8 #ifndef RRROADRUNNEROPTIONS_H_
9 #define RRROADRUNNEROPTIONS_H_
11 #include "rrExporter.h"
12 #include "Dictionary.h"
30 enum LLVM_BACKEND_VALUES {
37 enum LLJIT_OPTIMIZATION_LEVELS {
40 DEFAULT = (0x1 << 18),
41 AGGRESSIVE = (0x1 << 19)
47 static std::vector<LLVM_BACKEND_VALUES> getAllLLVMBackendValues() {
48 return std::vector<LLVM_BACKEND_VALUES>({
55 static std::vector<LLJIT_OPTIMIZATION_LEVELS> getAllLLJitOptimizationValues() {
56 return std::vector<LLJIT_OPTIMIZATION_LEVELS>({
75 CONSERVED_MOIETIES = (0x1 << 0),
88 RECOMPILE = (0x1 << 1),
99 READ_ONLY = (0x1 << 2),
105 MUTABLE_INITIAL_CONDITIONS = (0x1 << 3),
111 OPTIMIZE_GVN = (0x1 << 4),
117 OPTIMIZE_CFG_SIMPLIFICATION = (0x1 << 5),
124 OPTIMIZE_INSTRUCTION_COMBINING = (0x1 << 6),
131 OPTIMIZE_DEAD_INST_ELIMINATION = (0x1 << 7),
139 OPTIMIZE_DEAD_CODE_ELIMINATION = (0x1 << 8),
144 OPTIMIZE_INSTRUCTION_SIMPLIFIER = (0x1 << 9),
150 OPTIMIZE = OPTIMIZE_GVN | OPTIMIZE_CFG_SIMPLIFICATION |
151 OPTIMIZE_INSTRUCTION_COMBINING |
152 OPTIMIZE_DEAD_INST_ELIMINATION | OPTIMIZE_DEAD_CODE_ELIMINATION |
153 OPTIMIZE_INSTRUCTION_SIMPLIFIER,
163 USE_MCJIT = (0x1 << 10),
166 LLVM_SYMBOL_CACHE = (0x1 << 11),
171 TURN_ON_VALIDATION = (0x1 << 12),
181 NO_DEFAULT_SELECTIONS = (0x1 << 0),
186 NO_DEFAULT_STEADY_STATE_SELECTIONS = (0x1 << 1)
209 std::uint32_t modelGeneratorOpt;
211 std::uint32_t loadFlags;
217 void setItem(
const std::string& key,
const rr::Setting& value)
override;
222 Setting getItem(
const std::string& key)
const override;
229 bool hasKey(
const std::string& key)
const override;
234 size_t deleteItem(
const std::string& key)
override;
239 std::vector<std::string> getKeys()
const override;
241 bool getConservedMoietyConversion()
const {
242 return modelGeneratorOpt & CONSERVED_MOIETIES;
245 void setConservedMoietyConversion(
bool val) {
246 modelGeneratorOpt = val ?
247 modelGeneratorOpt | CONSERVED_MOIETIES :
248 modelGeneratorOpt & ~CONSERVED_MOIETIES;
251 void setValidation(
bool val) {
252 loadFlags = val ? loadFlags | TURN_ON_VALIDATION : loadFlags & ~TURN_ON_VALIDATION;
255 void setLLVMBackend(LoadSBMLOptions::LLVM_BACKEND_VALUES val);
257 ~LoadSBMLOptions()
override;
259 void setLLJitOptimizationLevel(LLJIT_OPTIMIZATION_LEVELS levels);
379 std::vector<double> times;
384 std::string toString()
const;
389 std::string toRepr()
const;
397 void loadSBMLSettings(
const std::string& filename);
401 virtual void initialize();
403 virtual double getNext(
size_t step);
408 virtual void reset();
434 DISABLE_PYTHON_DYNAMIC_PROPERTIES = (0x1 << 0),
447 double steadyStateThreshold;
448 double fluxThreshold;
RoadRunner's Gillespie SSA integrator.
This class is frozen, no new features Basic implementation of the Dictionary interface which uses a s...
Definition: Dictionary.h:140
This class is frozen, no new features A dictionary interface that objects can implement.
Definition: Dictionary.h:30
Options for loading SBML into RoadRunner.
Definition: rrRoadRunnerOptions.h:28
LoadOpt
Definition: rrRoadRunnerOptions.h:177
std::uint16_t size
sizeof this struct
Definition: rrRoadRunnerOptions.h:207
ModelGeneratorOpt
Definition: rrRoadRunnerOptions.h:65
std::uint16_t version
the version this struct
Definition: rrRoadRunnerOptions.h:202
Store a roadrunner option (or setting) as a Variant type.
Definition: Setting.h:78
This class is frozen, no new features RoadRunner simulation options.
Definition: rrRoadRunnerOptions.h:294
std::vector< std::string > variables
The variables (in addition to time) whose values will be saved in the result.
Definition: rrRoadRunnerOptions.h:359
std::string output_file
The ouptut file for simulation results.
Definition: rrRoadRunnerOptions.h:343
std::vector< std::string > amounts
A list of the variable whose output in the results file is in amount (not concentration) units.
Definition: rrRoadRunnerOptions.h:366
int steps
The number of steps at which the output is sampled.
Definition: rrRoadRunnerOptions.h:323
std::vector< std::string > concentrations
A list of the variable whose output in the results file is in concentration (not amount) units.
Definition: rrRoadRunnerOptions.h:373
bool reset_model
reset the model to the initial state.
Definition: rrRoadRunnerOptions.h:305
double duration
The duration of the simulation run, in the model's units of time.
Definition: rrRoadRunnerOptions.h:334
bool structured_result
Simulate should return a raw result matrix without adding any column names.
Definition: rrRoadRunnerOptions.h:310
bool copy_result
Make a copy of the simulation result in Python.
Definition: rrRoadRunnerOptions.h:315
double start
The start time of the simulation time-series data.
Definition: rrRoadRunnerOptions.h:329
C_DECL_SPEC bool rrcCallConv reset(RRHandle handle)
Resets all variables of the model to their current initial values. Does not change the parameters.
A set of options that determine how the top level RoadRunner class should behave.
Definition: rrRoadRunnerOptions.h:424
double jacobianStepSize
step size used for numeric Jacobian calculations.
Definition: rrRoadRunnerOptions.h:445
Options
Definition: rrRoadRunnerOptions.h:426
std::uint32_t flags
a bitmask of the options specified in the Options enumeration.
Definition: rrRoadRunnerOptions.h:440