bool ComplexDomainFlux::process(Ports<InputBuffer*>& inp, Ports<OutputBuffer*>& outp)
{
assert(inp.size()==1);
InputBuffer* in = inp[0].data;
assert(outp.size()==1);
OutputBuffer* out = outp[0].data;
if ((out->tokenno()==0) && (in->tokenno()!=-2))
in->prependZeros(2);
if (!in->hasTokens(3)) return false;
const int N = in->info().size/2;
ArrayXcd inPredPredRotator(N);
ArrayXcd inPredRotator(N);
rotatorOp<double> op;
{
Map<ArrayXcd> inPredPredData((complex<double>*) in->token(0),N);
inPredPredRotator = inPredPredData.unaryExpr(op);
}
while (in->hasTokens(3))
{
Map<ArrayXcd> inPredData((complex<double>*) in->token(1),N);
Map<ArrayXcd> inData((complex<double>*) in->token(2), N);
inPredRotator = inPredData.unaryExpr(op);
double* output = out->writeToken();
*output++ = (inData - (inPredData * (inPredRotator * inPredPredRotator.conjugate()))).abs().sum();
in->consumeToken();
inPredPredRotator.swap(inPredRotator);
}
return true;
}
bool EvoAlgoTestIndividual::loadGenotypes()
{
// Removing all old genotypes
freeGenotypes();
// Loading all genotypes
QFile inData(m_filename);
if (inData.open(QFile::ReadOnly)) {
QTextStream in(&inData);
while (!in.atEnd()) {
std::unique_ptr<Genotype> g(getPrototype()->clone());
bool loaded = g->loadGen(in);
if (!loaded) {
// This could be not a real error, only notifying the user
Logger::warning(QString("Error loading the genotype at index %1 from file %2").arg(m_genotypes.size()).arg(m_filename));
break;
}
m_genotypes.append(g.release());
}
inData.close();
} else {
Logger::error(QString("Cannot open file %1 to read genotypes").arg(m_filename));
return false;
}
return true;
}
void FFT::processToken(double* inPtr, const int N, double* out, const int outSize)
{
#ifdef WITH_FFTW3
double* inFFT = (double*) fftw_malloc(m_nfft*sizeof(double));
complex<double>* outFFT = (complex<double>*) fftw_malloc((m_nfft/2+1)*sizeof(complex<double>));
Map<VectorXd> infft(inFFT,m_nfft);
#else
VectorXd infft(m_nfft);
#endif
Map<VectorXd> inData(inPtr,N);
if (m_window.size()>0)
infft.segment(0,N) = m_window.array() * inData.array();
else
infft.segment(0,N) = inData;
if (N<m_nfft)
infft.segment(N,m_nfft-N).setZero();
#ifdef WITH_FFTW3
fftw_execute_dft_r2c(m_plan,inFFT,(fftw_complex*)outFFT);
memcpy(out,outFFT,outSize*sizeof(double));
fftw_free(inFFT);
fftw_free(outFFT);
#else
m_plan.fwd((std::complex<double>*) out,infft.data(),m_nfft);
#endif
}
void
wxPdfParser::GetStreamBytesRaw(wxPdfStream* stream)
{
wxPdfNumber* streamLength = (wxPdfNumber*) ResolveObject(stream->Get(_T("/Length")));
size_t size = streamLength->GetInt();
m_tokens->Seek(stream->GetOffset());
wxMemoryOutputStream* memoryBuffer = NULL;
wxMemoryOutputStream* streamBuffer = m_tokens->ReadBuffer(size);
if (m_encrypted && size > 0)
{
wxMemoryInputStream inData(*streamBuffer);
delete streamBuffer;
memoryBuffer = new wxMemoryOutputStream();
unsigned char* buffer = new unsigned char[size];
inData.Read(buffer, size);
if (inData.LastRead() == size)
{
m_decryptor->Encrypt(m_objNum, m_objGen, buffer, size);
memoryBuffer->Write(buffer, size);
}
delete [] buffer;
memoryBuffer->Close();
}
else
{
memoryBuffer = streamBuffer;
}
stream->SetBuffer(memoryBuffer);
if (streamLength->IsIndirect())
{
delete streamLength;
}
}
ReflectorSession* SetupProxySession(QTSS_StandardRTSP_Params* inParams, RTSPRelaySession* session)
{
if(session == NULL) return NULL;
UInt32 sdpLen = 0;
char* relaySDP = NULL;
relaySDP = session->GetSDPInfo()->GetLocalSDP(&sdpLen);
if(relaySDP == NULL) return NULL;
StrPtrLen inData(relaySDP);
return FindOrCreateProxySession(session->GetRef()->GetString(), inParams, &inData,0);
}
//void DebugStatsModule::SendRandomNetworkInPacket()
Console::CommandResult DebugStatsModule::SendRandomNetworkInPacket(const StringVector ¶ms)
{
if (params.size() == 0)
return Console::ResultSuccess();
int numMessages = atoi(params[0].c_str());
for(int i = 0; i < numMessages; ++i)
{
std::vector<char> data;
int dataLen = rand() % 1600 + 1;
for(int i = 0; i < dataLen; ++i)
data.push_back(rand() % 256);
int msgID = rand();
ProtocolUtilities::NetMessageManager *messageManager = current_world_stream_->GetCurrentProtocolModule()->GetNetworkMessageManager();
if (!messageManager)
return Console::ResultSuccess();
try
{
ProtocolUtilities::NetInMessage msg(msgID, (boost::uint8_t *)&data[0], dataLen, false);
#ifdef _DEBUG
msg.SetMessageID(msgID);
#endif
ProtocolUtilities::NetMsgID id = msgID;
ProtocolUtilities::NetworkEventInboundData inData(id , &msg);
const ProtocolUtilities::NetMessageInfo *messageInfo = messageManager->GetMessageInfoByID(msgID);
if (!messageInfo)
continue;
msg.SetMessageInfo(messageInfo);
framework_->GetEventManager()->SendEvent(networkEventCategory_, id, &inData);
}
catch(const Exception &e)
{
LogInfo(std::string("Exception thrown: ") + e.what());
}
catch(const std::exception &e)
{
LogInfo(std::string("std::exception thrown: ") + e.what());
}
catch(...)
