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Input_ODE_before_compile_mixed.h
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/*!
\brief Text file input handler
ALL IDS MUST START WITH AN ALPHABETIC LETTER, FOLLOWED BY LETTERS OR DIGITS
//read file
//parse by libxml2
//some check
//write data structure
//write to a file if need compile
//compile
*/
#ifndef _INPUT_ODE_BEFORE_COMPILE_MIXED_H_
#define _INPUT_ODE_BEFORE_COMPILE_MIXED_H_
#include "Input.h"
#include <fstream>
//#define _CUSTOM_PROPENSITY_FUNCTIONS_FILENAME_ "CustomPropensityFunctions.h"
namespace STOCHKIT
{
template<typename _populationVectorType,
typename _stoichiometryType,
typename _propensitiesFunctorType,
typename _dependencyGraphType>
class Input_ODE_before_compile_mixed :
public Input<_populationVectorType, _stoichiometryType, _propensitiesFunctorType, _dependencyGraphType>
{
std::vector<std::string> rightHandSide;
std::vector<std::string> jacobian;
bool ODE_ready;
double volume, NATIMESVOLUME;
static const double AvogadroConstant = 6.02214E23;
typedef Input<_populationVectorType, _stoichiometryType, _propensitiesFunctorType, _dependencyGraphType> Base;
typedef typename Base::_populationValueType _populationValueType;
using Base::ParametersList;
using Base::simpleCalculator;
using Base::NumberOfSpecies;
using Base::SpeciesList;
public:
Input_ODE_before_compile_mixed(char *xmlFilename):
Input<_populationVectorType, _stoichiometryType, _propensitiesFunctorType, _dependencyGraphType>(xmlFilename),
rightHandSide(this->NumberOfSpecies, "RCONST(0)"),
jacobian(this->NumberOfSpecies*this->NumberOfSpecies,"RCONST(0)"),
ODE_ready(false),
NATIMESVOLUME(1.0)
{
}
protected:
// calculate rate based on the value stored in parameterslist
double rateCalculation(std::string equation)
{
std::vector<unsigned int> ParametersAffectRate;
std::vector<unsigned int>::iterator para_it; // iterator of parameters in link graph
ParametersAffectRate = this->ParametersList.analyzeParameterExpression(equation);
bool calculationStatus = false;
for( para_it = ParametersAffectRate.begin(); para_it < ParametersAffectRate.end(); ++para_it ){
if( this->ParametersList[*para_it].CalculateFlag == -1 ){
calculationStatus = this->ParametersList.calculateParameter(*para_it);
if(!calculationStatus){
std::cerr << "StochKit ERROR (Input_mass_action::rateCalculation): while calculating rate " << equation << std::endl;
return BADRESULT;
}
}
}
std::string substitutedEquation = this->ParametersList.parameterSubstitution(equation);
if( substitutedEquation.empty() ){
std::cerr << "StochKit ERROR (Input_mass_action::rateCalculation): while calculating rate " << equation << std::endl;
return BADRESULT;
}
return this->simpleCalculator.calculateString(substitutedEquation);
}
bool getODEReady()
{
// double rate;
typename Input<_populationVectorType, _stoichiometryType, _propensitiesFunctorType, _dependencyGraphType>::Reaction *cur_reaction;
int volume_position;
if((volume_position = findParameterWithId("Volume")) != -1){
} else if((volume_position = findParameterWithId("VOLUME")) != -1){
} else if((volume_position = findParameterWithId("volume")) != -1){
} else {
std::cout << "StochKit WARNING (Input_ODE_before_compile_mixed::getODEReady): no volume parameter is specified, assuming model file is written in concentration style." << std::endl;
volume = 1.0;
NATIMESVOLUME = 1.0;
}
if(volume_position != -1){
if(this->ParametersList[volume_position].CalculateFlag != 1){
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): ParametersList not calculated." << std::endl;
exit(1);
}
volume = this->ParametersList[volume_position].Value;
NATIMESVOLUME = volume * AvogadroConstant;
}
std::string rate;
std::string customized_propensities;
std::ostringstream temp_expressions;
for(int i=0; i<this->NumberOfReactions; ++i){
cur_reaction = &this->ReactionsList[i];
