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spatialsimulator.cpp
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//============================================================================
// Name : SBMLSimulator.cpp
// Author :
// Version :
// Copyright : Your copyright notice
// Description : Hello World in C++, Ansi-style
//============================================================================
#include "spatialsim/spatialsimulator.h"
#include "spatialsim/mystruct.h"
#include "spatialsim/initializeFunction.h"
#include "spatialsim/freeFunction.h"
#include "spatialsim/searchFunction.h"
#include "spatialsim/astFunction.h"
#include "spatialsim/calcPDE.h"
#include "spatialsim/setInfoFunction.h"
#include "spatialsim/boundaryFunction.h"
#include "spatialsim/checkStability.h"
#include "spatialsim/checkFunc.h"
#include "spatialsim/options.h"
#include "spatialsim/outputHDF.h"
#include "spatialsim/outputImage.h"
//#include "spatialsim/cerealize.h"
#include "sbml/SBMLTypes.h"
#include "sbml/packages/spatial/common/SpatialExtensionTypes.h"
#include "sbml/packages/spatial/extension/SpatialModelPlugin.h"
#include "H5Cpp.h"
#include <float.h>
#include <opencv2/opencv.hpp>
#include <opencv2/highgui/highgui.hpp>
#include <iostream>
#include <fstream>
#include <vector>
#include <zlib.h>
#include <sys/stat.h>
#include <unistd.h>
#include <csignal>
LIBSBML_CPP_NAMESPACE_USE
using namespace H5;
using namespace cv;
using namespace std;
#ifdef __cplusplus
extern "C" {
#endif
void spatialSimulator(int argc, char **argv){
if (argc == 1 || access(argv[argc - 1], F_OK) == -1) {
printErrorMessage(argv[0]);
}
SBMLDocument *doc = readSBML(argv[argc - 1]);
if (doc->getErrorLog()->contains(XMLFileUnreadable) || doc->getErrorLog()->contains(BadlyFormedXML)
|| doc->getErrorLog()->contains(MissingXMLEncoding) || doc->getErrorLog()->contains(BadXMLDecl)) {
doc->printErrors();
delete doc;
exit(1);
}
//struct stat st;
//if(stat("./result", &st) != 0) system("mkdir ./result");
if (doc->getModel()->getPlugin("spatial") != 0 && doc->getPkgRequired("spatial")) {//PDE
simulate(getOptionList(argc, argv, doc));
} else {//ODE
}
delete doc;
}
void simulate(optionList options)
{
SBMLDocument *doc = 0;
if(options.docFlag != 0) {
// from java
doc = readSBMLFromString(options.document);
} else {
doc = readSBML(options.fname);
}
cout << "fname " << options.fname << endl;
cout << "outpath " << options.outpath << endl;
struct stat st;
unsigned int i, j, k;
//int X = 0, Y = 0, Z = 0, divIndex = 0, t = 0, count = 0, file_num = 0, percent = 0, index = 0;
int X = 0, Y = 0, Z = 0, t = 0, count = 0, file_num = 0, percent = 0, index = 0;
double *sim_time = new double(0.0);
double deltaX = 0.0, deltaY = 0.0, deltaZ = 0.0;
double mesh = 0.0;
double Xsize = 0.0, Ysize = 0.0, Zsize = 0.0;
unsigned int numOfASTNodes = 0;
char *xaxis = 0, *yaxis = 0, *zaxis = 0;
cout << "validating model..." << endl;
doc->checkConsistency();
doc->printErrors(cerr);
cout << "finished" << endl;
//sbml core
Model *model = doc->getModel();
ASTNode *ast = 0;
Species *s = 0;
SpeciesReference *sr = 0;
ListOfSpecies *los = model->getListOfSpecies();
ListOfCompartments *loc = model->getListOfCompartments();
SpatialCompartmentPlugin *cPlugin = 0;
//sbml spatial package
SpatialModelPlugin *spPlugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
Geometry *geometry = spPlugin->getGeometry();
//size of list
unsigned int numOfSpecies = model->getNumSpecies();
unsigned int numOfReactions = model->getNumReactions();
unsigned int numOfCompartments = model->getNumCompartments();
unsigned int numOfParameters = model->getNumParameters();
unsigned int numOfRules = model->getNumRules();
vector<variableInfo*> varInfoList = vector<variableInfo*>();
varInfoList.reserve(numOfCompartments + numOfSpecies + numOfParameters);
vector<GeometryInfo*> geoInfoList = vector<GeometryInfo*>();
geoInfoList.reserve(geometry->getNumGeometryDefinitions());
vector<reactionInfo*> rInfoList = vector<reactionInfo*>();
rInfoList.reserve(numOfReactions + numOfRules);
vector<reactionInfo*> fast_rInfoList = vector<reactionInfo*>();
fast_rInfoList.reserve(numOfReactions + numOfRules);
vector<const char*> memList = vector<const char*>();
memList.reserve(numOfCompartments);
vector<boundaryMembrane*> bMemInfoList = vector<boundaryMembrane*>();
bMemInfoList.reserve(numOfCompartments);