{
LogInfo("Unknown exception thrown.");
}
}
return Console::ResultSuccess();
}
bool MPEGDecoder::init( bool decodeOnly )
{
onlyDecode = decodeOnly;
QFile file( testFile );
if ( !file.open(QIODevice::ReadOnly) ) {
fprintf( stderr, "%s", QString("MPEGDecoder: FATAL: Can't open %1 !!\n").arg(testFile).toLatin1().data() );
return false;
}
QDataStream inData( &file );
inData.readRawData( (char*)&width, 4 );
inData.readRawData( (char*)&height, 4 );
inData.readRawData( (char*)&ratio, 8 );
inData.readRawData( (char*)&profile, 4 );
int i;
for ( i=0; i<FRAMESINSAMPLE; ++i ) {
MPEGFrame *frame = new MPEGFrame();
inData.readRawData( (char*)&frame->info, sizeof(frame->info) );
inData.readRawData( (char*)&frame->dataLength, 4 );
frame->data = new uint8_t[frame->dataLength];
inData.readRawData( (char*)frame->data, frame->dataLength );
frames.append( frame );
}
VdpStatus st = vc->vdp_decoder_create( vc->vdpDevice, profile, width, height, 2, &decoder );
if ( st != VDP_STATUS_OK ) {
fprintf( stderr, "MPEGDecoder: FATAL: Can't create decoder!!\n" );
return false;
}
for ( i=0; i<NUMSURFACES; ++i ) {
surfaces[ i ] = VDP_INVALID_HANDLE;
if ( onlyDecode && i>2 )
continue;
st = vc->vdp_video_surface_create( vc->vdpDevice, VDP_CHROMA_TYPE_420, width, height, &surfaces[i] );
if ( st != VDP_STATUS_OK ) {
fprintf( stderr, "MPEGDecoder: FATAL: Can't create required surfaces!!\n" );
return false;
}
}
forwardRef = backwardRef = VDP_INVALID_HANDLE;
currentSurface = surfaces[0];
currentFrame = 0;
//fprintf( stderr, "MPEGDecoder: profile = %d\n", profile );
return true;
}
bool Cepstrum::process(Ports<InputBuffer*>& inp, Ports<OutputBuffer*>& outp)
{
assert(inp.size()==1);
InputBuffer* in = inp[0].data;
if (in->empty())
return false;
assert(outp.size()==1);
OutputBuffer* out = outp[0].data;
safeLogOp<double> slop;
VectorXd outDct;
while (!in->empty())
{
Map<VectorXd> inData(in->readToken(),in->info().size);
outDct.noalias() = m_dctPlan * inData.unaryExpr(slop);
memcpy(out->writeToken(),outDct.data() + m_ignoreFirst, out->info().size*sizeof(double));
in->consumeToken();
}
return true;
}
bool SpecificLoudness::process(Ports<InputBuffer*>& inp, Ports<OutputBuffer*>& outp)
{
assert(inp.size()==1);
InputBuffer* in = inp[0].data;
if (in->empty()) return false;
assert(outp.size()==1);
OutputBuffer* out = outp[0].data;
const int N = in->info().size;
const int M = out->info().size;
while (!in->empty())
{
Map<VectorXd> inData(in->readToken(),N);
double* outData = out->writeToken();
for (int i=0;i<NB_BARK_BANDS;i++)
outData[i] = pow(inData.segment(m_bkBdLimits[i],m_bkBdLimits[i+1]-m_bkBdLimits[i]).sum(),0.23);
in->consumeToken();
}
return true;
}
bool MelFilterBank::process(Ports<InputBuffer*>& inp, Ports<OutputBuffer*>& outp)
{
assert(inp.size()==1);
InputBuffer* in = inp[0].data;
if (in->empty()) return false;
assert(outp.size()==1);
OutputBuffer* out = outp[0].data;
while (!in->empty()) {
Map<VectorXd> inData(in->readToken(),in->info().size);
double* outData = out->writeToken();
for (int f=0;f<m_filters.size();f++)
{
RowVectorXd& filter = m_filters[f];
outData[f] = filter * inData.segment(m_filterStart[f],filter.size());
}
in->consumeToken();
}
return true;
}
//--------------------------------------------------------------------------------------
// Name: TerrainClass::LoadTerrainFromFile()
// Desc: 加载地形高度信息以及纹理
//--------------------------------------------------------------------------------------
BOOL TerrainClass::LoadTerrainFromFile(wchar_t *pRawFileName, wchar_t *pTextureFile)
{
// 从文件中读取高度信息
std::ifstream inFile;
inFile.open(pRawFileName, std::ios::binary); //用二进制的方式打开文件
inFile.seekg(0,std::ios::end); //把文件指针移动到文件末尾
std::vector<BYTE> inData(inFile.tellg()); //用模板定义一个vector<BYTE>类型的变量inData并初始化，其值为缓冲区当前位置，即缓冲区大小
inFile.seekg(std::ios::beg); //将文件指针移动到文件的开头，准备读取高度信息
inFile.read((char*)&inData[0], inData.size()); //关键的一步，读取整个高度信息
inFile.close(); //操作结束，可以关闭文件了
m_vHeightInfo.resize(inData.size()); //将m_vHeightInfo尺寸取为缓冲区的尺寸
//遍历整个缓冲区，将inData中的值赋给m_vHeightInfo
for (unsigned int i=0; i<inData.size(); i++)
m_vHeightInfo[i] = inData[i];
// 加载地形纹理
if (FAILED(D3DXCreateTextureFromFile(m_pd3dDevice, pTextureFile, &m_pTexture)))
return FALSE;
return TRUE;
}
/** create a SlaterDeterminant
* @param cur xmlnode containing \<slaterdeterminant\>
* @return a SlaterDeterminant
*
* @warning MultiSlaterDeterminant is not working yet.