if(cur_reaction->Type == 0){
rate = customPropensitySubstitution(cur_reaction->Rate);
// if( rate == BADRESULT ){
// std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): while calculating rate of reaction " << cur_reaction->Id << "\n";
// return false;
// }
switch ( cur_reaction->Reactants.size() ){
case 0:
// std::cout << "0-th order: " << i << std::endl;
for(std::size_t j=0; j<cur_reaction->Products.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry/NATIMESVOLUME << ")*" << rate;
rightHandSide[cur_reaction->Products[j].Index] += temp_expressions.str();
}
break;
case 1:
if( cur_reaction->Reactants[0].Stoichiometry == -1 ) {
// std::cout << "1-st order: " << i << std::endl;
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[0].Stoichiometry << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
rightHandSide[cur_reaction->Reactants[0].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[0].Stoichiometry <<")*" << rate ;
jacobian[cur_reaction->Reactants[0].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
for(std::size_t j=0; j<cur_reaction->Products.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
rightHandSide[cur_reaction->Products[j].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry <<")*" << rate;
jacobian[cur_reaction->Products[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
}
}
else if( cur_reaction->Reactants[0].Stoichiometry == -2 ) {
// std::cout << "2-nd order of same species: " << i << std::endl;
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[0].Stoichiometry*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
rightHandSide[cur_reaction->Reactants[0].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[0].Stoichiometry*2*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
jacobian[cur_reaction->Reactants[0].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
for(std::size_t j=0; j<cur_reaction->Products.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
rightHandSide[cur_reaction->Products[j].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry*2*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
jacobian[cur_reaction->Products[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
}
}
else{
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): currently the highest order mass-action reaction supported is bi-molecular reaction while Reaction " << cur_reaction->Id << " is not\n";
return false;
}
break;
case 2:
if( cur_reaction->Reactants[0].Stoichiometry != -1 || cur_reaction->Reactants[1].Stoichiometry != -1 ){
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): currently the highest order mass-action reaction supported is bi-molecular reaction while Reaction " << cur_reaction->Id << " is not\n";
return false;
}
else{
// std::cout << "2-nd order of different species: " << i << std::endl;
for(std::size_t j=0; j<cur_reaction->Reactants.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[j].Stoichiometry*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")*Ith(y," << cur_reaction->Reactants[1].Index+1 << ")";
rightHandSide[cur_reaction->Reactants[j].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[j].Stoichiometry*NATIMESVOLUME << ")*" << rate << "*Ith(y," << cur_reaction->Reactants[1].Index+1 << ")";
jacobian[cur_reaction->Reactants[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[j].Stoichiometry*NATIMESVOLUME<< ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
jacobian[cur_reaction->Reactants[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[1].Index] += temp_expressions.str();
}
for(std::size_t j=0; j<cur_reaction->Products.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry*NATIMESVOLUME<< ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")*Ith(y," << cur_reaction->Reactants[1].Index+1 << ")";
