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setInfoFunction.cpp
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setInfoFunction.cpp
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#include "spatialsim/setInfoFunction.h"
#include "spatialsim/mystruct.h"
#include "spatialsim/initializeFunction.h"
#include "spatialsim/searchFunction.h"
#include "spatialsim/astFunction.h"
#include "spatialsim/options.h"
#include "sbml/SBMLTypes.h"
#include "sbml/packages/spatial/common/SpatialExtensionTypes.h"
#include "sbml/packages/spatial/extension/SpatialModelPlugin.h"
#include <vector>
#include <iostream>
#include <fstream>//added by Morita
#include <string>//added by Morita
using namespace std;
LIBSBML_CPP_NAMESPACE_USE
void setCompartmentInfo(Model *model, std::vector<variableInfo*> &varInfoList)
{
ListOfCompartments *loc = model->getListOfCompartments();
unsigned int numOfCompartments = static_cast<unsigned int>(model->getNumCompartments());
unsigned int i;
for (i = 0; i < numOfCompartments; i++) {
Compartment *c = loc->get(i);
variableInfo *info = new variableInfo;
InitializeVarInfo(info);
varInfoList.push_back(info);
info->com = c;
info->id = c->getId().c_str();
if (model->getRule(info->id) == 0) {
info->isResolved = true;
info->isUniform = true;
info->value = (c->isSetSize()) ? new double(c->getSize()) : new double(1.0);
}
}
}
void setSpeciesInfo(Model *model, std::vector<variableInfo*> &varInfoList, unsigned int volDimension, unsigned int memDimension, int Xindex, int Yindex, int Zindex)
{
SpatialModelPlugin *spPlugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));//added by Morita
ListOfSpecies *los = model->getListOfSpecies();
unsigned int numOfSpecies = static_cast<unsigned int>(model->getNumSpecies());
unsigned int i;
int X, Y, Z;
unsigned int Xdiv = (Xindex + 1)/2, Ydiv = (Yindex + 1)/2, Zdiv = (Zindex + 1)/2;//added by Morita
unsigned int numOfVolIndexes = Xindex * Yindex * Zindex;
for (i = 0; i < numOfSpecies; i++) {
Species *s = los->get(i);
SpatialSpeciesPlugin* splugin = static_cast<SpatialSpeciesPlugin*>(s->getPlugin("spatial"));
//species have spatial extension
if (splugin->getIsSpatial()) {
variableInfo *info = new variableInfo;
InitializeVarInfo(info);
varInfoList.push_back(info);
info->sp = s;
info->com = model->getCompartment(s->getCompartment());
info->id = s->getId().c_str();
info->name = s->getName().c_str();
if (info->com->getSpatialDimensions()== volDimension) {
info->inVol = true;
} else if (info->com->getSpatialDimensions()== memDimension) {
info->inVol = false;
}
info->isLeaked = false;
//Species have Local Concentration at a Compartment added by Morita
if( model->getInitialAssignment(s->getId()) ){
InitialAssignment* ia = model->getInitialAssignment(s->getId());
if( ia->isSetMath() ){
if(model->getParameter(ia->getMath()->getName())){
Parameter *p = model->getParameter(ia->getMath()->getName());
Geometry* geo = spPlugin->getGeometry();
ListOfSampledFields* losf = geo->getListOfSampledFields();
SampledField* sf = losf->get( p->getId() );
int* samples = new int[ Xdiv * Ydiv * Zdiv ];
//get intensity in model
sf->getSamples( samples );
//initialize matrix "info->value"
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
info->delta = new double[4 * numOfVolIndexes];
fill_n(info->delta, 4 * numOfVolIndexes, 0.0);
//converted into sparse matrix
double sum = 0;
for( Z = 0; Z < Zdiv; Z++ ){
for( Y = 0; Y < Ydiv; Y++ ){
for( X = 0; X < Xdiv; X++ ){
info->value[ (2*Z) * Yindex * Xindex + (2*Y) * Xindex + (2*X) ] = samples[ Z * Ydiv * Xdiv + (Ydiv -1 -Y) * Xdiv + X ];
sum += samples[ Z * Ydiv * Xdiv + (Ydiv -1 -Y) * Xdiv + X ];
//check samples value
/*if( samples[ Z * Ydiv * Xdiv + (Ydiv -1 -Y) * Xdiv + X ] > 0 ){
cout << endl;
cout << "X:" +to_string(X)+ " Y:" +to_string(Y)+ " Z:"+to_string(Z)+ " value:"; //<- Check Intensity
cout << samples[ Z * Ydiv * Xdiv + (Ydiv -1 -Y) * Xdiv + X ] << endl;
cout << endl;*/
}
}
}
delete[] samples;
}
}
}
//Species have Uniform Concentration at a Compartment
else if( model->getInitialAssignment(s->getId()) == 0 ){
//species value is specified by initial amount, initial value, rule or initial assignment
//species is spatially defined
if (s->isSetInitialAmount() || s->isSetInitialConcentration()) {//Initial Amount or Initial Concentration
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
//if (!s->isSetConstant() || !s->getConstant()) {
info->delta = new double[4 * numOfVolIndexes];
fill_n(info->delta, 4 * numOfVolIndexes, 0.0);
//}
if (s->isSetInitialAmount()) {//Initial Amount
info->isResolved = true;