unsigned int dimension = geometry->getNumCoordinateComponents();
vector<string> spIdList = vector<string>();
spIdList.reserve(numOfSpecies);
for (i = 0; i < numOfSpecies; i++) {
spIdList.push_back(model->getSpecies(i)->getId());
}
int Xplus1 = 0, Xminus1 = 0, Yplus1 = 0, Yminus1 = 0, Zplus1 = 0, Zminus1 = 0;
//simulation options
int Xdiv = options.Xdiv;
int Ydiv = options.Ydiv;
int Zdiv = options.Zdiv;
//if( options.mesh_size != 0 )
//mesh = options.mesh_size;
double range_max = options.range_max;
double range_min = options.range_min;
double end_time = options.end_time;
double dt = options.dt;
int out_step = options.out_step;
double out_time_csv = options.out_csv;
int slice = options.slice;
char slicedim = options.slicedim;
bool sliceFlag = (options.sliceFlag != 0);
string outpath(options.outpath);
//double pixelWidth = options.mesh_size;
//div
if (dimension <= 1) {
Ydiv = 1;
}
if (dimension <= 2) {
Zdiv = 1;
}
//filename
string fname(options.fname);
fname = fname.substr(static_cast<unsigned long>(fname.find_last_of("/")) + 1, static_cast<unsigned long>(fname.find_last_of("."))- static_cast<unsigned long>(fname.find_last_of("/")) - 1);
if(fname.empty()){
if(model -> isSetId())
fname = model->getId();
else
fname = "model";
}
cout << "File name: \n" << fname << endl;
if (stat(string(outpath + "/result/" + fname).c_str(), &st) != 0)
system(string("mkdir -p " + outpath + "/result/" + fname).c_str());
bool isImageBased = false;
for (i = 0; i < geometry->getNumGeometryDefinitions(); i++) {
if (geometry->getGeometryDefinition(i)->isSampledFieldGeometry() && geometry->getGeometryDefinition(i)->getIsActive()) {
//SampleFieldGeometry
//SampledFieldGeometry *sfGeo = static_cast<SampledFieldGeometry*>(geometry->getGeometryDefinition(i));
SampledField *samField = geometry->getListOfSampledFields()->get(0); //may need changes
cout << "image size:" << endl << "width * height * depth = " << samField->getNumSamples1() << " * " << samField->getNumSamples2() << " * " << samField->getNumSamples3() << endl << endl;
isImageBased = true;
Xdiv = samField->getNumSamples1();
Ydiv = samField->getNumSamples2();
Zdiv = samField->getNumSamples3();
}
}
cout << "x mesh num: " << ((isImageBased) ? Xdiv : Xdiv - 1) << endl;
if (dimension >= 2) cout << "y mesh num: " << ((isImageBased) ? Ydiv : Ydiv - 1) << endl;
if (dimension == 3) cout << "z mesh num: " << ((isImageBased) ? Zdiv : Zdiv - 1) << endl;
cout << "simulation time = " << end_time << endl;
cout << "dt = " << dt << endl;
cout << "output results every " << out_step << " step" << endl;
cout << "color bar range min: " << range_min << endl;
cout << "color bar range max: ";
if (range_max == -DBL_MAX) {
range_max = getDefaultRangeMax(model);
cout << "using default value: ";
}
cout << range_max << endl;
if (range_min >= range_max) {
cout << "Your range_min(" << range_min << ") is equal or larger than range_max(" << range_max << ")."<< endl;
cout << "This will cause corrupted output image." << endl;
cout << "Please specify correct range_min and range_max by using -c and -C option, " << endl;
cout << "or just remove these options." << endl;
exit(1);
}
int Xindex = 2 * Xdiv - 1, Yindex = 2 * Ydiv - 1, Zindex = 2 * Zdiv - 1;//num of mesh
unsigned int numOfVolIndexes = static_cast<unsigned int>(Xindex * Yindex * Zindex);
//unit
unsigned int volDimension = geometry->getListOfCoordinateComponents()->size();
unsigned int memDimension = volDimension - 1;
//set id and value
//compartment
setCompartmentInfo(model, varInfoList);
//species
setSpeciesInfo(model, varInfoList, volDimension, memDimension, Xindex, Yindex, Zindex);
//parameter
setParameterInfo(model, varInfoList, bMemInfoList, Xdiv, Ydiv, Zdiv, Xsize, Ysize, Zsize, deltaX, deltaY, deltaZ, xaxis, yaxis, zaxis, mesh);
//pixel width
if( options.mesh_size == 0 ){ // added by morita
ListOfCompartments *loc = model->getListOfCompartments();
Compartment *c = loc->get(0);
SpatialCompartmentPlugin *cplugin = static_cast<SpatialCompartmentPlugin*>(c->getPlugin("spatial"));
CompartmentMapping *cmap = cplugin->getCompartmentMapping();
if( cmap->getUnitSize() == 1.0 ){
if( dimension >= 1 ){
//deltaX = mesh;
cout << "default deltaX: " << deltaX << endl;
}
if( dimension >= 2 ){
//deltaY = mesh;
cout << "default deltaY: " << deltaY << endl;
}
if( dimension >= 3 ){
//deltaZ = mesh;
cout << "default deltaZ: " << deltaZ << endl;