rightHandSide[cur_reaction->Products[j].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry*NATIMESVOLUME<< ")*" << rate << "*Ith(y," << cur_reaction->Reactants[1].Index+1 << ")";
jacobian[cur_reaction->Products[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[0].Index] += temp_expressions.str();
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry*NATIMESVOLUME<< ")*" << rate << "*Ith(y," << cur_reaction->Reactants[0].Index+1 << ")";
jacobian[cur_reaction->Products[j].Index * this->NumberOfSpecies + cur_reaction->Reactants[1].Index] += temp_expressions.str();
}
}
break;
default:
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): more than 2 reactants in mass-action reaction " << cur_reaction->Id << "\n";
return false;
}
}
else if (cur_reaction->Type == 2) {
customized_propensities = customPropensitySubstitution(cur_reaction->Customized);
for(std::size_t j=0; j<cur_reaction->Reactants.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Reactants[j].Stoichiometry/NATIMESVOLUME << ")*" << customized_propensities;
rightHandSide[cur_reaction->Reactants[j].Index] += temp_expressions.str();
}
for(std::size_t j=0; j<cur_reaction->Products.size(); ++j){
temp_expressions.str("");
temp_expressions << " +RCONST(" << (double)cur_reaction->Products[j].Stoichiometry/NATIMESVOLUME<< ")*" << customized_propensities;
rightHandSide[cur_reaction->Products[j].Index] += temp_expressions.str();
}
} else{
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::getODEReady): reaction " << cur_reaction->Id << " is not a mass-action or customized reaction\n";
return false;
}
}
ODE_ready = true;
return true;
}
// substitute parameters and species in custom propensities
std::string customPropensitySubstitution(std::string equation)
{
// locate a parameter name in equation
unsigned int begin = 0, end = 0;
std::string substitutedEquation = equation;
while( begin < substitutedEquation.length() ){
if( (isalpha(substitutedEquation.at(begin)) || substitutedEquation.at(begin) == '_') && ( (begin==0) || ((substitutedEquation.at(begin) != 'e') && (substitutedEquation.at(begin) != 'E')) || !(isalnum(substitutedEquation.at(begin-1)) || substitutedEquation.at(begin-1) == '_') )){
end = begin+1;
while( (end<substitutedEquation.length()) && (isalnum(substitutedEquation.at(end)) || substitutedEquation.at(end) == '_') )
++end;
std::string parameterName = substitutedEquation.substr(begin,end-begin);
// search for the parameter in ParametersList
unsigned int i = 0;
while( (i < this->ParametersList.size()) && (parameterName.compare(this->ParametersList[i].Id)!=0) )
++i;
if( i != this->ParametersList.size() ){
// substitute parameter with its value
// std::ostringstream parameterValue;
// parameterValue << this->ParametersList[i].Value;
// substitutedEquation.replace(begin, end-begin, parameterValue.str());
std::ostringstream parameterValue;
parameterValue << "data->p[" << i << "]";
substitutedEquation.replace(begin, end-begin, parameterValue.str());
begin = begin + parameterValue.str().size();
}
else{
// search for species in SpeciessList
unsigned int j = 0;
while( (j < this->SpeciesList.size()) && (parameterName.compare(this->SpeciesList[j].Id)!=0) )
++j;
if( j != this->SpeciesList.size() ){
// substitute species name with its population variable
std::ostringstream speciesReference;
speciesReference << "Ith(y," << j+1 <<")*"<<NATIMESVOLUME;
substitutedEquation.replace(begin, end-begin, speciesReference.str());
begin = begin + speciesReference.str().size();
}
else{
std::cout << "StochKit WARNING (Input_ODE_before_compile_mixed::customPropensitySubstitution): function \"" << parameterName << "\" written into custom propensity function, please make sure it's a legitimate c++ function \n";
begin = begin + parameterName.size();
}
}
}
else if (substitutedEquation.at(begin) == '/'){
substitutedEquation.replace(begin, 1, "/(double)");
begin += 9;
}
else{
++begin;
}
}
