src

BaseSim

class BaseSim

Subclassed by sme::simulate::DuneSim, sme::simulate::PixelSim

Public Functions

virtual ~BaseSim() = default

virtual std::size_t run(double time, double timeout_ms, const std::function<bool()> &stopRunningCallback) = 0

virtual const std::vector<double> &getConcentrations(std::size_t compartmentIndex) const = 0

virtual std::size_t getConcentrationPadding() const = 0

virtual const std::string &errorMessage() const = 0

virtual const common::ImageStack &errorImages() const = 0

virtual void setStopRequested(bool stop) = 0

GridFunction

Warning

doxygenclass: Cannot find class “sme::simulate::GridFunction” in doxygen xml output for project “sme” from directory: build/xml

IniFile

class IniFile

Public Functions

const QString &getText() const

void addSection(const QString &str)

void addSection(const QString &str1, const QString &str2)

void addSection(const QString &str1, const QString &str2, const QString &str3)

void addSection(const QString &str1, const QString &str2, const QString &str3, const QString &str4)

void addSection(const QString &str1, const QString &str2, const QString &str3, const QString &str4, const QString &str5)

void addSection(const QString &str1, const QString &str2, const QString &str3, const QString &str4, const QString &str5, const QString &str6)

void addValue(const QString &var, const QString &value)

void addValue(const QString &var, int value)

void addValue(const QString &var, double value, int precision)

void clear()

DuneSim

class DuneSim : public sme::simulate::BaseSim

Public Functions

explicit DuneSim(const model::Model &sbmlDoc, const std::vector<std::string> &compartmentIds, const std::map<std::string, double, std::less<>> &substitutions = {})

~DuneSim() override

virtual std::size_t run(double time, double timeout_ms, const std::function<bool()> &stopRunningCallback) override

virtual const std::vector<double> &getConcentrations(std::size_t compartmentIndex) const override

virtual std::size_t getConcentrationPadding() const override

virtual const std::string &errorMessage() const override

virtual const common::ImageStack &errorImages() const override

virtual void setStopRequested(bool stop) override

DuneImpl

template<int DuneDimensions>
class DuneImpl

Public Functions

inline explicit DuneImpl(const DuneConverter &dc, const DuneOptions &options, const model::Model &sbmlDoc, const std::vector<std::string> &compartmentIds)

~DuneImpl() = default

inline void run(double time)

inline const std::vector<double> &getConcentrations(std::size_t compartmentIndex) const

PixelSim

class PixelSim : public sme::simulate::BaseSim

Public Functions

explicit PixelSim(const model::Model &sbmlDoc, const std::vector<std::string> &compartmentIds, const std::vector<std::vector<std::string>> &compartmentSpeciesIds, const std::map<std::string, double, std::less<>> &substitutions = {})

~PixelSim() override

virtual std::size_t run(double time, double timeout_ms, const std::function<bool()> &stopRunningCallback) override

virtual const std::vector<double> &getConcentrations(std::size_t compartmentIndex) const override

virtual std::size_t getConcentrationPadding() const override

const std::vector<double> &getDcdt(std::size_t compartmentIndex) const

double getLowerOrderConcentration(std::size_t compartmentIndex, std::size_t speciesIndex, std::size_t pixelIndex) const

virtual const std::string &errorMessage() const override

virtual const common::ImageStack &errorImages() const override

virtual void setStopRequested(bool stop) override

PagmoUDP

class PagmoUDP

Implements a Pagmo User Defined Problem to evolve.

Note

Needs to be (cheaply) copy-constructible, implement fitness() and get_bounds() functions, and be thread-safe, see https://esa.github.io/pagmo2/docs/cpp/problem.html

Public Functions

PagmoUDP() = default

explicit PagmoUDP(const OptConstData *optConstData, ThreadsafeModelQueue *modelQueue, Optimization *optimization)

pagmo::vector_double fitness(const pagmo::vector_double &dv) const

std::pair<pagmo::vector_double, pagmo::vector_double> get_bounds() const