*/
SPOSetBase*
SplineSetBuilder::createSPOSet(xmlNodePtr cur)
{
string hrefname("NONE");
int norb(0);
int degeneracy(1);
OhmmsAttributeSet aAttrib;
aAttrib.add(norb,"orbitals");
aAttrib.add(degeneracy,"degeneracy");
aAttrib.add(hrefname,"href");
aAttrib.put(cur);
if(norb ==0)
{
app_error() << "SplineSetBuilder::createSPOSet failed. Check the attribte orbitals." << endl;
return 0;
}
app_log() << " Degeneracy = " << degeneracy << endl;
std::vector<int> npts(3);
npts[0]=GridXYZ->nX;
npts[1]=GridXYZ->nY;
npts[2]=GridXYZ->nZ;
std::vector<RealType> inData(npts[0]*npts[1]*npts[2]);
SPOSetType* psi= new SPOSetType(norb);
vector<int> occSet(norb);
for(int i=0; i<norb; i++)
occSet[i]=i;
cur=cur->children;
while(cur != NULL)
{
string cname((const char*)(cur->name));
if(cname == "occupation")
{
string occ_mode("ground");
const xmlChar* o=xmlGetProp(cur,(const xmlChar*)"mode");
if(o!= NULL)
occ_mode = (const char*)o;
//Do nothing if mode == ground
if(occ_mode == "excited")
{
vector<int> occ_in, occRemoved;
putContent(occ_in,cur);
for(int k=0; k<occ_in.size(); k++)
{
if(occ_in[k]<0)
occRemoved.push_back(-occ_in[k]-1);
}
int kpopd=0;
for(int k=0; k<occ_in.size(); k++)
{
if(occ_in[k]>0)
occSet[occRemoved[kpopd++]]=occ_in[k]-1;
}
}
hid_t h_file = H5Fopen(hrefname.c_str(),H5F_ACC_RDWR,H5P_DEFAULT);
const xmlChar* h5path = xmlGetProp(cur,(const xmlChar*)"h5path");
string hroot("/eigenstates_3/twist_0");
if(h5path != NULL)
hroot=(const char*)h5path;
char wfname[128],wfshortname[16];
for(int iorb=0; iorb<norb; iorb++)
{
sprintf(wfname,"%s/band_%d/eigenvector",hroot.c_str(),occSet[iorb]/degeneracy);
sprintf(wfshortname,"b%d",occSet[iorb]/degeneracy);
SPOType* neworb=0;
map<string,SPOType*>::iterator it(NumericalOrbitals.find(wfshortname));
if(it == NumericalOrbitals.end())
{
neworb=new SPOType(GridXYZ);
HDFAttribIO<std::vector<RealType> > dummy(inData,npts);
dummy.read(h_file,wfname);
//neworb->reset(inData.begin(), inData.end(), targetPtcl.Lattice.BoxBConds[0]);
neworb->reset(inData.begin(), inData.end(), targetPtcl.Lattice.SuperCellEnum);
NumericalOrbitals[wfshortname]=neworb;
app_log() << " Reading spline function " << wfname << endl;
}
else
{
neworb = (*it).second;
app_log() << " Reusing spline function " << wfname << endl;
}
psi->add(neworb);
}
H5Fclose(h_file);
}
cur=cur->next;
}
SPOType* aorb=(*NumericalOrbitals.begin()).second;
string fname("spline3d.vti");
std::ofstream dfile(fname.c_str());
dfile.setf(ios::scientific, ios::floatfield);
dfile.setf(ios::left,ios::adjustfield);
dfile.precision(10);
dfile << "<?xml version=\"1.0\"?>" << endl;
dfile << "<VTKFile type=\"ImageData\" version=\"0.1\">" << endl;
dfile << " <ImageData WholeExtent=\"0 " << npts[0]-2 << " 0 " << npts[1]-2 << " 0 " << npts[2]-2
<< "\" Origin=\"0 0 0\" Spacing=\"1 1 1\">"<< endl;
dfile << " <Piece Extent=\"0 " << npts[0]-2 << " 0 " << npts[1]-2 << " 0 " << npts[2]-2 << "\">" << endl;
dfile << " <PointData Scalars=\"wfs\">" << endl;
dfile << " <DataArray type=\"Float32\" Name=\"wfs\">" << endl;
int ng=0;
GradType grad;
ValueType lap;
for(int ix=0; ix<npts[0]-1; ix++)
{
double x(GridXYZ->gridX->operator()(ix));
for(int iy=0; iy<npts[1]-1; iy++)
{
double y(GridXYZ->gridY->operator()(iy));
for(int iz=0; iz<npts[2]-1; iz++, ng++)
{
PosType p(x,y,GridXYZ->gridZ->operator()(iz));
//aorb.setgrid(p);
//Timing with the ofstream is not correct.
//Uncomment the line below and comment out the next two line.
//double t=aorb.evaluate(p,grad,lap);
dfile << setw(20) << aorb->evaluate(p,grad,lap);
if(ng%5 == 4)
dfile << endl;
}
}
}
dfile << " </DataArray>" << endl;
dfile << " </PointData>" << endl;
dfile << " </Piece>" << endl;
dfile << " </ImageData>" << endl;
dfile << "</VTKFile>" << endl;
abort();
return psi;
}
void XnesAlgo::runEvolution()
{
Eigen::MatrixXf expCovMat(m_numGenes,m_numGenes);
int startGeneration = 0;
char statfile[64];
char inFilename[128];
char outFilename[128];
char bestOutFilename[128];
int bestGeneration = -1;
int bestFitness = -1;
// Set the seed
setSeed(m_rngSeed);
// Initialise the individual and the covariance matrix
initialise();
// Check whether to recover a previous evolution
sprintf(statfile,"S%d.fit", seed());
// Check if the file exists
DataChunk statTest(QString("stattest"),Qt::blue,2000,false);
if (statTest.loadRawData(QString(statfile),0))
{
startGeneration = statTest.getIndex();
sprintf(inFilename, "S%dG%d.gen", (seed()), startGeneration);
Logger::info("Recovering from startGeneration: " + QString::number(startGeneration));
Logger::info(QString("Loading file: ") + inFilename);
QFile inData(inFilename);
if (inData.open(QFile::ReadOnly))
{
QTextStream in(&inData);
bool loaded = m_individual->loadGen(in);
// Check possible errors during the loading operation
if (!loaded)
{
Logger::error("Error in the loading of the genotype");
}
// Check the consistency of the genotype (i.e., the number of genes)
if (m_individual->getLength() != m_numGenes)
{
Logger::error("Wrong genotype length!");
}
// Load the covariance matrix
char covMatFilename[64];
sprintf(covMatFilename, "S%dG%d.cvm", (seed()), startGeneration);
QFile covMatData(covMatFilename);
if (covMatData.open(QFile::ReadOnly))
{
QTextStream covMatInput(&covMatData);
for (int i = 0; i < m_numGenes; i++)
