rrExecutableModel

class ExecutableModel

Base class for all code generation systems; allows compiling and evaluating the model.

The ExecutableModel interface provides a way to access an sbml model that was compiled, JIT’d or interpreted as executable (runnable) module.

An ExecutableModel holds a ModelData structure, all the simulation values are stored in the ModelData struct, i.e. the dynamic state of the model is fully contained in the ModelData structure.

An ExecutableModel should also contain all of the initial conditions, rules, functions and whatever other semantic information that was specified in the sbml model.

Subclassed by rr::CompiledExecutableModel, rrllvm::LLVMExecutableModel

Public Types

enum ExecutableModelFlags

Values:

enumerator INTEGRATION

A simulation is currently running.

This means that the model should not have to re-calculate the reaction rate std::vector as it was calculated in the previous integration step.

enumerator OPTIMIZE_REACTION_RATE_SELECTION

optimize not-recalculating the reaction rates during selection.

Public Functions

ExecutableModel()

Returns a human-readable description of the code generation backend, e.g. LLVM, legacy C, etc.

Author

JKM

Date

07/31/2015

virtual std::string getExecutableModelDesc() const = 0
virtual std::string getModelName() = 0

get the name of the model

virtual void setTime(double _time) = 0
virtual double getTime() = 0
virtual void reset() = 0

Loads the initial conditions into the current model state.

Initial conditions may have been updated at any time externally.

virtual int getNumDepFloatingSpecies() = 0

dependent species are defined by rules and the only way to change them is by changing the values on which they depend.

virtual int getNumFloatingSpecies() = 0

total number of floating species.

virtual int getFloatingSpeciesIndex(const std::string &eid) = 0
virtual std::string getFloatingSpeciesId(size_t index) = 0
virtual int getNumIndFloatingSpecies() = 0

independent species do are not defined by rules, they typically participate in reactions and can have thier values set at any time.

virtual int getFloatingSpeciesAmounts(size_t len, int const *indx, double *values) = 0

get the floating species amounts

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of floating species to return.

  • values – [out] an array of at least length len which will store the returned floating species amounts.

virtual int setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values) = 0
virtual int setFloatingSpeciesAmounts(size_t len, int const *indx, const double *values, bool strict) = 0
virtual int getFloatingSpeciesAmountRates(size_t len, int const *indx, double *values) = 0

get the floating species amount rates

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of floating species to return.

  • values – [out] an array of at least length len which will store the returned floating species amount rates.

virtual int getFloatingSpeciesConcentrationRates(size_t len, int const *indx, double *values) = 0

get the floating species concentration rates

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of floating species to return.

  • values – [out] an array of at least length len which will store the returned floating species concentration rates.

virtual int getFloatingSpeciesConcentrations(size_t len, int const *indx, double *values) = 0

get the floating species concentrations

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of floating species to return.

  • values – [out] an array of at least length len which will store the returned floating species amounts.

virtual int setFloatingSpeciesConcentrations(size_t len, int const *indx, double const *values) = 0

set the floating species concentrations

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of floating species to return.

  • values – [in] an array of at least length len which will store the returned boundary species amounts.

virtual int setFloatingSpeciesInitConcentrations(size_t len, int const *indx, double const *values) = 0

Set the initial concentrations of the floating species.

Takes the same indices as the other floating species methods.

Note, if a floating species has an initial assignment rule, than the initial conditions value can only be set by updating the values on which it depends, it can not be set directly.

virtual int getFloatingSpeciesInitConcentrations(size_t len, int const *indx, double *values) = 0

Get the initial concentrations of the floating species, uses the same indexing as the other floating species methods.

virtual int setFloatingSpeciesInitAmounts(size_t len, int const *indx, double const *values) = 0

Set the initial amounts of the floating species.

Takes the same indices as the other floating species methods.

Note, if a floating species has an initial assignment rule, than the initial conditions value can only be set by updating the values on which it depends, it can not be set directly.

virtual int getFloatingSpeciesInitAmounts(size_t len, int const *indx, double *values) = 0

Get the initial amounts of the floating species, uses the same indexing as the other floating species methods.

virtual int getNumBoundarySpecies() = 0

get the number of boundary species.

virtual int getBoundarySpeciesIndex(const std::string &eid) = 0
virtual std::string getBoundarySpeciesId(size_t index) = 0
virtual int getBoundarySpeciesAmounts(size_t len, int const *indx, double *values) = 0

get the boundary species amounts

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of boundary species to return.