}
} else if( cmap->getUnitSize() != 1.0 ){
if( dimension >= 1 ){
deltaX = cmap->getUnitSize();
cout << "model defining deltaX: " << deltaX << endl;
}
if( dimension >= 2 ){
deltaY = cmap->getUnitSize();
cout << "model defining deltaY: " << deltaY << endl;
}
if( dimension >= 3 ){
deltaZ = cmap->getUnitSize();
cout << "model defining deltaZ: " << deltaZ << endl;
}
}
} else if( options.mesh_size != 0 ) {
if( dimension >= 1 ){
deltaX = options.mesh_size;
cout << "assigned deltaX: " << deltaX << endl;
}
if( dimension >= 2 ){
deltaY = options.mesh_size;
cout << "assigned deltaY: " << deltaY << endl;
}
if( dimension >= 3 ){
deltaZ = options.mesh_size;
cout << "assigned deltaZ: " << deltaZ << endl;
}
} cout << endl;
//time
variableInfo *t_info = new variableInfo;
InitializeVarInfo(t_info);
varInfoList.push_back(t_info);
t_info->id = (const char*)malloc(sizeof(char) * 1 + 1);
strcpy(const_cast<char*>(t_info->id), "t");
t_info->value = sim_time;
t_info->isResolved = true;
t_info->isUniform = true;
//volume index
vector<unsigned int> volumeIndexList;
for (Z = 0; Z < Zindex; Z += 2) {
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
volumeIndexList.push_back(Z * Yindex * Xindex + Y * Xindex + X);
}
}
}
cout << "defining geometry... " << endl;
GeometryInfo* allAreaInfo = new GeometryInfo;
allAreaInfo->isDomain = new int[numOfVolIndexes];
int aaIndex;
for (Z = 0; Z < Zindex; ++Z) {
for (Y = 0; Y < Yindex; ++Y) {
for (X = 0; X < Xindex; ++X) {
aaIndex = Z * Xindex * Yindex + Y * Xindex + X;
allAreaInfo->isDomain[aaIndex] = 1;
allAreaInfo->domainIndex.push_back(aaIndex);
}
}
}
//geometryDefinition
double *tmp_isDomain = new double[numOfVolIndexes];
for (i = 0; i < geometry->getNumGeometryDefinitions(); i++) {
if(geometry->getGeometryDefinition(i)->isSetIsActive() && !(geometry->getGeometryDefinition(i)->getIsActive())) continue;
if (geometry->getGeometryDefinition(i)->isAnalyticGeometry()) {
//AnalyticVolumes
AnalyticGeometry *analyticGeo = static_cast<AnalyticGeometry*>(geometry->getGeometryDefinition(i));
//gather information of compartment, domainType, analyticVolume
ListOfAnalyticVolumes *loav = analyticGeo->getListOfAnalyticVolumes();
unsigned int numOfAnalyticVolume = analyticGeo->getNumAnalyticVolumes();
for (j = 0; j < numOfAnalyticVolume; j++) {
AnalyticVolume *analyticVol = loav->get(j);
Compartment *c = 0;
//use the first compartment that is mapped to the domaintype
for(k = 0; k< numOfCompartments; k++) {
c = loc->get(k);
cPlugin = static_cast<SpatialCompartmentPlugin*>(c->getPlugin("spatialspatial"));
if(analyticVol->getDomainType() == cPlugin->getCompartmentMapping()->getDomainType())
break;
}
GeometryInfo *geoInfo = new GeometryInfo;
InitializeAVolInfo(geoInfo);
geoInfo->compartmentId = c->getId().c_str();
geoInfo->domainTypeId = analyticVol->getDomainType().c_str();
geoInfo->domainId = 0;
geoInfo->bType = new boundaryType[numOfVolIndexes];
for (k = 0; k < numOfVolIndexes; k++) {
geoInfo->bType[k].isBofXp = false;
geoInfo->bType[k].isBofXm = false;
geoInfo->bType[k].isBofYp = false;
geoInfo->bType[k].isBofYm = false;
geoInfo->bType[k].isBofZp = false;
geoInfo->bType[k].isBofZm = false;
}
geoInfo->isVol = true;
ast = const_cast<ASTNode*>(analyticVol->getMath());
rearrangeAST(ast);
numOfASTNodes = 0;
countAST(ast, numOfASTNodes);
geoInfo->rpInfo = new reversePolishInfo();
geoInfo->rpInfo->varList = new double*[numOfASTNodes];
fill_n(geoInfo->rpInfo->varList, numOfASTNodes, reinterpret_cast<double*>(0));
geoInfo->rpInfo->constList = new double*[numOfASTNodes];
fill_n(geoInfo->rpInfo->constList, numOfASTNodes, reinterpret_cast<double*>(0));
geoInfo->rpInfo->opfuncList = new int[numOfASTNodes];
fill_n(geoInfo->rpInfo->opfuncList, numOfASTNodes, 0);
geoInfo->rpInfo->listNum = numOfASTNodes;
geoInfo->isDomain = new int[numOfVolIndexes];
fill_n(geoInfo->isDomain, numOfVolIndexes, 0);
geoInfo->isBoundary = new int[numOfVolIndexes];
fill_n(geoInfo->isBoundary, numOfVolIndexes, 0);
geoInfo->adjacent0 = 0;
geoInfo->adjacent1 = 0;
parseAST(ast, geoInfo->rpInfo, varInfoList, numOfASTNodes);
//judge if the coordinate point is inside the analytic volume
fill_n(tmp_isDomain, numOfVolIndexes, 0);
reversePolishInitial(volumeIndexList, geoInfo->rpInfo, tmp_isDomain, numOfASTNodes, Xindex, Yindex, Zindex, false);
for (k = 0; k < numOfVolIndexes; k++) {
index = k;