{
for (int j = 0; j < m_numGenes; j++)
{
QString str;
covMatInput >> str;
bool ok = false;
float elem = str.toFloat(&ok);
if (!ok || (covMatInput.status() != QTextStream::Ok))
{
Logger::error("Error in the loading of the covariance matrix");
}
m_covMat(i,j) = elem;
expCovMat(i,j) = 0.0;
}
}
covMatData.close();
}
int main(){
int gender;
int wealthpercentile;
int i,j,l;
int deductgrid;
int wealth;
int wx;
int grid;
int temp_test;
int Sstart;
double alpha;
int offset;
char filename[11]={"table.txt"};
task_group tasks;
time_t time_began,time_end;
/*
output variable
*/
//memset(&CalcStruct[0],0,sizeof(CALCSTRUCT));
gender=1; //0 is female 1 is male
deductgrid=DEDUCTGRID;
//wealthpercentile=3; //0-9 different wealth distribution
/*
calculating declaration:
this time run for gird*4 total size
from 4-8
so the program make some adjustment
*/
cout<<"calculating declaration: this time run for gird*4 total size from 4-8 \n so the program make some adjustment"<<endl;
cur_time();
offset =0;
Sstart=START;
Parallel_LTCI *LTCI[10];
{
for(gender=1;gender<2;gender++){
// initilize the class of LTCI
for(wealthpercentile=Sstart;wealthpercentile<10-offset;wealthpercentile ++)
{
switch (wealthpercentile){
case 0: wealth=40000; alpha=0.98; wx=0; grid=20; break;
case 1: wealth=58450; alpha=0.98; wx=0; grid=20; break;
case 2: wealth=93415; alpha=0.91; wx=20000; grid=40; break;
case 3: wealth=126875; alpha=0.82; wx=30000; grid=75; break;
case 4: wealth=169905; alpha=0.70; wx=10000; grid=100; break;
case 5: wealth=222570; alpha=0.60; wx=50000; grid=130; break;
case 6: wealth=292780; alpha=0.52; wx=20000; grid=175; break;
case 7: wealth=385460; alpha=0.41; wx=40000; grid=225; break;
case 8: wealth=525955; alpha=0.35; wx=40000; grid=300; break;
case 9: wealth=789475; alpha=0.26; wx=75000; grid=450; break;
}
//wealth =wealth*224.937/172.192;
LTCI[int(wealthpercentile)-Sstart]=new Parallel_LTCI(wealthpercentile,gender,deductgrid,wealth,wx,grid,alpha);
}
calcSetup();
inputData(gender);
for(i=0;i<10-Sstart-offset;i++){
Setup(LTCI[i]);
inData(gender,LTCI[i]);
}
cout<<"calculating for 0:female 1: male ------"<<gender<<endl;
cout<<"deductile period is : \t"<<deductgrid<<endl;
cout<<"**********************************************"<<endl;
cout<<"**********************************************"<<endl;
/*task for 1 to 4*/
tasks.run([&gender,<CI,&offset,&Sstart](){
// int wealthpercentile;
for(int wealthpercentile=Sstart;wealthpercentile<5-offset;wealthpercentile++)
LTCI[wealthpercentile-Sstart]->comput();
});
//// /*task for 4*/
//tasks.run([&gender,<CI,&Sstart](){
// int wealthpercentile=4-Sstart;
// LTCI[wealthpercentile]->comput();
//});
// /*task for 5*/
tasks.run([&gender,<CI,&Sstart](){
int wealthpercentile=5-Sstart;
LTCI[wealthpercentile]->comput();
});
/*task for 6*/
tasks.run([&gender,<CI,&Sstart](){
int wealthpercentile=6-Sstart;
LTCI[wealthpercentile]->comput();
});
// /*task for 7*/
tasks.run([&gender,<CI,&Sstart](){
int wealthpercentile=7-Sstart;
LTCI[wealthpercentile]->comput();
});
/*task for 8*/
tasks.run([&gender,<CI,&Sstart](){
int wealthpercentile=8-Sstart;
LTCI[wealthpercentile]->comput();
});
/*task for 9*/
tasks.run_and_wait([&gender,<CI,&Sstart](){
int wealthpercentile=9-Sstart;
LTCI[wealthpercentile]->comput();
});
}
// output some variables
if(para.MWcount==0){if (gender==0) para.MW=1.058; else para.MW=0.5;}
else if(para.MWcount==1){if (gender==0) para.MW=0.6; else para.MW=0.3;}
else if(para.MWcount==2){if (gender==0) para.MW=1.358127; else para.MW=0.6418727;}
else if(para.MWcount==3){if (gender==0) para.MW=1.358127; else para.MW=0.6418727;}
else if(para.MWcount==4){if (gender==0) para.MW=1; else para.MW=1;}
ofstream out(filename, ios::app);
if (out.is_open())
{
// out<<"*********************************************************************"<<endl;
out<<"deductile grid is :"<<deductgrid<<endl;
for(i=0;i<10-offset-Sstart;i++) record_result(i,LTCI[i]);
// out<<"table "<<endl;
// for(i=0;i<10-offset-Sstart;i++){
// out<<i+Sstart<<"0th : \t 1 \t 2 \t 3 \t 4"<<endl;
// out<<record.MUstar[i]/record.EPDVMedical[i]<<'\t';
// out<<record.Mstar[i]/record.EPDVMedical[i]<<"\t";
// out<<(record.MUstar[i] - record.Mstar[i])/record.Istarown[i]<<"\t";
// out<<(1-(record.Istarown[i]-(record.MUstar[i]-record.Mstar[i]))/(record.Istarown[i]/para.MW))<<"\t";
// out<<record.wequiv[i]<<"\t";
// out<<endl;
// }
out<<"*********************************************************************"<<endl;
out<<"----------------------------------------------------------------------"<<endl;
out<<"---------------------------------raw data---------------------------- "<<endl;
out<<"----------------------------------------------------------------------"<<endl;
out<<"index for the data: S_Madicaid \t S_Insurance \t S_Madicaid_NI \t S_Medcost \t S_wequiv \t S_medicare \t S_med_joint_NI \t S_med_joint \t S_OOP \t S_OOP_NI"<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_Madicaid[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_Insurance[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_Madicaid_NI[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_Medcost[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_wequiv[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_medicare[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_med_joint_NI[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_med_joint[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_OOP[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.S_OOP_NI[i]<<"\t";