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
if( X%2==0 && Y%2==0 ){ // original point
if( s->getCompartment().find("membrane") == std::string::npos ){
info->value[Z * Yindex * Xindex + Y * Xindex + X] = s->getInitialAmount();
} else
info->value[Z * Yindex * Xindex + Y * Xindex + X] = 0.0;
} else { // for membrane
if( s->getCompartment().find("membrane") == std::string::npos ){
info->value[Z * Yindex * Xindex + Y * Xindex + X] = 0.0;
} else
info->value[Z * Yindex * Xindex + Y * Xindex + X] = s->getInitialAmount();
}
}
}
}
} else if (s->isSetInitialConcentration()) {//Initial Concentration
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
if( X%2==0 && Y%2==0 ){ // original pixels
if( s->getCompartment().find("membrane") == std::string::npos ){
info->value[Z * Yindex * Xindex + Y * Xindex + X] = s->getInitialConcentration();
} else
info->value[Z * Yindex * Xindex + Y * Xindex + X] = 0.0;
} else { // for membrane
if( s->getCompartment().find("membrane") == std::string::npos ){
info->value[Z * Yindex * Xindex + Y * Xindex + X] = 0.0;
} else
info->value[Z * Yindex * Xindex + Y * Xindex + X] = s->getInitialConcentration();
}
}
}
}
}
}
}
info -> isResolved = true;
}
}
}
void setParameterInfo(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<boundaryMembrane*> &bMemInfoList, int Xdiv, int Ydiv, int Zdiv, double &Xsize, double &Ysize, double &Zsize, double &deltaX, double &deltaY, double &deltaZ, char *&xaxis, char *&yaxis, char *&zaxis, double mesh)
{
SpatialModelPlugin *spPlugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
Geometry *geometry = spPlugin->getGeometry();
ListOfParameters *lop = model->getListOfParameters();
unsigned int numOfParameters = static_cast<unsigned int>(model->getNumParameters());
unsigned int i;
int X, Y, Z;
int Xindex = 2 * Xdiv - 1, Yindex = 2 * Ydiv - 1, Zindex = 2 * Zdiv - 1;//num of mesh
int numOfVolIndexes = Xindex * Yindex * Zindex;
string XmaxId = "", XminId = "", YmaxId = "", YminId = "", ZmaxId = "", ZminId = "";
//id of coordinate boundary
//cc = geometry->getCoordinateComponent(p->getId());
for (i = 0; i < geometry->getNumCoordinateComponents(); i++) {
CoordinateComponent *cc = geometry->getCoordinateComponent(i);
if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_X) {
XmaxId = cc->getBoundaryMax()->getId();
XminId = cc->getBoundaryMin()->getId();
}
if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_Y) {
YmaxId = cc->getBoundaryMax()->getId();
YminId = cc->getBoundaryMin()->getId();
}
if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_Z) {
ZmaxId = cc->getBoundaryMax()->getId();
ZminId = cc->getBoundaryMin()->getId();
}
}
for (i = 0; i < numOfParameters; i++) {
Parameter *p = lop->get(i);
SpatialParameterPlugin *pPlugin = static_cast<SpatialParameterPlugin*>(p->getPlugin("spatial"));
variableInfo *info = new variableInfo;
BoundaryCondition *bcon;
CoordinateComponent *cc;
variableInfo *sInfo;
InitializeVarInfo(info);
varInfoList.push_back(info);
info->para = p;
info->id = p->getId().c_str();
if (!pPlugin->isSpatialParameter()) {//normal parameters
if (model->getRule(info->id) == 0 && p->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
info->value = new double(p->getValue());
}
} else {//spatial parameter plugin
switch (pPlugin->getType()) {
case SBML_SPATIAL_DIFFUSIONCOEFFICIENT://diffusion coefficient
{
sInfo = searchInfoById(varInfoList, pPlugin->getDiffusionCoefficient()->getVariable().c_str());
if (sInfo->diffCInfo == 0) {
sInfo->diffCInfo = new variableInfo*[3];
fill_n(sInfo->diffCInfo, 3, reinterpret_cast<variableInfo*>(0));
}
DiffusionCoefficient* dc = pPlugin->getDiffusionCoefficient();
switch (dc->getType()) {
case SPATIAL_DIFFUSIONKIND_ISOTROPIC:
sInfo->diffCInfo[0] = info;
sInfo->diffCInfo[1] = info;
if(Zindex > 1) sInfo->diffCInfo[2] = info;
break;
case SPATIAL_DIFFUSIONKIND_ANISOTROPIC:
sInfo->diffCInfo[dc->getCoordinateReference1() - 1] = info;
break;
case SPATIAL_DIFFUSIONKIND_TENSOR:
sInfo->diffCInfo[dc->getCoordinateReference1() - 1] = info;
sInfo->diffCInfo[dc->getCoordinateReference2() - 1] = info;
break;
case SPATIAL_DIFFUSIONKIND_INVALID:
cerr << "warning: Diffusion_Kind == Unknown" << endl;
break;
}
if (model->getRule(info->id) == 0 && p->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
switch (dc->getType()) {
case SPATIAL_DIFFUSIONKIND_ISOTROPIC:
info->value = new double(p->getValue());
break;
case SPATIAL_DIFFUSIONKIND_ANISOTROPIC:
info->value = new double(p->getValue());
break;
case SPATIAL_DIFFUSIONKIND_TENSOR:
info->value = new double(p->getValue());
break;
case SPATIAL_DIFFUSIONKIND_INVALID:
cerr << "warning: Diffusion_Kind == Unknown" << endl;
break;
}
}
}
break;
case SBML_SPATIAL_ADVECTIONCOEFFICIENT://advection coefficient
sInfo = searchInfoById(varInfoList, pPlugin->getAdvectionCoefficient()->getVariable().c_str());
if (sInfo->adCInfo == 0) {
sInfo->adCInfo = new variableInfo*[3];
fill_n(sInfo->adCInfo, 3, reinterpret_cast<variableInfo*>(0));
}
sInfo->adCInfo[pPlugin->getAdvectionCoefficient()->getCoordinate() - 1] = info;
if (model->getRule(info->id) == 0 && p->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
info->value = new double(p->getValue());
}
break;
case SBML_SPATIAL_BOUNDARYCONDITION://boundary condition
{
sInfo = searchInfoById(varInfoList, pPlugin->getBoundaryCondition()->getVariable().c_str());
bcon = pPlugin->getBoundaryCondition();
if (sInfo->boundaryInfo == 0) {
sInfo->boundaryInfo = new variableInfo*[6];
fill_n(sInfo->boundaryInfo, 6, reinterpret_cast<variableInfo*>(0));
}
if (sInfo != 0 &&bcon != 0) {
//image edge
if( bcon->getCoordinateBoundary().find("membrane") == std::string::npos ){
int boundaryIndex = -1;
if (bcon->getCoordinateBoundary() == XmaxId) boundaryIndex = Xmax;
if (bcon->getCoordinateBoundary() == XminId) boundaryIndex = Xmin;
if (bcon->getCoordinateBoundary() == YmaxId) boundaryIndex = Ymax;
if (bcon->getCoordinateBoundary() == YminId) boundaryIndex = Ymin;
if (bcon->getCoordinateBoundary() == ZmaxId) boundaryIndex = Zmax;
if (bcon->getCoordinateBoundary() == ZminId) boundaryIndex = Zmin;
if (boundaryIndex != -1) {
sInfo->boundaryInfo[boundaryIndex] = info;
if (model->getRule(info->id) == 0 && p->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
info->value = new double(p->getValue());
}
}
} else { //membrane
if (model->getRule(info->id) == 0 && p->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
boundaryMembrane *bMem = new boundaryMembrane;
InitializeBMemInfo(bMem);
bMemInfoList.push_back(bMem);
bMem->name = bcon->getCoordinateBoundary().c_str();
switch(pPlugin->getBoundaryCondition()->getType()){
case SPATIAL_BOUNDARYKIND_NEUMANN:
bMem->bcType = 1;//neumann
break;
case SPATIAL_BOUNDARYKIND_DIRICHLET:
bMem->bcType = 2;//neumann
break;
default:
bMem->bcType = 3;//others
break;
}
bMem->value = p->getValue();
bMem->sId = sInfo->sp->getId().c_str();
bMem->sName = sInfo->sp->getName().c_str();
bMem->sCompartment = sInfo->com->getId().c_str();
variableInfo *originalSpecies = searchInfoById(varInfoList,bMem->sId);
originalSpecies->isLeaked = true;
bMem->position = new double[numOfVolIndexes];
fill_n(bMem->position, numOfVolIndexes, 0);
//adjacent compartment
unsigned int geoAdDnum = 0;
for (geoAdDnum = 0; geoAdDnum < geometry->getNumAdjacentDomains(); geoAdDnum++) {
AdjacentDomains *adDomain = geometry->getAdjacentDomains(geoAdDnum);
Domain *ad1 = geometry->getDomain(adDomain->getDomain1());
Domain *ad2 = geometry->getDomain(adDomain->getDomain2());
if( strcmp(ad1->getDomainType().c_str(),bMem->name)==0 || strcmp(ad2->getDomainType().c_str(),bMem->name)==0 ){
if( strcmp(bMem->name, ad1->getDomainType().c_str()) != 0 && strcmp(bMem->sCompartment, ad1->getDomainType().c_str()) != 0 ){
bMem->tCompartment = ad1->getDomainType().c_str();
}
if( strcmp(bMem->name, ad2->getDomainType().c_str()) != 0 && strcmp(bMem->sCompartment, ad2->getDomainType().c_str()) != 0 ){
bMem->tCompartment = ad2->getDomainType().c_str();
}
}
}
bMem->tId = searchSInfoByCompartment_Name(varInfoList,sInfo->name,bMem->tCompartment)->id;
variableInfo *psInfo = searchInfoById(varInfoList, bMem->tId);
if( psInfo!=0 ){//model has leaked species
psInfo->isLeaked = false; // required to consider
} else {//model has no leaked species
cout<< bMem->tId <<endl;
//making new species in model
Species* newSpecies = model->createSpecies();
newSpecies->setId(std::string(bMem->tId));
model->addSpecies(newSpecies);
//making new species variable
variableInfo *newSInfo = new variableInfo;
InitializeVarInfo(newSInfo);
varInfoList.push_back(newSInfo);
newSInfo->sp = newSpecies;
newSInfo->com = model->getCompartment(std::string(bMem->tCompartment));
newSInfo->id = newSpecies->getId().c_str();
newSInfo->isLeaked = true;
newSInfo->value = new double[numOfVolIndexes];
fill_n(newSInfo->value, numOfVolIndexes, 0);
newSInfo->delta = new double[4 * numOfVolIndexes];
fill_n(newSInfo->delta, 4 * numOfVolIndexes, 0.0);
}
}
}
}
}
break;
case SBML_SPATIAL_SPATIALSYMBOLREFERENCE: {//spatial symbol reference
// if (pPlugin->getSpatialSymbolReference()->getType() == "coordinateComponent")
cc = geometry->getCoordinateComponent(pPlugin->getSpatialSymbolReference()->getSpatialRef());
if(cc != NULL){//added by Morita