return substitutedEquation;
}
public:
bool writeODEFile(char *ODETemplateFileName, char *ODEFileName, std::vector<std::size_t> output_species_index, std::vector<std::string> output_species_names, std::vector<std::string> parameters_subset, double RTOL, double ATOL, unsigned int MXSTEPS)
{
if(!ODE_ready){
getODEReady();
}
std::size_t num_of_par;
std::vector<std::size_t> parameters_index;
if(parameters_subset.size() == 0){
num_of_par = this->NumberOfParameters;
parameters_index.resize(num_of_par);
for (std::size_t i=0; i<num_of_par; ++i) {
parameters_index[i] = i;
}
} else{
num_of_par = parameters_subset.size();
parameters_index.resize(num_of_par);
for (std::size_t i=0; i<num_of_par; ++i) {
parameters_index[i] = -1;
std::istringstream iss(parameters_subset[i]);
std::size_t index;
iss >> index;
if (!iss.fail()) {
std::cout << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): parameter \""<<parameters_subset[i]<<"\" should not be an integer, full parameter name only.\n";
exit(1);
} else {
for (std::size_t j=0; j<this->NumberOfParameters; ++j) {
if (parameters_subset[i].compare(this->ParametersList[j].Id)==0) {
parameters_index[i] = j;
break;
}
}
if(parameters_index[i] == -1){
std::cout << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): parameter \""<<parameters_subset[i]<<"\" can not be found in parameters' list.\n";
exit(1);
}
}
}
}
if(output_species_index.size() != output_species_names.size()){
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): output_species_index.size() != output_species_names.size(), something is seriously wrong." << std::endl;
exit(1);
} else if(output_species_index.size() == 0){
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): output_species_index.size() == 0. Please set approapriate species to output." << std::endl;
exit(1);
}
std::ifstream ODETemplateFile;
std::ofstream ODEFile;
ODETemplateFile.open(ODETemplateFileName);
ODEFile.open(ODEFileName);
if( !ODETemplateFile.is_open() ){
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): open ODE template file " << ODETemplateFileName << " failed." << std::endl;
exit(1);
} else if( !ODEFile.is_open() ) {
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): open write-to ODE file " << ODEFileName << " failed." << std::endl;
exit(1);
}
_populationVectorType initialPop = writeInitialConcentration();
std::string line;
std::size_t insert_found;
while(ODETemplateFile.good()){
getline(ODETemplateFile, line);
insert_found = line.find("INSERT GENERATED");
if(insert_found == std::string::npos){
ODEFile << line << std::endl;
} else {
if(line.find("CONSTANTS") != std::string::npos){
ODEFile << line << std::endl;
ODEFile << "#define RTOL RCONST(" << RTOL << ") /* scalar relative tolerance */" << std::endl;
ODEFile << "#define ATOL RCONST(" << ATOL << ") /* scalar absolute tolerance components */" << std::endl;
ODEFile << "#define MXSTEPS " << MXSTEPS << " /* max steps before tout */" << std::endl;
ODEFile << "#define NEQ " << this->NumberOfSpecies << " /* number of equations */" << std::endl;
ODEFile << "#define OUTPUT_SPECIES_NUMBER " << output_species_index.size() << " /* number of species in output */" << std::endl;
ODEFile << "#define NUMPAR " << this->NumberOfParameters << " /* number of parameters */" << std::endl;
ODEFile << "#define NUMPAR_SENSI " << num_of_par << " /* number of parameters/rate constants in sensitivity analysis */" << std::endl;
} else if (line.find("INITIAL CONDITION") != std::string::npos){
ODEFile << line << std::endl;
for(int i=0;i<this->NumberOfSpecies;++i){
ODEFile << " Ith(y," << i+1 << ") = RCONST(" << (double)initialPop[i]/volume <<");" << std::endl;
}
} else if (line.find("PARAMETERS LIST") != std::string::npos){
ODEFile << line << std::endl;
for(int i=0;i<this->NumberOfParameters;++i){
ODEFile << " data->p[" << i << "] = RCONST(" << this->ParametersList[i].Value <<");" << std::endl;