  • values – [out] an array of at least length len which will store the returned boundary species amounts.

virtual int getBoundarySpeciesConcentrations(size_t len, int const *indx, double *values) = 0

get the boundary species concentrations

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of boundary species to return.

  • values – [out] an array of at least length len which will store the returned boundary species amounts.

virtual int setBoundarySpeciesConcentrations(size_t len, int const *indx, double const *values) = 0

set the boundary species concentrations

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of boundary species to return.

  • values – [in] an array of at least length len which will store the returned boundary species concentrations.

virtual int setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values) = 0
virtual int setBoundarySpeciesAmounts(size_t len, int const *indx, double const *values, bool strict) = 0
virtual int setBoundarySpeciesInitConcentrations(size_t len, int const *indx, double const *values) = 0

Set the initial concentrations of the boundary species.

Takes the same indices as the other boundary species methods.

Note, if a boundary species has an initial assignment rule, than the initial conditions value can only be set by updating the values on which it depends, it can not be set directly.

virtual int getBoundarySpeciesInitConcentrations(size_t len, int const *indx, double *values) = 0

Get the initial concentrations of the boundary species, uses the same indexing as the other boundary species methods.

virtual int setBoundarySpeciesInitAmounts(size_t len, int const *indx, double const *values) = 0

Set the initial amounts of the boundary species.

Takes the same indices as the other boundary species methods.

Note, if a boundary species has an initial assignment rule, than the initial conditions value can only be set by updating the values on which it depends, it can not be set directly.

virtual int getBoundarySpeciesInitAmounts(size_t len, int const *indx, double *values) = 0

Get the initial amounts of the boundary species, uses the same indexing as the other boundary species methods.

virtual int getNumGlobalParameters() = 0

get the number of global parameters

virtual int getGlobalParameterIndex(const std::string &eid) = 0

index of the global parameter id, -1 if it does not exist.

virtual std::string getGlobalParameterId(size_t index) = 0

id of the indexed global parameter.

virtual int getGlobalParameterValues(size_t len, int const *indx, double *values) = 0

get the global parameter values

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of boundary species to return.

  • values – [out] an array of at least length len which will store the returned boundary species amounts.

virtual int setGlobalParameterValues(size_t len, int const *indx, const double *values) = 0
virtual int setGlobalParameterValues(size_t len, int const *indx, const double *values, bool strict) = 0
virtual int setGlobalParameterInitValues(size_t len, int const *indx, double const *values) = 0

Set the initial value of the global parameter.

Takes the same indices as the other global parameter methods.

virtual int getGlobalParameterInitValues(size_t len, int const *indx, double *values) = 0

Get the initial amounts of the global parameter, uses the same indexing as the other global parameter methods.

virtual int getNumCompartments() = 0
virtual int getCompartmentIndexForFloatingSpecies(size_t index) = 0
virtual int getCompartmentIndexForBoundarySpecies(size_t index) = 0
virtual int getCompartmentIndex(const std::string &eid) = 0
virtual std::string getCompartmentId(size_t index) = 0
virtual int getCompartmentVolumes(size_t len, int const *indx, double *values) = 0

get the compartment volumes

Parameters:

  • len – [in] the length of the indx and values arrays.

  • indx – [in] an array of length len of boundary species to return.

  • values – [out] an array of at least length len which will store the returned boundary species amounts.

virtual int setCompartmentVolumes(size_t len, int const *indx, const double *values) = 0
virtual int setCompartmentVolumes(size_t len, int const *indx, const double *values, bool strict) = 0
virtual int setCompartmentInitVolumes(size_t len, int const *indx, double const *values) = 0

Set the initial volumes of the compartments.

Takes the same indices as the other compartment methods.

Note, if a compartment has an initial assignment rule, than the initial conditions value can only be set by updating the values on which it depends, it can not be set directly.

virtual int getCompartmentInitVolumes(size_t len, int const *indx, double *values) = 0

Get the initial volume of the compartments, uses the same indexing as the other compartment methods.

virtual void getIds(int types, std::list<std::string> &ids) = 0

populates a given list with all the ids that this class can accept.

Parameters:

  • ids – a list of strings that will be filled by this class.

  • types – the types of ids that are requested. Can be set to 0xffffffff to request all the ids that this class supports. This should by a bitwise OR of the filelds in SelectionRecord::SelectionType

virtual int getSupportedIdTypes() = 0

returns a bit field of the ids that this class supports.

virtual double getValue(const std::string &id) = 0

gets the value for the given id std::string.