geoInfo->isDomain[k] = (int)tmp_isDomain[k];
}
geoInfoList.push_back(geoInfo);
}
} else if (geometry->getGeometryDefinition(i)->isSampledFieldGeometry()) {
//SampleFieldGeometry
SampledFieldGeometry *sfGeo = static_cast<SampledFieldGeometry*>(geometry->getGeometryDefinition(i));
for (j = 0; j < numOfCompartments; j++) {
Compartment *c = loc->get(j);
if (c->getSpatialDimensions() == volDimension) {
cPlugin = static_cast<SpatialCompartmentPlugin*>(c->getPlugin("spatial"));
if (cPlugin != 0) {
SampledField *samField = geometry->getListOfSampledFields()->get(sfGeo->getSampledField());
SampledVolume *samVol = 0;
for (k = 0; k < sfGeo->getNumSampledVolumes(); k++) {
if (sfGeo->getSampledVolume(k)->getDomainType() == cPlugin->getCompartmentMapping()->getDomainType()) {
samVol = sfGeo->getSampledVolume(k);
}
}
if(samVol != 0){
int *uncompr;
int length;
if(samField->getCompression() == SPATIAL_COMPRESSIONKIND_UNCOMPRESSED) {
length = samField->getUncompressedLength();
samField->getUncompressedData(uncompr, length);
} else if(samField->getCompression() == SPATIAL_COMPRESSIONKIND_DEFLATED) {
length = samField->getUncompressedLength();
samField->getUncompressedData(uncompr, length);
} else {
cerr << "base64 not supported" << endl;
exit(1);
}
GeometryInfo *geoInfo = new GeometryInfo;
InitializeAVolInfo(geoInfo);
geoInfo->compartmentId = c->getId().c_str();
geoInfo->domainTypeId = cPlugin->getCompartmentMapping()->getDomainType().c_str();
geoInfo->domainId = 0;
geoInfo->bType = new boundaryType[numOfVolIndexes];
for (k = 0; k < numOfVolIndexes; k++) {
geoInfo->bType[k].isBofXp = false;
geoInfo->bType[k].isBofXm = false;
geoInfo->bType[k].isBofYp = false;
geoInfo->bType[k].isBofYm = false;
geoInfo->bType[k].isBofZp = false;
geoInfo->bType[k].isBofZm = false;
}
geoInfo->isVol = true;
geoInfo->isDomain = new int[numOfVolIndexes];
fill_n(geoInfo->isDomain, numOfVolIndexes, 0);
geoInfo->isBoundary = new int[numOfVolIndexes];
fill_n(geoInfo->isBoundary, numOfVolIndexes, 0);
geoInfoList.push_back(geoInfo);
for (Z = 0; Z < Zindex; Z += 2) {
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
if (static_cast<unsigned int>(uncompr[Z / 2 * samField->getNumSamples2() * samField->getNumSamples1() + (samField->getNumSamples2() - Y / 2 - 1) * samField->getNumSamples1() + X / 2]) == static_cast<unsigned int>(samVol->getSampledValue())) {
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
} else {
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 0;
}
}
}
}
for (k = 0; k < geoInfo->domainIndex.size(); k++) {
index = geoInfo->domainIndex[k];
Z = index / (Xindex * Yindex);
Y = (index - Z * Xindex * Yindex) / Xindex;
X = index - Z * Xindex * Yindex - Y * Xindex;
if ((dimension == 2 && (X == 0 || X == Xindex - 1 || Y == 0 || Y == Yindex - 1)) ||
(dimension == 3 && (X == 0 || X == Xindex - 1 || Y == 0 || Y == Yindex - 1 || Z == 0 || Z == Zindex - 1))) {
geoInfo->isBoundary[index] = 1;
geoInfo->boundaryIndex.push_back(index);
if (dimension >= 2) {
if (X == 0) geoInfo->bType[index].isBofXm = true;
if (X == Xindex - 1) geoInfo->bType[index].isBofXp = true;
if (Y == 0) geoInfo->bType[index].isBofYm = true;
if (Y == Yindex - 1) geoInfo->bType[index].isBofYp = true;
}
if (dimension == 3) {
if (Z == 0) geoInfo->bType[index].isBofZm = true;
if (Z == Zindex - 1) geoInfo->bType[index].isBofZp = true;
}
} else {
if (dimension >= 2) {
if (geoInfo->isDomain[Z * Xindex * Yindex + Y * Xindex + (X + 2)] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofXp = true;
}
if (geoInfo->isDomain[Z * Xindex * Yindex + Y * Xindex + (X - 2)] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofXm = true;
}
if (geoInfo->isDomain[Z * Xindex * Yindex + (Y + 2) * Xindex + X] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofYp = true;
}
if (geoInfo->isDomain[Z * Xindex * Yindex + (Y - 2) * Xindex + X] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofYm = true;
}
}
if (dimension == 3) {
if (geoInfo->isDomain[(Z + 2) * Xindex * Yindex + Y * Xindex + X] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofZp = true;
}
if (geoInfo->isDomain[(Z - 2) * Xindex * Yindex + Y * Xindex + X] == 0) {
geoInfo->isBoundary[index] = 1;
geoInfo->bType[index].isBofZm = true;
}
}
}
}
//free(compr_int);
//free(compr);
free(uncompr);
}
}
}
}
} else if (geometry->getGeometryDefinition(i)->isCSGeometry()) {
//CSGeometry