double min = cc->getBoundaryMin()->getValue();
double max = cc->getBoundaryMax()->getValue();
if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_X) {
//if( mesh == 0 ){
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
xaxis = const_cast<char*>(p->getId().c_str());
Xsize = max - min;
deltaX = (max - min) / (Xdiv - 1);
info->isResolved = true;
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
info->value[Z * Yindex * Xindex + Y * Xindex + X] = min + static_cast<double>(X) * deltaX / 2.0;
}
}
}
//}
} else if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_Y) {
//if( mesh == 0 ){
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
yaxis = const_cast<char*>(p->getId().c_str());
Ysize = max - min;
deltaY = (max - min) / (Ydiv - 1);
info->isResolved = true;
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
info->value[Z * Yindex * Xindex + Y * Xindex + X] = min + static_cast<double>(Y) * deltaY / 2.0;
}
}
}
//}
} else if (cc->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_Z) {
//if( mesh == 0 ){
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
zaxis = const_cast<char*>(p->getId().c_str());
Zsize = max - min;
deltaZ = (max - min) / (Zdiv - 1);
info->isResolved = true;
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
info->value[Z * Yindex * Xindex + Y * Xindex + X] = min + static_cast<double>(Z) * deltaZ / 2.0;
}
}
}
//}
}
//cout << endl;
}
}
break;
default:
break;
}
}
}
}
void setReactionInfo(Model *model, std::vector<variableInfo*> &varInfoList, vector<reactionInfo*> &rInfoList, vector<reactionInfo*> &fast_rInfoList, unsigned int numOfVolIndexes)
{
ListOfReactions *lor = model->getListOfReactions();
unsigned int numOfReactions = static_cast<unsigned int>(model->getNumReactions());
unsigned int i, j, k;
ASTNode *ast = 0;
unsigned int numOfASTNodes = 0;
Species *s;
for (i = 0; i < numOfReactions; i++) {
Reaction *r = lor->get(i);
const KineticLaw *kl = r->getKineticLaw();
if (kl != 0) {
for (j = 0; j < kl->getNumLocalParameters(); j++) {
const LocalParameter *lp = kl->getLocalParameter(j);
variableInfo *info = new variableInfo;
InitializeVarInfo(info);
info->id = lp->getId().c_str();
if (model->getRule(info->id) == 0 && lp->isSetValue()) {
info->isResolved = true;
info->isUniform = true;
info->value = new double(lp->getValue());
}
varInfoList.push_back(info);
}
reactionInfo *rInfo = new reactionInfo;
rInfo->reaction = r;
for (j = 0; j < r->getNumReactants(); j++) {
SpeciesReference *sr_re = r->getReactant(j);
Species *reactant = model->getSpecies(sr_re->getSpecies());
for (k = 0; k < r->getNumProducts(); k++) {
SpeciesReference *sr_pro = r->getProduct(k);
Species *product = model->getSpecies(sr_pro->getSpecies());
if (reactant->getCompartment() != product->getCompartment()) {
rInfo->isMemTransport = true;
goto end;
}
}
}
rInfo->isMemTransport = false;
end:
for (j = 0; j < r->getNumReactants(); j++) {
rInfo->spRefList.push_back(searchInfoById(varInfoList, r->getReactant(j)->getSpecies().c_str()));
rInfo->srStoichiometry.push_back(r->getReactant(j)->getStoichiometry());
s = model->getSpecies(r->getReactant(j)->getSpecies());
if (!s->isSetConstant() || !s->getConstant() || !s->getBoundaryCondition()) {
rInfo->isVariable.push_back(true);
} else {
rInfo->isVariable.push_back(false);
}
}
for (j = 0; j < r->getNumProducts(); j++) {
rInfo->spRefList.push_back(searchInfoById(varInfoList, r->getProduct(j)->getSpecies().c_str()));
rInfo->srStoichiometry.push_back(r->getProduct(j)->getStoichiometry());
s = model->getSpecies(r->getProduct(j)->getSpecies());
if (!s->isSetConstant() || !s->getConstant() || !s->getBoundaryCondition()) {
rInfo->isVariable.push_back(true);
} else {
rInfo->isVariable.push_back(false);
}
}
//mashimo
for (j = 0; j < r->getNumModifiers(); j++) {
rInfo->spRefList.push_back(searchInfoById(varInfoList, r->getModifier(j)->getSpecies().c_str()));
//rInfo->srStoichiometry.push_back();//Modifierはstoichiometry持ってない
s = model->getSpecies(r->getModifier(j)->getSpecies());
if (!s->isSetConstant() || !s->getConstant() || !s->getBoundaryCondition()) {
rInfo->isVariable.push_back(true);
} else {
rInfo->isVariable.push_back(false);
}
}
rInfo->id = r->getId().c_str();
rInfo->value = new double[numOfVolIndexes];
fill_n(rInfo->value, numOfVolIndexes, 0);
ast = const_cast<ASTNode*>(kl->getMath());
unsigned int tmp = 0;
countAST(ast, tmp);
//cout << "before reaction: " << SBML_formulaToString(ast) << endl;
//cerr << "num_of_nodes: " << tmp << endl;
rearrangeAST(ast);
if (rInfo->isMemTransport == false) {
cout << "reaction: " << SBML_formulaToString(ast) << endl;
