", "real"],
         ["surface", "Surface", "real"],
         ["patchPos", "PatchPos", "real4"],
         ["patchVector", "PatchVector", "real4"],
         ["parentIndex", "ParentIndex", "int"],
         ["anisotropy", "Anisotropy", "real"],
         ["magneticField", "MagneticField", "real4"],
         ["magnetization", "Magnetization", "real4"],
         ["tentativeState", "TentativeState", "int4"],
         ["transitionProbability", "TransitionProbability", "real"],
         ["selectedId", "SelectedId", "int"],
         ["hessian", "Hessian", "tensor3"],
         ["lambdaDerivative","LambdaDerivative","real"],
         ["polarizability","Polarizability","real"],
         ["pairwiseForce","PairwiseForce","real4"],
         ["myProperty","MyProperty","DataType"]
     ],

Finally, if you want the property to be initialized from the input through State, also add it to the “State” section of the Data.json file.

 "State": [
     ["velocity", "Vel", "real3"],
     ["direction", "Dir", "real4"],
     ["innerRadius", "InnerRadius", "real"],
     ["magnetization", "Magnetization", "real4"],
     ["anisotropy", "Anisotropy", "real"],
     ["mass", "Mass", "real"],
     ["polarizability","Polarizability","real"],
     ["radius", "Radius", "real"],
     ["charge", "Charge", "real"],
     ["myProperty","MyProperty","DataType"]
 ],