} else if (geometry->getGeometryDefinition(i)->isParametricGeometry()) {
//ParametricGeometry
}
}
delete[] tmp_isDomain;
//merge external and internal analytic volumes and get boundary points of the geometry
for (i = 0; i < geometry->getNumGeometryDefinitions(); i++) {
if (geometry->getGeometryDefinition(i)->isAnalyticGeometry()) {
AnalyticGeometry *analyticGeo = static_cast<AnalyticGeometry*>(geometry->getGeometryDefinition(i));
for (j = 0; j < analyticGeo->getNumAnalyticVolumes(); j++) {
AnalyticVolume *analyticVolEx = analyticGeo->getAnalyticVolume(j);
GeometryInfo *geoInfoEx = searchAvolInfoByDomainType(geoInfoList, analyticVolEx->getDomainType().c_str());
for (k = 0; k < analyticGeo->getNumAnalyticVolumes(); k++) {
AnalyticVolume *analyticVolIn = analyticGeo->getAnalyticVolume(k);
if (analyticVolEx->getOrdinal() < analyticVolIn->getOrdinal()) {//ex's ordinal is smaller than in's ordinal
GeometryInfo *geoInfoIn = searchAvolInfoByDomainType(geoInfoList, analyticVolIn->getDomainType().c_str());
//merge
for (Z = 0; Z < Zindex; Z += 2) {
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
index = Z * Yindex * Xindex + Y * Xindex + X;
if (geoInfoEx->isDomain[index] == 1 && geoInfoIn->isDomain[index] == 1) {
geoInfoEx->isDomain[index] = 0;
}
}
}
}
}
}
//domainの位置(analytic geo)
for (Z = 0; Z < Zindex; Z += 2) {
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
index = Z * Xindex * Yindex + Y * Xindex + X;
if (geoInfoEx->isDomain[index] == 1) {
geoInfoEx->domainIndex.push_back(index);
}
}
}
}
//boundary
switch(dimension) {
case 1://1D
for (X = 0; X < Xindex; X += 2) {
geoInfoEx->isBoundary[X] = 0;//initialize
if (geoInfoEx->isDomain[X] == 1) {
if (X == 0 || X == Xindex - 1) {//bounary of the domain
geoInfoEx->isBoundary[X] = 1;
geoInfoEx->boundaryIndex.push_back(X);
} else if (geoInfoEx->isDomain[X + 2] == 0 || geoInfoEx->isDomain[X - 2] == 0) {
geoInfoEx->isBoundary[Y * Xindex + X] = 1;
geoInfoEx->boundaryIndex.push_back(X);
}
}
}
break;
case 2://2D
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
geoInfoEx->isBoundary[Y * Xindex + X] = 0;//initialize
if (geoInfoEx->isDomain[Y * Xindex + X] == 1) {
if (X == 0 || X == Xindex - 1 || Y == 0 || Y == Yindex - 1) {//boundary of the domain
geoInfoEx->isBoundary[Y * Xindex + X] = 1;
geoInfoEx->boundaryIndex.push_back(Y * Xindex + X);
} else if (geoInfoEx->isDomain[Y * Xindex + (X + 2)] == 0
|| geoInfoEx->isDomain[Y * Xindex + (X - 2)] == 0
|| geoInfoEx->isDomain[(Y + 2) * Xindex + X] == 0
|| geoInfoEx->isDomain[(Y - 2) * Xindex + X] == 0) {
geoInfoEx->isBoundary[Y * Xindex + X] = 1;
geoInfoEx->boundaryIndex.push_back(Y * Xindex + X);
}
}
}
}
break;
case 3://3D
for (Z = 0; Z < Zindex; Z += 2) {
for (Y = 0; Y < Yindex; Y += 2) {
for (X = 0; X < Xindex; X += 2) {
geoInfoEx->isBoundary[Z * Yindex * Xindex + Y * Xindex + X] = 0;//initialize
if (geoInfoEx->isDomain[Z * Yindex * Xindex + Y * Xindex + X] == 1) {
if (X == 0 || X == Xindex - 1 || Y == 0 || Y == Yindex - 1 || Z == 0 || Z == Zindex - 1) {//boundary of th domain
geoInfoEx->isBoundary[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfoEx->boundaryIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
} else if (geoInfoEx->isDomain[Z * Yindex * Xindex + Y * Xindex + (X + 2)] == 0
|| geoInfoEx->isDomain[Z * Yindex * Xindex + Y * Xindex + (X - 2)] == 0
|| geoInfoEx->isDomain[Z * Yindex * Xindex + (Y + 2) * Xindex + X] == 0
|| geoInfoEx->isDomain[Z * Yindex * Xindex + (Y - 2) * Xindex + X] == 0
|| geoInfoEx->isDomain[(Z + 2) * Yindex * Xindex + Y * Xindex + X] == 0
|| geoInfoEx->isDomain[(Z - 2) * Yindex * Xindex + Y * Xindex + X] == 0) {
geoInfoEx->isBoundary[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfoEx->boundaryIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
}
}
}
}
}
break;
default:
break;
}
}
}
}
//membrane compartment
for (i = 0; i < numOfCompartments; i++) {
cPlugin = static_cast<SpatialCompartmentPlugin*>(loc->get(i)->getPlugin("spatial"));
if (cPlugin == 0 || !(cPlugin->isSetCompartmentMapping())) continue;
DomainType *dType = geometry->getDomainType(cPlugin->getCompartmentMapping()->getDomainType());
GeometryInfo *geoInfo = searchAvolInfoByCompartment(geoInfoList, loc->get(i)->getId().c_str());
if (geoInfo == 0) {
geoInfo = new GeometryInfo;
InitializeAVolInfo(geoInfo);
geoInfo->compartmentId = loc->get(i)->getId().c_str();