out<<endl;
out<<"EPDVMedical wequive Mstar Istar MUstar Istarnon "<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.EPDVMedical[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.wequiv[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.Mstar[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.Istarown[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.MUstar[i]<<"\t";
out<<endl;
for(i=0;i<10-offset-Sstart;i++) out<<record.Istarnone[i]<<"\t";
out<<endl;
out.close();
}
for(i=0;i<10-offset-START;i++) delete LTCI[i];
}
system("pause");
return 0;
}
int main(int argc, char** argv) {
double ri = 0.0;
double rf = 1.0;
std::vector<int> npts(3);
npts[0]=51;npts[1]=51;npts[2]=51;
double xcut=0.23;
double ycut=0.67;
const int nk0=1;
const int nk1=1;
const int nk2=1;
//Create one-dimensional grids for three orthogonal directions
typedef LinearGrid<double> GridType;
GridType gridX, gridY, gridZ;
gridX.set(ri,rf,npts[0]);
gridY.set(ri,rf,npts[1]);
gridZ.set(ri,rf,npts[2]);
//Create an analytic function for assignment
ComboFunc infunc;
infunc.push_back(0.5,new TestFunc(1,1,1));
//infunc.push_back(0.3,new TestFunc(1,1,2));
//infunc.push_back(0.1,new TestFunc(1,2,1));
//infunc.push_back(0.01,new TestFunc(2,1,1));
//infunc.push_back(0.01,new TestFunc(2,2,1));
//infunc.push_back(0.001,new TestFunc(2,1,2));
//infunc.push_back(0.001,new TestFunc(2,2,2));
//infunc.push_back(0.001,new TestFunc(5,5,5));
//infunc.push_back(-0.3,new TestFunc(7,2,3));
//infunc.push_back(0.01,new TestFunc(7,7,7));
//infunc.push_back(0.001,new TestFunc(5,5,5));
//Write to an array
std::vector<double> inData(npts[0]*npts[1]*npts[2]);
std::vector<double>::iterator it(inData.begin());
Pooma::Clock timer;
timer.start();
//Assign the values
for(int ix=0; ix<npts[0]; ix++) {
double x(gridX(ix));
for(int iy=0; iy<npts[1]; iy++) {
double y(gridY(iy));
for(int iz=0; iz<npts[2]; iz++) {
(*it)=infunc.f(x,y,gridZ(iz));++it;
}
}
}
timer.stop();
cout << "Time to evaluate " << timer.cpu_time() << endl;
//Test TriCubicSplineT function
//Create XYZCubicGrid
XYZCubicGrid<double> grid3(&gridX,&gridY,&gridZ);
//Create a TriCubicSpline with PBC: have to think more about fixed-boundary conditions
TriCubicSplineT<double> aorb(&grid3);
//Reset the coefficients
aorb.reset(inData.begin(), inData.end());
double lap,val;
TinyVector<double,3> grad;
//aorb.reset();
//Write for vtk ImageData
string fname("spline3d.vti");
std::ofstream dfile(fname.c_str());
dfile.setf(ios::scientific, ios::floatfield);
dfile.setf(ios::left,ios::adjustfield);
dfile.precision(10);
dfile << "<?xml version=\"1.0\"?>" << endl;
dfile << "<VTKFile type=\"ImageData\" version=\"0.1\">" << endl;
dfile << " <ImageData WholeExtent=\"0 " << npts[0]-2 << " 0 " << npts[1]-2 << " 0 " << npts[2]-2
<< "\" Origin=\"0 0 0\" Spacing=\"1 1 1\">"<< endl;
dfile << " <Piece Extent=\"0 " << npts[0]-2 << " 0 " << npts[1]-2 << " 0 " << npts[2]-2 << "\">" << endl;
dfile << " <PointData Scalars=\"wfs\">" << endl;
dfile << " <DataArray type=\"Float32\" Name=\"wfs\">" << endl;
timer.start();
int ng=0;
for(int ix=0; ix<npts[0]-1; ix++) {
double x(gridX(ix));
for(int iy=0; iy<npts[1]-1; iy++) {
double y(gridY(iy));
for(int iz=0; iz<npts[2]-1; iz++, ng++) {
TinyVector<double,3> p(x,y,gridZ(iz));
//aorb.setgrid(p);
//Timing with the ofstream is not correct.
//Uncomment the line below and comment out the next two line.
//double t=aorb.evaluate(p,grad,lap);
dfile << setw(20) << aorb.evaluate(p,grad,lap);
if(ng%5 == 4) dfile << endl;
}
}
}
timer.stop();
cout << "Time to evaluate with spline " << timer.cpu_time() << endl;
dfile << " </DataArray>" << endl;
dfile << " </PointData>" << endl;
dfile << " </Piece>" << endl;
dfile << " </ImageData>" << endl;
dfile << "</VTKFile>" << endl;
hid_t h_file = H5Fcreate("spline3d.h5",H5F_ACC_TRUNC,H5P_DEFAULT,H5P_DEFAULT);
HDFAttribIO<std::vector<double> > dump(inData,npts);
dump.write(h_file,"orb0000");
HDFAttribIO<TriCubicSplineT<double> > dump1(aorb);
dump1.write(h_file,"spline0000");
H5Fclose(h_file);
//double lap;
//TinyVector<double,3> grad;
//for(int k=0; k<nptY-1; k++) {
// //TinyVector<double,3> p(xcut,ycut,gridZ(k)+0.11*gridZ.dr(k));
// TinyVector<double,3> p(xcut,gridY(k)+0.11*gridY.dr(k),ycut);
// aorb.setgrid(p);
// double y=aorb.evaluate(p,grad,lap);
// dfile << setw(30) << p[1] << setw(30) << infunc.f(p) << setw(30) << y << setw(30) << infunc.d2f(p) << setw(30) << lap << endl;
//}
return 0;
}
void PWOrbitalBuilder::transform2GridData(PWBasis::GIndex_t& nG, int spinIndex, PWOrbitalSet& pwFunc)
{
ostringstream splineTag;
splineTag << "eigenstates_"<<nG[0]<<"_"<<nG[1]<<"_"<<nG[2];
herr_t status = H5Eset_auto(NULL, NULL);
app_log() << " splineTag " << splineTag.str() << endl;
hid_t es_grp_id;
status = H5Gget_objinfo (hfileID, splineTag.str().c_str(), 0, NULL);
if(status)
{
es_grp_id = H5Gcreate(hfileID,splineTag.str().c_str(),0);
HDFAttribIO<PWBasis::GIndex_t> t(nG);
t.write(es_grp_id,"grid");