The std::string must be a SelectionRecord std::string that is accepted by this class.

virtual void setValue(const std::string &id, double value) = 0

sets the value coresponding to the given selection stringl

virtual int setStoichiometries(size_t len, int const *indx, const double *values) = 0
virtual int setStoichiometries(size_t len, int const *indx, const double *values, bool strict) = 0
virtual int setStoichiometry(int index, double value) = 0
virtual int setStoichiometry(int speciesIndex, int reactionIndex, double value) = 0
virtual double getStoichiometry(int index) = 0

Get the current stiochiometry value with the given index.

If either are not valid, NaN is returned.

virtual double getStoichiometry(int speciesIndex, int reactionIndex) = 0

Get the current stiochiometry value for the given species / reaction.

If either are not valid, NaN is returned.

virtual int getNumConservedMoieties() = 0
virtual int getConservedMoietyIndex(const std::string &eid) = 0
virtual std::string getConservedMoietyId(size_t index) = 0
virtual int getConservedMoietyValues(size_t len, int const *indx, double *values) = 0
virtual int setConservedMoietyValues(size_t len, int const *indx, const double *values) = 0
virtual int getNumRateRules() = 0
virtual std::vector<std::string> getRateRuleSymbols() const = 0

Gets the symbols defined by rate rules, i.e. returns all x such that x’ = f(x) is a rule which defines parameter x.

Author

JKM

Date

07/31/2015

virtual int getNumReactions() = 0

get the number of reactions the model has

virtual int getReactionIndex(const std::string &eid) = 0

get the index of a named reaction

Returns:

>= 0 on success, < 0 on failure.

virtual std::string getReactionId(size_t index) = 0

get the name of the specified reaction

virtual int getStoichiometryIndex(const std::string&) = 0

get the index of a named stoichiometry

Returns:

>= 0 on success, < 0 on failure.

virtual int getStoichiometryIndex(const std::string&, const std::string&) = 0

get the index of a named stoichiometry

Returns:

>= 0 on success, < 0 on failure.

virtual std::string getStoichiometryId(size_t index) = 0

get the name of the specified stoichiometry

virtual int getReactionRates(size_t len, int const *indx, double *values) = 0

get the std::vector of reaction rates.

Parameters:

  • len – the length of the supplied buffer, must be >= reaction rates size.

  • indx – pointer to index array. If NULL, then it is ignored and the reaction rates are copied directly into the supplied buffer.

  • values – pointer to user supplied buffer where rates will be stored.

virtual void getRateRuleValues(double *rateRuleValues) = 0

get the ‘values’ i.e.

the what the rate rule integrates to, and store it in the given array.

The length of rateRuleValues obviously must be the number of rate rules we have.

virtual int getRateRuleRates(size_t len, int const *indx, double *values)

get the ‘rates’ i.e.

the what the rate rule integrates to, and store it in the given array.

Parameters:

  • len – the length of the supplied buffer, must be >= reaction rates size.

  • indx – pointer to index array. If NULL, then it is ignored and the rates are copied directly into the supplied buffer.

  • values – pointer to user supplied buffer where rates will be stored.

virtual std::string getStateVectorId(size_t index) = 0

get the id of an element of the state std::vector.

virtual int getStateVector(double *stateVector) = 0

The state std::vector is a std::vector of elements that are defined by differential equations (rate rules) or independent floating species are defined by reactions.

To get the ids of the state std::vector elements, use getStateVectorId.

copies the internal model state std::vector into the provided buffer.

Parameters:

stateVector – [out] a buffer to copy the state std::vector into, if NULL, return the size required.

Returns:

the number of items coppied into the provided buffer, if stateVector is NULL, returns the length of the state std::vector.

virtual int setStateVector(const double *stateVector) = 0

sets the internal model state to the provided packed state std::vector.

Parameters:

stateVector – [in] an array which holds the packed state std::vector, must be at least the size returned by getStateVector.

Returns:

the number of items copied from the state std::vector, negative on failure.

virtual void getStateVectorRate(double time, const double *y, double *dydt = 0) = 0

the state std::vector y is the rate rule values and floating species concentrations concatenated.

y is of length numFloatingSpecies + numRateRules.

The state std::vector is packed such that the first n raterule elements are the values of the rate rules, and the last n floatingspecies are the floating species values.