geoInfo->domainTypeId = cPlugin->getCompartmentMapping()->getDomainType().c_str();
//geoInfo->bt = new boundaryType[numOfVolIndexes];
if (dType->getSpatialDimensions() == (int)volDimension) {
geoInfo->isVol = true;
} else if (dType->getSpatialDimensions() == (int)memDimension) {
geoInfo->isVol = false;
}
geoInfoList.push_back(geoInfo);
}
for (j = 0; j < geometry->getNumDomains(); j++) {//Domain
Domain *domain = geometry->getDomain(j);
if (domain->getDomainType() == geoInfo->domainTypeId) {
geoInfo->domainIdList.push_back(domain->getId().c_str());
}
}
}
for (i = 0; i < geometry->getNumAdjacentDomains(); i++) {//AdjacentDomain
AdjacentDomains *adDomain = geometry->getAdjacentDomains(i);
Domain *ad1 = geometry->getDomain(adDomain->getDomain1());
Domain *ad2 = geometry->getDomain(adDomain->getDomain2());
GeometryInfo *geoi1 = searchAvolInfoByDomainType(geoInfoList, ad1->getDomainType().c_str());
GeometryInfo *geoi2 = searchAvolInfoByDomainType(geoInfoList, ad2->getDomainType().c_str());
if (geoi1->adjacentGeo1 == 0) {
geoi1->adjacentGeo1 = geoi2;
} else if (geoi1->adjacentGeo2 == 0 && geoi1->adjacentGeo1 != geoi2) {
geoi1->adjacentGeo2 = geoi2;
}
if (geoi2->adjacentGeo1 == 0) {
geoi2->adjacentGeo1 = geoi1;
} else if (geoi2->adjacentGeo2 == 0 && geoi2->adjacentGeo1 != geoi1) {
geoi2->adjacentGeo2 = geoi1;
}
}
//membrane position
for (i = 0; i < geoInfoList.size(); i++) {
GeometryInfo *geoInfo = geoInfoList[i];
boundaryMembrane *bMem = searchBMemInfoByCompartment(bMemInfoList, geoInfo->compartmentId);// membrane's boundary condition
if (geoInfo->isVol == false) {//avol is membrane
geoInfo->isDomain = new int[numOfVolIndexes];
fill_n(geoInfo->isDomain, numOfVolIndexes, 0);
geoInfo->isBoundary = new int[numOfVolIndexes];
fill_n(geoInfo->isBoundary, numOfVolIndexes, 0);
geoInfo->bType = new boundaryType[numOfVolIndexes];
for (j = 0; j < numOfVolIndexes; j++) {
geoInfo->bType[j].isBofXp = false;
geoInfo->bType[j].isBofXm = false;
geoInfo->bType[j].isBofYp = false;
geoInfo->bType[j].isBofYm = false;
geoInfo->bType[j].isBofZp = false;
geoInfo->bType[j].isBofZm = false;
}
switch (dimension) {
case 1:
for (X = 0; X < Xindex; X++) {
if (X % 2 != 0) {
Xplus1 = Y * Xindex + (X + 1);
Xminus1 = Y * Xindex + (X - 1);
if (X != 0 && X != (Xindex - 1)) {
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {
//position
geoInfo->isDomain[X] = 1;
geoInfo->domainIndex.push_back(X);
//boundary condition
if( bMem != 0 )
bMem->position[X] = bMem->bcType;
}
}
}
}
break;
case 2:
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
if ((Y * Xindex + X) % 2 != 0) {
Xplus1 = Y * Xindex + (X + 1);
Xminus1 = Y * Xindex + (X - 1);
Yplus1 = (Y + 1) * Xindex + X;
Yminus1 = (Y - 1) * Xindex + X;
if (X != 0 && X != (Xindex - 1) && Y != 0 && Y != (Yindex - 1)) {
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Y * Xindex + X].isBofXp = true;
geoInfo->bType[Y * Xindex + X].isBofXm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Yplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Yminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yplus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Y * Xindex + X].isBofYp = true;
geoInfo->bType[Y * Xindex + X].isBofYm = true;
}
} else if (X == 0 || X == Xindex - 1) {
if ((geoInfo->adjacentGeo1->isDomain[Yplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Yminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yplus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Y * Xindex + X].isBofYp = true;
geoInfo->bType[Y * Xindex + X].isBofYm = true;
}
} else if (Y == 0 || Y == Yindex - 1) {
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(X);
if( bMem != 0 ) // boundary condition
bMem->position[Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Y * Xindex + X].isBofXp = true;
geoInfo->bType[Y * Xindex + X].isBofXm = true;
}
}
}
}
}
//pseudo membrane
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
if ((X % 2 != 0 && Y % 2 != 0)) {
Xplus1 = Y * Xindex + (X + 1);
Xminus1 = Y * Xindex + (X - 1);
Yplus1 = (Y + 1) * Xindex + X;
Yminus1 = (Y - 1) * Xindex + X;
if (X != 0 && X != Xindex - 1 && Y != 0 && Y != Yindex - 1) {
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Yminus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 2;
geoInfo->pseudoMemIndex.push_back(Y * Xindex + X);
}
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Yplus1] == 1) ||
(geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Yminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Xminus1] == 1)) {
geoInfo->isDomain[Y * Xindex + X] = 2;
geoInfo->pseudoMemIndex.push_back(Y * Xindex + X);
}
} else if (X == 0 || X == Xindex - 1) {
if (geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Yminus1] == 1) {
geoInfo->isDomain[Y * Xindex + X] = 2;
geoInfo->pseudoMemIndex.push_back(Y * Xindex + X);
}
} else if (Y == 0 || Y == Yindex - 1) {
if (geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) {
geoInfo->isDomain[Y * Xindex + X] = 2;
geoInfo->pseudoMemIndex.push_back(Y * Xindex + X);
}
}
}
}
}
break;
case 3:
for (Z = 0; Z < Zindex; Z++) {
for (Y = 0; Y < Yindex; Y++) {
for (X = 0; X < Xindex; X++) {
if ((Z * Yindex * Xindex + Y * Xindex + X) % 2 != 0) {
Xplus1 = Z * Yindex * Xindex + Y * Xindex + (X + 1);
Xminus1 = Z * Yindex * Xindex + Y * Xindex + (X - 1);
Yplus1 = Z * Yindex * Xindex + (Y + 1) * Xindex + X;
Yminus1 = Z * Yindex * Xindex + (Y - 1) * Xindex + X;
Zplus1 = (Z + 1) * Yindex * Xindex + Y * Xindex + X;
Zminus1 = (Z - 1) * Yindex * Xindex + Y * Xindex + X;
if ((X * Y * Z) != 0 && X != (Xindex - 1) && Y != (Yindex - 1) && Z != (Zindex - 1)) {//not at the edge of simulation space
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {//X
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Yplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Yminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yplus1] == 1)) {//Y
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Zplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Zminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zplus1] == 1)) {//Z
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofZp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofZm = true;
}
} else if (X == 0 || X == Xindex - 1) {
if ((geoInfo->adjacentGeo1->isDomain[Yplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Yminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yplus1] == 1)) {//Y
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Zplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Zminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zplus1] == 1)) {//Z
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex +Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofZp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofZm = true;
}
} else if (Y == 0 || Y == Yindex - 1) {
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {//X
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Zplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Zminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Zplus1] == 1)) {//Y
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex +Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYm = true;
}
} else if (Z == 0 || Z == Zindex - 1) {
if ((geoInfo->adjacentGeo1->isDomain[Xplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Xminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Xplus1] == 1)) {//X
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex + Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofXm = true;
} else if ((geoInfo->adjacentGeo1->isDomain[Yplus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yminus1] == 1) ||
(geoInfo->adjacentGeo1->isDomain[Yminus1] == 1 && geoInfo->adjacentGeo2->isDomain[Yplus1] == 1)) {//Y
geoInfo->isDomain[Z * Yindex * Xindex + Y * Xindex + X] = 1;
geoInfo->domainIndex.push_back(Z * Yindex * Xindex +Y * Xindex + X);
if( bMem != 0 ) // boundary condition
bMem->position[Z * Yindex * Xindex + Y * Xindex + X] = bMem->bcType;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYp = true;
geoInfo->bType[Z * Yindex * Xindex + Y * Xindex + X].isBofYm = true;
}
}
}
}
}
}//mashimodao
//pseudo membrane
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) || (Y % 2 != 0 && Z % 2 != 0) || (Z % 2 != 0 && X % 2 != 0)) {
index = Z * Yindex * Xindex + Y * Xindex + X;
Xplus1 = Z * Yindex * Xindex + Y * Xindex + (X + 1);
Xminus1 = Z * Yindex * Xindex + Y * Xindex + (X - 1);
Yplus1 = Z * Yindex * Xindex + (Y + 1) * Xindex + X;
Yminus1 = Z * Yindex * Xindex + (Y - 1) * Xindex + X;
Zplus1 = (Z + 1) * Yindex * Xindex + Y * Xindex + X;
Zminus1 = (Z - 1) * Yindex * Xindex + Y * Xindex + X;
if (X != 0 && X != Xindex - 1 && Y != 0 && Y != Yindex - 1 && Z != 0 && Z != Zindex - 1) {