}
else
{
es_grp_id = H5Gopen(hfileID,splineTag.str().c_str());
}
string tname=myParam->getTwistName();
hid_t twist_grp_id;
status = H5Gget_objinfo (es_grp_id, tname.c_str(), 0, NULL);
if(status)
twist_grp_id = H5Gcreate(es_grp_id,tname.c_str(),0);
else
twist_grp_id = H5Gopen(es_grp_id,tname.c_str());
HDFAttribIO<PosType> hdfobj_twist(TwistAngle);
hdfobj_twist.write(twist_grp_id,"twist_angle");
ParticleSet::ParticleLayout_t& lattice(targetPtcl.Lattice);
RealType dx=1.0/static_cast<RealType>(nG[0]-1);
RealType dy=1.0/static_cast<RealType>(nG[1]-1);
RealType dz=1.0/static_cast<RealType>(nG[2]-1);
#if defined(VERYTINYMEMORY)
typedef Array<ValueType,3> StorageType;
StorageType inData(nG[0],nG[1],nG[2]);
int ib=0;
while(ib<myParam->numBands)
{
string bname(myParam->getBandName(ib));
status = H5Gget_objinfo (twist_grp_id, bname.c_str(), 0, NULL);
hid_t band_grp_id, spin_grp_id=-1;
if(status)
{
band_grp_id = H5Gcreate(twist_grp_id,bname.c_str(),0);
}
else
{
band_grp_id = H5Gopen(twist_grp_id,bname.c_str());
}
hid_t parent_id=band_grp_id;
if(myParam->hasSpin)
{
bname=myParam->getSpinName(spinIndex);
status = H5Gget_objinfo (band_grp_id, bname.c_str(), 0, NULL);
if(status)
{
spin_grp_id = H5Gcreate(band_grp_id,bname.c_str(),0);
}
else
{
spin_grp_id = H5Gopen(band_grp_id,bname.c_str());
}
parent_id=spin_grp_id;
}
for(int ig=0; ig<nG[0]; ig++)
{
RealType x=ig*dx;
for(int jg=0; jg<nG[1]; jg++)
{
RealType y=jg*dy;
for(int kg=0; kg<nG[2]; kg++)
{
inData(ig,jg,kg)= pwFunc.evaluate(ib,lattice.toCart(PosType(x,y,kg*dz)));
}
}
}
app_log() << " Add spline data " << ib << " h5path=" << tname << "/eigvector" << endl;
HDFAttribIO<StorageType> t(inData);
t.write(parent_id,myParam->eigvecTag.c_str());
if(spin_grp_id>=0) H5Gclose(spin_grp_id);
H5Gclose(band_grp_id);
++ib;
}
#else
typedef Array<ValueType,3> StorageType;
vector<StorageType*> inData;
int nb=myParam->numBands;
for(int ib=0; ib<nb; ib++)
inData.push_back(new StorageType(nG[0],nG[1],nG[2]));
PosType tAngle=targetPtcl.Lattice.k_cart(TwistAngle);
PWOrbitalSet::ValueVector_t phi(nb);
for(int ig=0; ig<nG[0]; ig++)
{
RealType x=ig*dx;
for(int jg=0; jg<nG[1]; jg++)
{
RealType y=jg*dy;
for(int kg=0; kg<nG[2]; kg++)
{
targetPtcl.R[0]=lattice.toCart(PosType(x,y,kg*dz));
pwFunc.evaluate(targetPtcl,0,phi);
RealType x(dot(targetPtcl.R[0],tAngle));
ValueType phase(std::cos(x),-std::sin(x));
for(int ib=0; ib<nb; ib++)
(*inData[ib])(ig,jg,kg)=phase*phi[ib];
}
}
}
for(int ib=0; ib<nb; ib++)
{
string bname(myParam->getBandName(ib));
status = H5Gget_objinfo (twist_grp_id, bname.c_str(), 0, NULL);
hid_t band_grp_id, spin_grp_id=-1;
if(status)
{
band_grp_id = H5Gcreate(twist_grp_id,bname.c_str(),0);
}
else
{
band_grp_id = H5Gopen(twist_grp_id,bname.c_str());
}
hid_t parent_id=band_grp_id;
if(myParam->hasSpin)
{
bname=myParam->getSpinName(spinIndex);
status = H5Gget_objinfo (band_grp_id, bname.c_str(), 0, NULL);
if(status)
{
spin_grp_id = H5Gcreate(band_grp_id,bname.c_str(),0);
}
else
{
spin_grp_id = H5Gopen(band_grp_id,bname.c_str());
}
parent_id=spin_grp_id;
}
app_log() << " Add spline data " << ib << " h5path=" << tname << "/eigvector" << endl;
HDFAttribIO<StorageType> t(*(inData[ib]));
t.write(parent_id,myParam->eigvecTag.c_str());
if(spin_grp_id>=0) H5Gclose(spin_grp_id);
H5Gclose(band_grp_id);
}
for(int ib=0; ib<nb; ib++) delete inData[ib];
#endif
H5Gclose(twist_grp_id);
H5Gclose(es_grp_id);
}
void TrainModelNN (_String* model, _String* matrix)
{
_String errMsg;
long modelIdx = modelNames.Find(model);
_Parameter verbI;
checkParameter (VerbosityLevelString, verbI, 0.0);
char buffer [128];
if (modelIdx < 0) {
errMsg = *model & " did not refer to an existring model";
} else {
_Variable* boundsMatrix = FetchVar (LocateVarByName (*matrix));
if (boundsMatrix && (boundsMatrix->ObjectClass() == MATRIX)) {
_Matrix * bmatrix = (_Matrix*) boundsMatrix->GetValue ();
if (bmatrix->IsAStringMatrix() && (bmatrix->GetVDim () == 3)) {
_Variable* modelMatrix = LocateVar (modelMatrixIndices.lData[modelIdx]);
_SimpleList modelVariableList;
{
_AVLList mvla (&modelVariableList);
modelMatrix->ScanForVariables (mvla, true);
mvla.ReorderList();
}
if (bmatrix->GetHDim () == modelVariableList.lLength) {
// now map model variables to bounds matrix
_SimpleList variableMap;
_String *myName;
for (long k = 0; k < modelVariableList.lLength; k++) {
myName = ((_FString*)bmatrix->GetFormula(k,0)->Compute())->theString;
long vID = LocateVarByName (*myName);
if (vID < 0) {
break;
}
vID = variableNames.GetXtra (vID);
vID = modelVariableList.Find(vID);
if (vID < 0) {
break;
}
variableMap << vID;
}
if (variableMap.lLength == modelVariableList.lLength) {
_Matrix vBounds (variableMap.lLength,2, false, true);
long k2 = 0;
for (; k2 < variableMap.lLength; k2++) {
_Parameter lb = ((_FString*)bmatrix->GetFormula(k2,1)->Compute())->theString->toNum(),
ub = ((_FString*)bmatrix->GetFormula(k2,2)->Compute())->theString->toNum();
if ( ub>lb || k2) {
vBounds.Store (k2,0,lb);
vBounds.Store (k2,1,ub);
if (ub<=lb && vBounds (k2-1,0) <= vBounds (k2-1,1) && (!CheckEqual(vBounds (k2-1,0),0.0) || !CheckEqual(vBounds (k2-1,1),1.0))) {
break;
}
}
}
if (k2 == modelVariableList.lLength) {
// set up the sampling now
_String fName = ProcessLiteralArgument (&ModelNNFile,nil);