Parameters:

  • time – [in] current simulator time

  • y – [in] state std::vector, must be either null, or have a size of that speciefied by getStateVector. If y is null, then the model is evaluated using its current state. If y is not null, then the y is considered the state std::vector.

  • dydt – [out] calculated rate of change of the state std::vector, if null, it is ignored.

virtual void testConstraints() = 0
virtual std::string getInfo() = 0
virtual void print(std::ostream &stream) = 0
virtual int getNumEvents() = 0
virtual int getEventTriggers(size_t len, const int *indx, unsigned char *values) = 0

get the event status, false if the even is not triggered, true if it is.

The reason this returns an unsigned char instead of a bool array is this array is typically stuffed into an std::vector, and std::vector<bool> is well, weird as it’s actually implemented as a bitfield, and can not be used as a C array.

So, on every modern system I’m aware of, bool is an unsigned char, so use that data type here.

virtual int applyEvents(double timeEnd, const unsigned char *previousEventStatus, const double *initialState, double *finalState) = 0

Itterate through all of the current and pending events and apply them.

If any events trigger a state change which triggers any additional events, these are applied as well. After this method finishes, all events are processed.

Parameters:

  • timeEnd – model time when the event occured.

  • previousEventStatus – array of previous event triggered states.

  • initialState – (optional): initial state std::vector, may be NULL, in which the current state is used.

  • finalState – (optional): final state std::vector, where the final state is coppied to. May be NULL, in which case, ignored.

virtual void getEventRoots(double time, const double *y, double *gdot) = 0

evaluate the event ‘roots’ &#8212; when events transition form triggered - non-triggered or triggered to non-triggered state.

Simplest method is to return 1 for triggered, -1 for not-triggered, so long as there is a zero crossing.

Parameters:

  • time – [in] current time

  • y – [in] the state std::vector

  • gdot – [out] result event roots, this is of length numEvents.

virtual void getPiecewiseTriggerRoots(double time, const double *y, double *gdot) = 0
virtual double getNextPendingEventTime(bool pop) = 0
virtual int getPendingEventSize() = 0
virtual void resetEvents() = 0
virtual int getNumPiecewiseTriggers() = 0

We do root-finding for ‘piecewise triggers’: those times in a piecewise function that transition from one condition to the next.

inline virtual ~ExecutableModel()

need a virtual destructor as object implementing this interface can be deleted directly, i.e.

ExecutableModel *p = createModel(…); delete p;

virtual int getEventIndex(const std::string &eid) = 0

Gets the index for an event id.

If there is no event with this id, returns -1.

virtual std::string getEventId(size_t index) = 0
virtual void getEventIds(std::list<std::string>&) = 0
virtual void getAssignmentRuleIds(std::list<std::string>&) = 0
virtual void getRateRuleIds(std::list<std::string>&) = 0
virtual void getInitialAssignmentIds(std::list<std::string>&) = 0
virtual void setEventListener(size_t index, EventListenerPtr eventHandler) = 0
virtual EventListenerPtr getEventListener(size_t index) = 0
virtual double getFloatingSpeciesAmountRate(size_t index, const double *reactionRates) = 0

Get the amount rate of change for the i’th floating species given a reaction rates std::vector.

TODO: This should be merged with getFloatingSpeciesAmountRates, but that will break inteface, will do in next point release.

TODO: If the conversion factor changes in between getting the reaction rates std::vector via getReactionRates

Parameters:

  • index – index of the desired floating speceis rate.

  • reactionRates – pointer to buffer of reaction rates.

virtual void reset(int options) = 0

reset the model accordign to a bitfield specified by the SelectionRecord::SelectionType values.

virtual void setRandomSeed(int64_t) = 0

set the seed used by the random number generator.

This will by definition reset the RNG.

virtual int64_t getRandomSeed() = 0

get the seed used by the RNG.

virtual double getRandom() = 0

Get a uniform random number between 0 and 1 created by the RNG.

The type of RNG can be specified in the config file with the RANDOM_GENERATOR_TYPE key.

virtual uint32_t getFlags() const = 0

Get the current set of flags.

virtual void setFlags(uint32_t) = 0

Set certain options that determine the state of the ExecutableModel, these are listed in.

inline void computeAllRatesOfChange()

for source compatability

inline virtual void saveState(std::ostream &out)
virtual void setIntegrationStartTime(double time)

Protected Functions

inline void setIntegration(bool value)

is integration is currently proceeding.

Protected Attributes

double mIntegrationStartTime

Friends

friend class RoadRunner