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Yminus1] == 1) ||
(geoInfo->isDomain[Zplus1] == 1 && geoInfo->isDomain[Zminus1] == 1)) {
geoInfo->isDomain[index] = 2;
geoInfo->pseudoMemIndex.push_back(index);
}
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Yplus1] == 1) ||
(geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Yminus1] == 1) ||
(geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Xminus1] == 1 && geoInfo->isDomain[Yplus1] == 1) ||
(geoInfo->isDomain[Xminus1] == 1 && geoInfo->isDomain[Yminus1] == 1) ||
(geoInfo->isDomain[Xminus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Xminus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zminus1] == 1)) {
geoInfo->isDomain[index] = 2;
geoInfo->pseudoMemIndex.push_back(index);
}
} else if (X == 0 || X == Xindex - 1) {
if ((geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Yminus1] == 1) ||
(geoInfo->isDomain[Zplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zminus1] == 1)) {
geoInfo->isDomain[index] = 2;
geoInfo->pseudoMemIndex.push_back(index);
}
} else if (Y == 0 || Y == Yindex - 1) {
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) ||
(geoInfo->isDomain[Zplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Zminus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zplus1] == 1) ||
(geoInfo->isDomain[Yminus1] == 1 && geoInfo->isDomain[Zminus1] == 1)) {
geoInfo->isDomain[index] = 2;
}
} else if (Z == 0 || Z == Zindex - 1) {
if ((geoInfo->isDomain[Xplus1] == 1 && geoInfo->isDomain[Xminus1] == 1) ||
(geoInfo->isDomain[Yplus1] == 1 && geoInfo->isDomain[Yminus1] == 1)) {
geoInfo->isDomain[index] = 2;
geoInfo->pseudoMemIndex.push_back(index);
}
}
}
}
}
}
break;
default:
break;
}
}
}
cout << "finished" << endl << endl;
//make directories to output result (txt and img)
if(stat(string(outpath + "/result/" + fname + "/img").c_str(), &st) != 0) {
system(string("mkdir " + outpath + "/result/" + fname + "/img").c_str());
}
if(stat(string(outpath + "/result/" + fname + "/HDF5").c_str(), &st) != 0) {//added by mashimo
system(string("mkdir " + outpath + "/result/" + fname + "/HDF5").c_str());
}
makeHDF(fname, los, outpath);//added by mashimo
if (dimension == 3)
make3DHDF(fname, los, outpath);
for (i = 0; i < numOfSpecies; i++) {
s = los->get(i);
variableInfo *sInfo = searchInfoById(varInfoList, s->getId().c_str());
if (sInfo != 0 && stat(string(outpath + "/result/" + fname + "/img/" + s->getId()).c_str(), &st) != 0) {
system(string("mkdir " + outpath + "/result/" + fname + "/img/" + s->getId()).c_str());
}
}
//draw geometries
variableInfo *xInfo = 0, *yInfo = 0, *zInfo = 0;
if (dimension >= 1) {
xInfo = searchInfoById(varInfoList, xaxis);
}
if (dimension >= 2) {
yInfo = searchInfoById(varInfoList, yaxis);
}
if (dimension >= 3) {
zInfo = searchInfoById(varInfoList, zaxis);
}
//set species' initial condition
//boundary type(Xp, Xm, Yp, Ym, Zx, Zm)
//parse dependence among species, compartments, parameters
cout << "assigning initial conditions of species and parameters..." << endl;
vector<variableInfo*> notOrderedInfo;
for (i = 0; i < varInfoList.size(); i++) {
variableInfo *info = varInfoList[i];
ast = 0;
std::string SFId = info->id;
SFId += "_initialConcentration";
if ( (model->getInitialAssignment(info->id) != 0 ) && (geometry->getListOfSampledFields()->get( SFId ) == 0 ) ) {//initial assignment which does not mean local concentration modified by morita
if (info->value == 0) {//value is not set yet
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
if (info->sp != 0 && (!info->sp->isSetConstant() || !info->sp->getConstant())) {
info->delta = new double[4 * numOfVolIndexes];
fill_n(info->delta, 4 * numOfVolIndexes, 0);
}
}
ast = const_cast<ASTNode*>((model->getInitialAssignment(info->id))->getMath());
} else if (model->getRule(info->id) != 0 && model->getRule(info->id)->isAssignment()) {//assignment rule
info->hasAssignmentRule = true;
if (info->value == 0) {//value is not set yet
info->value = new double[numOfVolIndexes];
fill_n(info->value, numOfVolIndexes, 0);
if (info->sp != 0 && (!info->sp->isSetConstant() || !info->sp->getConstant())) {
//the species is variable
info->delta = new double[4 * numOfVolIndexes];
fill_n(info->delta, 4 * numOfVolIndexes, 0);
}
}
ast = const_cast<ASTNode*>((static_cast<AssignmentRule*>(model->getRule(info->id)))->getMath());
}
if (ast != 0) {
rearrangeAST(ast);
numOfASTNodes = 0;