FILE* nnFile = doFileOpen (fName.getStr(), "w");
if (nnFile) {
_Matrix* modelMatrix = (_Matrix*) LocateVar(modelMatrixIndices.lData[modelIdx])->GetValue();
_Parameter mainSteps,
checkSteps,
errorTerm,
loopMax,
hiddenNodes,
absError,
nn1,
nn2;
long fullDimension = modelMatrix->GetHDim() * modelMatrix->GetVDim();
checkParameter (ModelNNTrainingSteps, mainSteps, 10000.0);
checkParameter (ModelNNVerificationSample, checkSteps, 500.0);
checkParameter (ModelNNPrecision, errorTerm, 0.01);
checkParameter (ModelNNTrainingSteps, loopMax, 10);
checkParameter (ModelNNHiddenNodes, hiddenNodes, 5);
checkParameter (ModelNNLearningRate, nn1, .3);
checkParameter (ModelNNPersistenceRate, nn2, .1);
Net** matrixNet = new Net* [fullDimension] ;
for (long i = 0; i < fullDimension; i++) {
checkPointer (matrixNet [i] = new Net (variableMap.lLength,(long)hiddenNodes,1,errorTerm,nn1,nn2,100,200,true));
//matrixNet[i]->verbose = true;
}
checkPointer (matrixNet);
_List tIn,
tOut;
FILE* varSamples = doFileOpen ("variableSamples.out", "w");
fprintf (varSamples, "%s" ,LocateVar(modelVariableList.lData[0])->GetName()->getStr());
for (long vc = 1; vc < modelVariableList.lLength; vc++) {
fprintf (varSamples, ",%s" ,LocateVar(modelVariableList.lData[variableMap.lData[vc]])->GetName()->getStr());
}
fprintf (varSamples, "\n");
for (long itCount = 0; itCount < loopMax; itCount ++) {
if (verbI > 5) {
snprintf (buffer, sizeof(buffer), "\nNeural Network Pass %ld. Building a training set...\n", itCount);
BufferToConsole (buffer);
}
while (tIn.countitems() < mainSteps) {
NNMatrixSampler (0, vBounds, modelVariableList, variableMap, modelMatrix, tIn, tOut);
}
_Matrix inData (mainSteps, variableMap.lLength, false, true);
_Parameter *md = inData.theData;
for (long matrixC = 0; matrixC < mainSteps; matrixC++) {
_Parameter * ed = ((_Matrix*)tIn (matrixC))->theData;
fprintf (varSamples, "\n%g",*ed);
*md = *ed;
ed++;
md++;
for (long entryC = 1; entryC < variableMap.lLength; entryC++, ed++, md++) {
*md = *ed;
fprintf (varSamples, ",%g", *md);
}
}
tIn.Clear();
if (verbI > 5) {
BufferToConsole ( "Done Building Training Set. Training...\n");
}
long lastDone = 0;
for (long cellCount = 0; cellCount < fullDimension; cellCount++) {
Net* thisCell = matrixNet[cellCount];
_Matrix outVector (mainSteps, 1, false, true);
for (long oc = 0; oc < mainSteps; oc++) {
outVector.theData[oc] = ((_Matrix*)tOut(oc))->theData[cellCount];
}
thisCell->studyAll (inData.theData, outVector.theData, mainSteps);
long nowDone = (cellCount+1)*100./fullDimension;
if (nowDone > lastDone) {
snprintf (buffer, sizeof(buffer),"%ld%% done\n", lastDone = nowDone);
BufferToConsole (buffer);
}
}
tOut.Clear();
if (verbI > 5) {
BufferToConsole ( "Done Training. Resampling...\n");
}
_PMathObj tObj = _Constant(0).Time();
_Parameter time1 = tObj->Value(),
time2;
while (tIn.countitems() < checkSteps) {
NNMatrixSampler (0, vBounds, modelVariableList, variableMap, modelMatrix, tIn, tOut);
}
absError = 0.0;
DeleteObject (tObj);
tObj = _Constant(0).Time();
time2 = tObj->Value();
if (verbI > 5) {
snprintf (buffer, sizeof(buffer),"Done Resampling in %g seconds. Computing Error...\n", time2-time1);
BufferToConsole (buffer);
}
_Parameter maxValT,
maxValE;
for (long verCount = 0; verCount < checkSteps; verCount++) {
_Parameter* inData = ((_Matrix*)tIn(verCount))->theData,
* outData = ((_Matrix*)tOut(verCount))->theData;
for (long cellCount = 0; cellCount < fullDimension; cellCount++) {
Net *thisCell = matrixNet[cellCount];
_Parameter estVal = thisCell->eval(inData)[0],
trueVal = outData[cellCount],
localError;
localError = estVal-trueVal;
if (localError < 0) {
localError = -localError;
}
if (absError < localError) {
maxValT = trueVal;
maxValE = estVal;
absError = localError;
}
}
}
DeleteObject (tObj);
tObj = _Constant(0).Time();
time1 = tObj->Value();
DeleteObject (tObj);
if (verbI > 5) {
snprintf (buffer, sizeof(buffer), "Done Error Checking in %g seconds. Got max abs error %g on the pair %g %g\n", time1-time2, absError, maxValT, maxValE);
BufferToConsole (buffer);
}
if (absError <= errorTerm) {
break;
}
}
if (absError > errorTerm) {
ReportWarning (_String("Couldn't achive desired precision in TrainModelNN. Achieved error of ") & absError);
}
fclose (varSamples);
fprintf (nnFile,"{{\n\"%s\"", LocateVar(modelVariableList.lData[0])->GetName()->getStr());
_Matrix newBounds (modelVariableList.lLength, 2, false, true);
if (vBounds(0,0)>vBounds(0,1)) {
newBounds.Store (variableMap.lData[0],0,0.);
newBounds.Store (variableMap.lData[0],1,1.);
} else {
newBounds.Store (variableMap.lData[0],0,vBounds(0,0));
newBounds.Store (variableMap.lData[0],1,vBounds(0,1));
}
for (long varCounter = 1; varCounter < modelVariableList.lLength; varCounter ++) {
fprintf (nnFile,",\n\"%s\"", LocateVar(modelVariableList.lData[varCounter])->GetName()->getStr());
if (vBounds(varCounter,0)>vBounds(varCounter,1)) {
newBounds.Store (variableMap.lData[varCounter],0,0.);
newBounds.Store (variableMap.lData[varCounter],1,1.);
} else {
newBounds.Store (variableMap.lData[varCounter],0,vBounds(varCounter,0));
newBounds.Store (variableMap.lData[varCounter],1,vBounds(varCounter,1));
}
}
fprintf (nnFile,"\n}}\n");
newBounds.toFileStr (nnFile);