}
} else if (line.find("RIGHT HAND SIDE") != std::string::npos){
ODEFile << line << std::endl;
for(int i=0;i<this->NumberOfSpecies;++i){
ODEFile << " Ith(ydot," << i+1 << ") = " << rightHandSide[i] << ";" << std::endl;
}
} else if (line.find("OUTPUT SPECIES NAMES") != std::string::npos){
ODEFile << line << std::endl;
ODEFile << " char *species_names[" << output_species_index.size() << "];" << std::endl;
for(std::size_t i=0;i<output_species_index.size();++i){
ODEFile << " species_names[" << i << "] = \"" << output_species_names[i] << "\";" << std::endl;
}
} else if (line.find("OUTPUT SPECIES INDEX") != std::string::npos){
ODEFile << line << std::endl;
ODEFile << " int species_index[" << output_species_index.size() << "] = { ";
for(std::size_t i=0;i<output_species_index.size()-1;++i){
ODEFile << " " << output_species_index[i] << ", ";
}
ODEFile << " " << output_species_index[output_species_index.size()-1] << " ";
ODEFile << " };" << std::endl;
} else if (line.find("PLIST") != std::string::npos){
ODEFile << line << std::endl;
ODEFile << " int plist[NUMPAR_SENSI] = {";
for(int j=0;j<num_of_par-1;++j){
ODEFile << " " << parameters_index[j] << ",";
}
ODEFile << " " << parameters_index[num_of_par-1];
ODEFile << "};" << std::endl;
} else if (line.find("OUTPUT PARAMETERS NAMES") != std::string::npos){
ODEFile << line << std::endl;
ODEFile << " char *parameters_names[NUMPAR_SENSI];" << std::endl;
for(int j=0;j<num_of_par;++j){
ODEFile << " parameters_names[" << j << "] = \"" << this->ParametersList[parameters_index[j]].Id << "\";" << std::endl;
}
} else{
std::cerr << "StochKit ERROR (Input_ODE_before_compile_mixed::writeODEFile): template file corrupted, indication line not recognized: " << line;
ODETemplateFile.close();
ODEFile.close();
exit(1);
}
/*
while(ODETemplateFile.good()){
getline(ODETemplateFile, line);
end_found = line.find("END OF GENERATED");
if(end_found != std::string::npos){
ODEFile << line;
break;
}
}
*/
}
}
ODETemplateFile.close();
ODEFile.close();
return true;
}
protected:
int findParameterWithId(std::string givenId)
{
int found = -1;
for( unsigned int i = 0; i < this->ParametersList.size(); ++i ){
if(this->ParametersList[i].Id.compare(givenId) == 0){
found = (int)i;
break;
}
}
return found;
}
_populationValueType concentrationCalculation(std::string equation)
{
std::vector<unsigned int> ParametersAffectRate;
std::vector<unsigned int>::iterator para_it; // iterator of parameters in link graph
ParametersAffectRate = ParametersList.analyzeParameterExpression(equation);
bool calculationStatus = false;
for( para_it = ParametersAffectRate.begin(); para_it < ParametersAffectRate.end(); ++para_it ){
if( ParametersList[*para_it].CalculateFlag == -1 ){
calculationStatus = ParametersList.calculateParameter(*para_it);
if(!calculationStatus){
std::cerr << "StochKit ERROR (Input::populationCalculation): while calculating rate " << equation << std::endl;
return BADRESULT;
}
}
}
std::string substitutedEquation = customPropensitySubstitution(equation);
if( substitutedEquation.empty() ){
std::cerr << "StochKit ERROR (Input::populationCalculation): while calculating initial population " << equation << std::endl;
return BADRESULT;
}
double calculatedPopulation = simpleCalculator.calculateString(substitutedEquation);
return (_populationValueType)calculatedPopulation;
}
_populationVectorType writeInitialConcentration()
{
_populationValueType cur_population;
_populationVectorType X(NumberOfSpecies);
for(int i=0; i<NumberOfSpecies; ++i){
cur_population = concentrationCalculation(SpeciesList[i].InitialPopulation);
if( cur_population == BADRESULT ){
std::cerr << "StochKit ERROR (Input_ODE_before_compilation::writeInitialConcentration): while calculating initial population of " << SpeciesList[i].Id << std::endl;
exit(1);
}
X[i] = cur_population;
}
return X;
}
};
}
#endif