Ksolve

class Ksolve

xCompt

void (shared message field) Shared message for pool exchange for cross-compartment reactions. Exchanges latest values of all pools that participate in such reactions.

proc

void (shared message field) Shared message for process and reinit. These are used for all regular Ksolve calculations including interfacing with the diffusion calculations by a Dsolve.

init

void (shared message field) Shared message for initProc and initReinit. This is used when the system has cross-compartment reactions.

setMethod()

(destination message field) Assigns field value.

getMethod()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setEpsAbs()

(destination message field) Assigns field value.

getEpsAbs()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setEpsRel()

(destination message field) Assigns field value.

getEpsRel()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setCompartment()

(destination message field) Assigns field value.

getCompartment()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getNumLocalVoxels()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setNVec()

(destination message field) Assigns field value.

getNVec()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setNumAllVoxels()

(destination message field) Assigns field value.

getNumAllVoxels()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setNumPools()

(destination message field) Assigns field value.

getNumPools()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getEstimatedDt()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getStoich()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

voxelVol()

(destination message field) Handles updates to all voxels. Comes from parent ChemCompt object.

xComptIn()

(destination message field) Handles arriving pool 'n' values used in cross-compartment reactions.

process()

(destination message field) Handles process call from Clock

reinit()

(destination message field) Handles reinit call from Clock

initProc()

(destination message field) Handles initProc call from Clock

initReinit()

(destination message field) Handles initReinit call from Clock

xComptOut

Id,vector<double> (source message field) Sends 'n' of all molecules participating in cross-compartment reactions between any juxtaposed voxels between current compt and another compartment. This includes molecules local to this compartment, as well as proxy molecules belonging elsewhere. A(t+1) = (Alocal(t+1) + AremoteProxy(t+1)) - Alocal(t) A(t+1) = (Aremote(t+1) + Aproxy(t+1)) - Aproxy(t) Then we update A on the respective solvers with: Alocal(t+1) = Aproxy(t+1) = A(t+1) This is equivalent to sending dA over on each timestep.

method

string (value field) Integration method, using GSL. So far only explict. Options are:rk5: The default Runge-Kutta-Fehlberg 5th order adaptive dt methodgsl: alias for the aboverk4: The Runge-Kutta 4th order fixed dt methodrk2: The Runge-Kutta 2,3 embedded fixed dt methodrkck: The Runge-Kutta Cash-Karp (4,5) methodrk8: The Runge-Kutta Prince-Dormand (8,9) method

epsAbs

double (value field) Absolute permissible integration error range.

epsRel

double (value field) Relative permissible integration error range.

compartment

Id (value field) Compartment in which the Ksolve reaction system lives.

numLocalVoxels

unsigned int (value field) Number of voxels in the core reac-diff system, on the current solver.

numAllVoxels

unsigned int (value field) Number of voxels in the entire reac-diff system, including proxy voxels to represent abutting compartments.

numPools

unsigned int (value field) Number of molecular pools in the entire reac-diff system, including variable, function and buffered.

estimatedDt

double (value field) Estimated timestep for reac system based on Euler error

stoich

Id (value field) Id for stoichiometry object tied to this Ksolve

nVec

unsigned int,vector<double> (lookup field) vector of pool counts. Index specifies which voxel.