} else {
cout << "mem trans: " << SBML_formulaToString(ast) << endl;
}
numOfASTNodes = 0;
countAST(ast, numOfASTNodes);
//cerr << "num_of_nodes: " << numOfASTNodes << endl;
rInfo->rpInfo = new reversePolishInfo();
rInfo->rpInfo->varList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->varList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->deltaList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->deltaList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->constList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->constList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->opfuncList = new int[numOfASTNodes];
fill_n(rInfo->rpInfo->opfuncList, numOfASTNodes, 0);
rInfo->rpInfo->listNum = numOfASTNodes;
parseAST(ast, rInfo->rpInfo, varInfoList, numOfASTNodes);
if (!r->getFast()) {
rInfoList.push_back(rInfo);
} else {
fast_rInfoList.push_back(rInfo);
}
}
}
}
void setRateRuleInfo(Model *model, std::vector<variableInfo*> &varInfoList, std::vector<reactionInfo*> &rInfoList, unsigned int numOfVolIndexes)
{
unsigned int numOfRules = static_cast<unsigned int>(model->getNumRules());
unsigned int i;
ASTNode *ast = 0;
unsigned int numOfASTNodes = 0;
Species *s;
for (i = 0; i < numOfRules; i++) {
if (model->getRule(i)->isRate()) {
RateRule *rrule = static_cast<RateRule*>(model->getRule(i));
reactionInfo *rInfo = new reactionInfo;
rInfo->id = rrule->getVariable().c_str();
rInfo->value = new double[numOfVolIndexes];
fill_n(rInfo->value, numOfVolIndexes, 0);
ast = const_cast<ASTNode*>(rrule->getMath());
rearrangeAST(ast);
cout << "rate rule: " << SBML_formulaToString(ast) << endl;
numOfASTNodes = 0;
countAST(ast, numOfASTNodes);
rInfo->rpInfo = new reversePolishInfo();
rInfo->rpInfo->varList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->varList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->deltaList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->deltaList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->constList = new double*[numOfASTNodes];
fill_n(rInfo->rpInfo->constList, numOfASTNodes, reinterpret_cast<double*>(0));
rInfo->rpInfo->opfuncList = new int[numOfASTNodes];
fill_n(rInfo->rpInfo->opfuncList, numOfASTNodes, 0);
rInfo->rpInfo->listNum = numOfASTNodes;
parseAST(ast, rInfo->rpInfo, varInfoList, numOfASTNodes);
rInfo->spRefList.push_back(searchInfoById(varInfoList, rrule->getVariable().c_str()));
rInfo->srStoichiometry.push_back(1.0);
s = model->getSpecies(rrule->getVariable());
if (!s->isSetConstant() || !s->getConstant() || !s->getBoundaryCondition()) {
rInfo->isVariable.push_back(true);
} else {
rInfo->isVariable.push_back(false);
}
rInfoList.push_back(rInfo);
}
}
}
normalUnitVector* setNormalAngle(std::vector<GeometryInfo*> &geoInfoList, double Xsize, double Ysize, double Zsize, int dimension, int Xindex, int Yindex, int Zindex, unsigned int numOfVolIndexes)
{
unsigned int i, j, k, step_kXY = 0, step_kYZ = 0, step_kXZ = 0;
int X, Y, Z, index;
normalUnitVector *nuVec = new normalUnitVector[numOfVolIndexes];
int *isD = 0;
GeometryInfo *geoInfo = 0;
double X1 = 0.0, X2 = 0.0, Y1 = 0.0, Y2 = 0.0, Z1 = 0.0, Z2 = 0.0, len, rhoXY = 0.0, rhoYZ = 0.0, rhoXZ = 0.0;
double a = 0.0, b = 0.0, c = 0.0;//length of triangle
double max_radiusXY = 0.0, max_radiusYZ = 0.0, max_radiusXZ = 0.0;
int startX, startY, startZ;
int preD = -1;
int Xdiv = (Xindex + 1) / 2;
int Ydiv = (Yindex + 1) / 2;
int Zdiv = (Zindex + 1) / 2;
double hX = 1.0, hY = 1.0, hZ = 1.0;//grid size
double hXY = 1.0, hYZ = 1.0, hXZ = 1.0;
//double XYratio = Ysize / Xsize, XZratio = Zsize / Xsize;// unused varibale
int xyPlaneX[2] = {0}, xyPlaneY[2] = {0}, yzPlaneY[2] = {0}, yzPlaneZ[2] = {0}, xzPlaneX[2] = {0}, xzPlaneZ[2] = {0};
/*
hX = 1.0 / (Xdiv - 1);
hY = XYratio / (Ydiv - 1);
if (dimension == 2) {
hXY = (hX + hY) / 2.0;
} else if (dimension == 3) {
hZ = XZratio / (Zdiv - 1);
hXY = (hX + hY) / 2.0;
hYZ = (hY + hZ) / 2.0;
hXZ = (hX + hZ) / 2.0;
}
*/
hX = Xsize / (Xdiv - 1);
hY = Ysize / (Ydiv - 1);
if (dimension == 2) {
hXY = (hX + hY) / 2.0;
} else if (dimension == 3) {
hZ = Zsize / (Zdiv - 1);
hXY = (hX + hY) / 2.0;
hYZ = (hY + hZ) / 2.0;
hXZ = (hX + hZ) / 2.0;
}
if (dimension >= 2) {
for (i = 0; i < geoInfoList.size(); i++) {
geoInfo = geoInfoList[i];
isD = geoInfo->isDomain;
if (geoInfo->isVol == false) {//avol is membrane
//calc max_radius
for (j = 0; j < geoInfo->domainIndex.size(); j++) {
index = geoInfo->domainIndex[j];
Z = index / (Xindex * Yindex);
Y = (index - Z * Xindex * Yindex) / Xindex;
X = index - Z * Xindex * Yindex - Y * Xindex;
startX = X;
startY = Y;
startZ = Z;
preD = -1;
//calc max|r_i - r_j|
max_radiusXY = 0.0;
max_radiusYZ = 0.0;
max_radiusXZ = 0.0;
if ((geoInfo->bType[index].isBofXp && geoInfo->bType[index].isBofXm) || (geoInfo->bType[index].isBofYp && geoInfo->bType[index].isBofYm)) {//xy plane
for (k = 0; k < geoInfo->domainIndex.size(); k++) {
if ((Y + 2 < Yindex) &&
(isD[Z * Yindex * Xindex + (Y + 2) * Xindex + X] == 1 && isD[Z * Yindex * Xindex + (Y + 1) * Xindex + X] == 2 && preD != S)) {//north
//X = X;//self assign
Y = Y + 2;
preD = N;
} else if (isD[Z * Yindex * Xindex + (Y + 1) * Xindex + (X + 1)] == 1 && preD != SW) {//northeast
X = X + 1;
Y = Y + 1;
preD = NE;
} else if (isD[Z * Yindex * Xindex + Y * Xindex + (X + 2)] == 1 && isD[Z * Yindex * Xindex + Y * Xindex + (X + 1)] == 2 && preD != W) {//east
X = X + 2;
//Y = Y;//self assign
preD = E;
} else if (isD[Z * Yindex * Xindex + (Y - 1) * Xindex + (X + 1)] == 1 && preD != NW) {//southeast
X = X + 1;
Y = Y - 1;
preD = SE;
} else if ((Y - 2 >= 0) &&
(isD[Z * Yindex * Xindex + (Y - 2) * Xindex + X] == 1 && isD[Z * Yindex * Xindex + (Y - 1) * Xindex + X] == 2 && preD != N)) {//south
//X = X;//self assign
Y = Y - 2;
preD = S;
} else if (isD[Z * Yindex * Xindex + (Y - 1) * Xindex + (X - 1)] == 1 && preD != NE) {//southwest
X = X - 1;
Y = Y - 1;
preD = SW;
} else if (isD[Z * Yindex * Xindex + Y * Xindex + (X - 2)] == 1 && isD[Z * Yindex * Xindex + Y * Xindex + (X - 1)] == 2 && preD != E) {//west
X = X - 2;
//Y = Y;//self assign
preD = W;
} else if (isD[Z * Yindex * Xindex + (Y + 1) * Xindex + (X - 1)] == 1 && preD != SE) {//northwest
X = X - 1;
Y = Y + 1;
preD = NW;
}
max_radiusXY = max(max_radiusXY, sqrt(pow(((X - startX) / 2) * hX, 2) + pow(((Y - startY) / 2) * hY, 2)) / 2.0);
if (X == startX && Y == startY) {
break;
}
}
}
X = startX;
Y = startY;
Z = startZ;
preD = -1;
if (dimension == 3) {
if ((geoInfo->bType[index].isBofYp && geoInfo->bType[index].isBofYm) || (geoInfo->bType[index].isBofZp && geoInfo->bType[index].isBofZm)) {//yz plane
for (k = 0; k < geoInfo->domainIndex.size(); k++) {
if ((Z + 2 < Zindex) &&
(isD[(Z + 2) * Yindex * Xindex + Y * Xindex + X] == 1 && isD[(Z + 1) * Yindex * Xindex + Y * Xindex + X] == 2 && preD != S)) {//north
//Y = Y;//self assign
Z = Z + 2;
preD = N;
} else if (isD[(Z + 1) * Yindex * Xindex + (Y + 1) * Xindex + X] == 1 && preD != SW) {//northeast
Y = Y + 1;
Z = Z + 1;
preD = NE;
} else if (isD[Z * Yindex * Xindex + (Y + 2) * Xindex + X] == 1 && isD[Z * Yindex * Xindex + (Y + 1) * Xindex + X] == 2 && preD != W) {//east
Y = Y + 2;
//Z = Z;//self assign
preD = E;
} else if (isD[(Z - 1) * Yindex * Xindex + (Y + 1) * Xindex + X] == 1 && preD != NW) {//southeast
Y = Y + 1;
Z = Z - 1;
preD = SE;
} else if ((Z - 2 >= 0) &&
(isD[(Z - 2) * Yindex * Xindex + Y * Xindex + X] == 1 && isD[(Z - 1) * Yindex * Xindex + Y * Xindex + X] == 2 && preD != N)) {//south
//Y = Y;//self assign
Z = Z - 2;
preD = S;
} else if (isD[(Z - 1) * Yindex * Xindex + (Y - 1) * Xindex + X] == 1 && preD != NE) {//southwest
Y = Y - 1;
Z = Z - 1;
preD = SW;
} else if (isD[Z * Yindex * Xindex + (Y - 2) * Xindex + X] == 1 && isD[Z * Yindex * Xindex + (Y - 1) * Xindex + X] == 2 && preD != E) {//west
Y = Y - 2;
//Z = Z;//self assign
preD = W;
} else if (isD[(Z + 1) * Yindex * Xindex + (Y - 1) * Xindex + X] == 1 && preD != SE) {//northwest
Y = Y - 1;
Z = Z + 1;
preD = NW;
}
max_radiusYZ = max(max_radiusYZ, sqrt(pow(((Y - startY) / 2) * hY, 2) + pow(((Z - startZ) / 2) * hZ, 2)) / 2.0);
if (Y == startY && Z == startZ) {
break;
}
}
}
X = startX;
Y = startY;
Z = startZ;
preD = -1;
if ((geoInfo->bType[index].isBofXp && geoInfo->bType[index].isBofXm) || (geoInfo->bType[index].isBofZp && geoInfo->bType[index].isBofZm)) {//xz plane
for (k = 0; k < geoInfo->domainIndex.size(); k++) {
if ((Z + 2 < Zindex) &&
(isD[(Z + 2) * Yindex * Xindex + Y * Xindex + X] == 1 && isD[(Z + 1) * Yindex * Xindex + Y * Xindex + X] == 2 && preD != S)) {//north
//X = X;//self assign
Z = Z + 2;
preD = N;
} else if (isD[(Z + 1) * Yindex * Xindex + Y * Xindex + (X + 1)] == 1 && preD != SW) {//northeast
X = X + 1;
Z = Z + 1;
preD = NE;
} else if (isD[Z * Yindex * Xindex + Y * Xindex + (X + 2)] == 1 && isD[Z * Yindex * Xindex + Y * Xindex + (X + 1)] == 2 && preD != W) {//east
X = X + 2;
//Z = Z;//self assign
preD = E;
} else if (isD[(Z - 1) * Yindex * Xindex + Y * Xindex + (X + 1)] == 1 && preD != NW) {//southeast
X = X + 1;
Z = Z - 1;
preD = SE;
} else if ((Z - 2 >= 0) &&
(isD[(Z - 2) * Yindex * Xindex + Y * Xindex + X] == 1 && isD[(Z - 1) * Yindex * Xindex + Y * Xindex + X] == 2 && preD != N)) {//south
//X = X;//self assign
Z = Z - 2;
preD = S;
} else if (isD[(Z - 1) * Yindex * Xindex + Y * Xindex + (X - 1)] == 1 && preD != NE) {//southwest
X = X - 1;
Z = Z - 1;
preD = SW;
} else if (isD[Z * Yindex * Xindex + Y * Xindex + (X - 2)] == 1 && isD[Z * Yindex * Xindex + Y * Xindex + (X - 1)] == 2 && preD != E) {//west
X = X - 2;
//Z = Z;//self assign
preD = W;
} else if (isD[(Z + 1) * Yindex * Xindex + Y * Xindex + (X - 1)] == 1 && preD != SE) {//northwest
X = X - 1;
Z = Z + 1;
preD = NW;
}
max_radiusXZ = max(max_radiusXZ, sqrt(pow(((X - startX) / 2) * hX, 2) + pow(((Z - startZ) / 2) * hZ, 2)) / 2.0);
if (X == startX && Z == startZ) {
break;
}
}
}
X = startX;
Y = startY;
Z = startZ;
}
/* calc local radius of curvature */
//calc tmp step_k to calc local radius of curvature
step_kXY = static_cast<int>(pow(hXY, -(2.0 / 3.0)) + 0.5);
step_kYZ = static_cast<int>(pow(hYZ, -(2.0 / 3.0)) + 0.5);
step_kXZ = static_cast<int>(pow(hXZ, -(2.0 / 3.0)) + 0.5);
//step_kXY = static_cast<int>(pow(hXY, -(2.0 / 3.0)));
//step_kYZ = static_cast<int>(pow(hYZ, -(2.0 / 3.0)));
//step_kXZ = static_cast<int>(pow(hXZ, -(2.0 / 3.0)));
if (step_kXY == 0) step_kXY = 1;
if (step_kYZ == 0) step_kYZ = 1;
if (step_kXZ == 0) step_kXZ = 1;
if ((geoInfo->bType[index].isBofXp && geoInfo->bType[index].isBofXm) || (geoInfo->bType[index].isBofYp && geoInfo->bType[index].isBofYm)) {//xy plane
//calc the radius of circumscribed circle
oneStepSearch(1, step_kXY, X, Y, Z, Xindex, Yindex, Zindex, xyPlaneX, xyPlaneY, isD, "xy");
a = sqrt(pow(((X - xyPlaneX[0]) * hX) / 2.0, 2) + pow(((Y - xyPlaneY[0]) * hY) / 2.0, 2));
b = sqrt(pow(((X - xyPlaneX[1]) * hX) / 2.0, 2) + pow(((Y - xyPlaneY[1]) * hY) / 2.0, 2));
c = sqrt(pow(((xyPlaneX[0] - xyPlaneX[1]) * hX) / 2.0, 2) + pow(((xyPlaneY[0] - xyPlaneY[1]) * hY) / 2.0, 2));
//calc step_k
if ((a + b + c) * (-a + b + c) * (a - b + c) * (a + b - c) == 0) {//r_i+k, r_i, r_i-k are on the straight line
step_kXY = 1;
//step_kXY = static_cast<int>(pow((max_radiusXY / hXY), 2.0 / 3.0) + 0.5);
} else {
rhoXY = min(max_radiusXY, (a * b * c) / sqrt((a + b + c) * (-a + b + c) * (a - b + c) * (a + b - c)));
step_kXY = static_cast<int>(pow((rhoXY / hXY), 2.0 / 3.0) + 0.5);
//step_kXY = static_cast<int>(pow((rhoXY / hXY), 2.0 / 3.0));
}
//step_kXY = 1;
//cout << X / 2 * hX << " " << Y / 2 * hY << " " << step_kXY << endl;
//cout << X / 2 * hX << " " << Y / 2 * hY << " " << rhoXY << " " << max_radiusXY << " " << hXY << endl;
//calc tangent vector
oneStepSearch(1, step_kXY, X, Y, Z, Xindex, Yindex, Zindex, xyPlaneX, xyPlaneY, isD, "xy");
}
if (dimension == 3) {
//yz-plane
if ((geoInfo->bType[index].isBofYp && geoInfo->bType[index].isBofYm) || (geoInfo->bType[index].isBofZp && geoInfo->bType[index].isBofZm)) {//yz plane
//calc the radius of circumscribed circle
oneStepSearch(1, step_kYZ, X, Y, Z, Xindex, Yindex, Zindex, yzPlaneY, yzPlaneZ, isD, "yz");
a = sqrt(pow(((Y - yzPlaneY[0]) * hY) / 2.0, 2) + pow(((Z - yzPlaneZ[0]) * hZ) / 2.0, 2));
b = sqrt(pow(((Y - yzPlaneY[1]) * hY) / 2.0, 2) + pow(((Z - yzPlaneZ[1]) * hZ) / 2.0, 2));
c = sqrt(pow(((yzPlaneY[0] - yzPlaneY[1]) * hY) / 2.0, 2) + pow(((yzPlaneZ[0] - yzPlaneZ[1]) * hZ) / 2.0, 2));
//calc step_k
if ((a + b + c) == 0 || (-a + b + c) == 0 || (a - b + c) == 0 || (a + b - c) == 0) {
step_kYZ = 1;
//step_kYZ = static_cast<int>(pow((max_radiusYZ / hYZ), 2.0 / 3.0) + 0.5);
} else {
rhoYZ = min(max_radiusYZ, (a * b * c) / sqrt((a + b + c) * (-a + b + c) * (a - b + c) * (a + b - c)));
step_kYZ = static_cast<int>(pow((rhoYZ / hYZ), 2.0 / 3.0) + 0.5);
//step_kYZ = static_cast<int>(pow((rhoYZ / hYZ), 2.0 / 3.0));
}
//calc tangent vector
oneStepSearch(1, step_kYZ, X, Y, Z, Xindex, Yindex, Zindex, yzPlaneY, yzPlaneZ, isD, "yz");
}
//xz-plane
if ((geoInfo->bType[index].isBofXp && geoInfo->bType[index].isBofXm) || (geoInfo->bType[index].isBofZp && geoInfo->bType[index].isBofZm)) {//xz plane
//calc the radius of circumscribed circle
oneStepSearch(1, step_kXZ, X, Y, Z, Xindex, Yindex, Zindex, xzPlaneX, xzPlaneZ, isD, "xz");
a = sqrt(pow(((X - xzPlaneX[0]) * hX) / 2.0, 2) + pow(((Z - xzPlaneZ[0]) * hZ) / 2.0, 2));
b = sqrt(pow(((X - xzPlaneX[1]) * hX) / 2.0, 2) + pow(((Z - xzPlaneZ[1]) * hZ) / 2.0, 2));
c = sqrt(pow(((xzPlaneX[0] - xzPlaneX[1]) * hX) / 2.0, 2) + pow(((xzPlaneZ[0] - xzPlaneZ[1]) * hZ) / 2.0, 2));
//calc step_k
if ((a + b + c) == 0 || (-a + b + c) == 0 || (a - b + c) == 0 || (a + b - c) == 0) {
step_kXZ = 1;
//step_kXZ = static_cast<int>(pow((max_radiusXZ / hXZ), 2.0 / 3.0) + 0.5);
} else {
rhoXZ = min(max_radiusXZ, (a * b * c) / sqrt((a + b + c) * (-a + b + c) * (a - b + c) * (a + b - c)));
step_kXZ = static_cast<int>(pow((rhoXZ / hXZ), 2.0 / 3.0) + 0.5);
//step_kXZ = static_cast<int>(pow((rhoXZ / hXZ), 2.0 / 3.0));
}
//calc tangent vector
oneStepSearch(1, step_kXZ, X, Y, Z, Xindex, Yindex, Zindex, xzPlaneX, xzPlaneZ, isD, "xz");
}
}
//set normal unit vector
//calc extended product
if (dimension == 2) {
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = 0.0;
Y2 = 0.0;
Z2 = 1.0;
//cout << "(" << xyPlaneX[0] << ", " << xyPlaneY[0] << ") " << "(" << X << ", " << Y << ") " << "(" << xyPlaneX[1] << ", " << xyPlaneY[1] << ") " << endl;
} else if (dimension == 3) {
if (geoInfo->bType[index].isBofXp || geoInfo->bType[index].isBofXm) {//xy * xz
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = xzPlaneX[0] - xzPlaneX[1];
Y2 = 0.0;
Z2 = xzPlaneZ[0] - xzPlaneZ[1];
}
if (geoInfo->bType[index].isBofYp || geoInfo->bType[index].isBofYm) {//xy * yz
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = 0.0;
Y2 = yzPlaneY[0] - yzPlaneY[1];
Z2 = yzPlaneZ[0] - yzPlaneZ[1];
}
if (geoInfo->bType[index].isBofZp || geoInfo->bType[index].isBofZm) {//xz * yz
X1 = xzPlaneX[0] - xzPlaneX[1];
Y1 = 0.0;
Z1 = xzPlaneZ[0] - xzPlaneZ[1];
X2 = 0.0;
Y2 = yzPlaneY[0] - yzPlaneY[1];
Z2 = yzPlaneZ[0] - yzPlaneZ[1];
}
//これ、z境界かつy境界とかだと、あとが優先？
}
//cout << sqrt(pow(coord_x, 2) + pow(coord_y, 2) + pow(coord_z, 2)) << endl;
nuVec[index].nx = Y1 * Z2 - Z1 * Y2;
nuVec[index].ny = Z1 * X2 - X1 * Z2;
nuVec[index].nz = X1 * Y2 - Y1 * X2;
len = sqrt(pow(nuVec[index].nx, 2) + pow(nuVec[index].ny, 2) + pow(nuVec[index].nz, 2));
//double phi = atan2(nuVec[index].ny, nuVec[index].nx);
//double theta = acos(nuVec[index].nz / len);
nuVec[index].nx /= len;
nuVec[index].ny /= len;
//nuVec[index].nx = sin(theta) * cos(phi);
//nuVec[index].ny = sin(theta) * sin(phi);
//cout << " " << nuVec[index].nx << " " << nuVec[index].ny << " " << pow(nuVec[index].nx, 2) + pow(nuVec[index].ny, 2) <<endl;
nuVec[index].nz /= len;
//cout << "(" << X << ", " << Y << ", " << Z << ") " << nuVec[index].nx << " " << nuVec[index].ny << " " << nuVec[index].nz << endl;
/*
double coord_x = -1.0 + (double)X * hX / 2.0;
double coord_y = -1.0 + (double)Y * hY / 2.0;
double coord_z = -1.0 + (double)Z * hZ / 2.0;
//cout << fabs(fabs(nuVec[index].nx) - fabs(coord_x)) + fabs(fabs(nuVec[index].ny) - fabs(coord_y)) + fabs(fabs(nuVec[index].nz) - fabs(coord_z)) << " ";
nuVec[index].nx = coord_x;
nuVec[index].ny = coord_y;
nuVec[index].nz = coord_z;
*/
//set normal unit vector
//calc extended product
if (dimension == 2) {
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = 0.0;
Y2 = 0.0;
Z2 = 1.0;
} else if (dimension == 3) {
if (geoInfo->bType[index].isBofXp || geoInfo->bType[index].isBofXm) {//xy * xz
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = xzPlaneX[0] - xzPlaneX[1];
Y2 = 0.0;
Z2 = xzPlaneZ[0] - xzPlaneZ[1];
}
if (geoInfo->bType[index].isBofYp || geoInfo->bType[index].isBofYm) {//xy * yz
X1 = xyPlaneX[0] - xyPlaneX[1];
Y1 = xyPlaneY[0] - xyPlaneY[1];
Z1 = 0.0;
X2 = 0.0;
Y2 = yzPlaneY[0] - yzPlaneY[1];
Z2 = yzPlaneZ[0] - yzPlaneZ[1];
}
if (geoInfo->bType[index].isBofZp || geoInfo->bType[index].isBofZm) {//xz * yz
X1 = xzPlaneX[0] - xzPlaneX[1];
Y1 = 0.0;
Z1 = xzPlaneZ[0] - xzPlaneZ[1];
X2 = 0.0;
Y2 = yzPlaneY[0] - yzPlaneY[1];
Z2 = yzPlaneZ[0] - yzPlaneZ[1];
}
}
nuVec[index].nx = Y1 * Z2 - Z1 * Y2;
nuVec[index].ny = Z1 * X2 - X1 * Z2;
nuVec[index].nz = X1 * Y2 - Y1 * X2;
len = sqrt(pow(nuVec[index].nx, 2) + pow(nuVec[index].ny, 2) + pow(nuVec[index].nz, 2));
nuVec[index].nx /= len;
nuVec[index].ny /= len;
nuVec[index].nz /= len;
}
}
}
}
return nuVec;
}
normalUnitVector* setNormalAngle_modify(std::vector<GeometryInfo*> &geoInfoList, double Xsize, double Ysize, double Zsize, int dimension, int Xindex, int Yindex, int Zindex, unsigned int numOfVolIndexes)
{
unsigned int i, j, k, step_kXY = 0, step_kYZ = 0, step_kXZ = 0;
int X, Y, Z, index;
normalUnitVector *nuVec = new normalUnitVector[numOfVolIndexes];
int *isD = 0;
GeometryInfo *geoInfo = 0;
double X1 = 0.0, X2 = 0.0, Y1 = 0.0, Y2 = 0.0, Z1 = 0.0, Z2 = 0.0, len, rhoXY = 0.0, rhoYZ = 0.0, rhoXZ = 0.0;
double a = 0.0, b = 0.0, c = 0.0;//length of triangle
double max_radiusXY = 0.0, max_radiusYZ = 0.0, max_radiusXZ = 0.0;
int startX, startY, startZ;
int preD = -1;
int Xdiv = (Xindex + 1) / 2;
int Ydiv = (Yindex + 1) / 2;
int Zdiv = (Zindex + 1) / 2;
double hX = 1.0, hY = 1.0, hZ = 1.0;//grid size
double hXY = 1.0, hYZ = 1.0, hXZ = 1.0;
int xyPlaneX[2] = {0}, xyPlaneY[2] = {0}, yzPlaneY[2] = {0}, yzPlaneZ[2] = {0}, xzPlaneX[2] = {0}, xzPlaneZ[2] = {0};
hX = Xsize / (Xdiv - 1);