for (long i2 = 0; i2 < fullDimension; i2++) {
matrixNet[i2]->save(nnFile);
delete matrixNet [i2];
}
fclose (nnFile);
delete matrixNet;
} else {
errMsg = _String ("Failed to open ") & fName & " for writing";
}
} else {
errMsg = _String ("Invalid variable bounds in row ") & (k2+1) & " of the bounds matrix";
}
} else {
errMsg = *myName & " was not one of the model parameters";
}
} else {
errMsg = *matrix & " must be a have the same number of rows as the number of model parameters";
}
} else {
errMsg = *matrix & " must be a string matrix with 3 columns";
}
} else {
errMsg = *matrix & " was not the identifier of a valid matrix variable";
}
}
if (errMsg.sLength) {
errMsg = errMsg & _String(" in call to TrainModelNN.");
WarnError (errMsg);
}
}
void SteadyStateAlgo::runEvolution()
{
int startGeneration = 0;
char statfile[64];
char inFilename[128];
char outFilename[128];
char bestOutFilename[128];
int bestGeneration = -1;
float bestFitness = -1.0;
// Define the final mutation rate (i.e., the lower bound for the mutation rate)
const double finalMutRate = m_mutRate;
// Initialise the mutation rate
m_mutRate = m_initMutRate; // initially mutation (default 50%)
// Set the seed
setSeed(m_rngSeed);
// Initialise the population
randomisePopulation();
// Check whether to recover a previous evolution
sprintf(statfile, "S%d.fit", seed());
// Check if the file exists
DataChunk statTest(QString("stattest"), Qt::blue, 2000, false);
if (statTest.loadRawData(QString(statfile), 0))
{
startGeneration = statTest.getIndex();
sprintf(inFilename, "S%dG%d.gen", (seed()), startGeneration);
Logger::info("Recovering from startGeneration: " + QString::number(startGeneration));
Logger::info(QString("Loading file: ") + inFilename);
QFile inData(inFilename);
if (inData.open(QFile::ReadOnly))
{
QTextStream in(&inData);
for (int i = 0; i < m_popSize; i++)
{
bool loaded = m_population[i]->loadGen(in);
// Check possible errors during the loading operation
if (!loaded)
{
Logger::error("Error in the loading of the genotype");
}
// Check the consistency of the genotype (i.e., the number of genes)
if (m_population[i]->getLength() != m_numGenes)
{
Logger::error("Wrong genotype length!");
}
}
inData.close();
}
}
// Flow control
pauseFlow();
if (stopFlow())
{
// Cleanup
return;
}
// Do all generations
for (int gn = startGeneration; gn < m_numGenerations; gn++)
{
// Define a fitness array for all the individuals to be tested
QVector<float> fit(m_popSize * 2);
m_gae->setIndividualCounter();
m_gae->initGeneration(gn);
// Evaluate all the individuals
for (int i = 0; i < m_popSize; i++)
{
// Set the genotype to be tested
m_gt->setGenotype(m_population[i]);
// Evaluate the genotype
m_gae->evaluate();
// Get the fitness
fit[i] = m_gae->getFitness();
// Set the fitness of the current genotype
m_population[i]->setFitness(fit[i]);
// Use subclasses for modifying and/or getting elements (i.e., genes)
GenotypeInt* ind = dynamic_cast<GenotypeInt*>(m_population[i]);
GenotypeInt* off = dynamic_cast<GenotypeInt*>(m_population[i + m_popSize]);
// Now generate an offspring and evaluate it
for (int g = 0; g < m_numGenes; g++)
{
int val = ind->getGene(g);
// Mutate the value
int newVal = mutate(val, m_mutRate);
off->setGene(g, newVal);
}
m_gt->setGenotype(m_population[i + m_popSize]);
// Evaluate the genotype
m_gae->evaluate();
// Get the fitness
fit[i + m_popSize] = m_gae->getFitness();
// Flow control
pauseFlow();
if (stopFlow())
{
return;
}
}
m_gae->resetIndividualCounter();
// Select the best <popSize> individuals
QVector<int> indices = sortFit(fit);
// Define a temporary array for storing
// the best <popSize> individuals
QVector<float*> tmpPop(m_popSize);
// Define a temporary array for storing
// the fitnesses of the best individuals
QVector<float> tmpFit(m_popSize);
for (int i = 0; i < m_popSize; i++)
{
tmpPop[i] = new float[m_numGenes];
int idx = indices[i];
GenotypeInt* ind = dynamic_cast<GenotypeInt*>(m_population[idx]);
for (int g = 0; g < m_numGenes; g++)
{
tmpPop[i][g] = ind->getGene(g);
}
tmpFit[i] = fit[idx];
}
// Swap individuals
for (int i = 0; i < m_popSize; i++)
{
GenotypeInt* ind = dynamic_cast<GenotypeInt*>(m_population[i]);
for (int g = 0; g < m_numGenes; g++)
{
ind->setGene(g, tmpPop[i][g]);
ind->setFitness(tmpFit[i]);
}
}
// Flow control
pauseFlow();
if (stopFlow())
{
break;
}
// Save fitness statistics
char fitStatFilename[64];
sprintf(fitStatFilename, "S%d.fit", seed());
QFile fitStatData(fitStatFilename);
bool openOk = false;
if (gn == 0)
{
openOk = fitStatData.open(QIODevice::WriteOnly);
}
else
{
openOk = fitStatData.open(QIODevice::Append);
}
if (openOk)
{
QTextStream fitStat(&fitStatData);
// Compute maximum, minimum and average fitness and store them in a vector
QVector<float> fitArray(3);
// Max
float maxFit = fit[indices[0]];
fitArray[0] = maxFit;
// Average
float avgFit = 0.0;
for (int i = 0; i < m_popSize; i++)
{
avgFit += fit[indices[i]];
}
avgFit /= m_popSize;
fitArray[1] = avgFit;
// Min
float minFit = fit[indices[m_popSize - 1]];
fitArray[2] = minFit;
saveFitStats(fitArray, fitStat);
fitStatData.close();
}
// Save all fitness statistics if <saveFitnessAllIndividuals> flag is set to true
if (m_saveFitnessAllIndividuals)
{
char allFitStatFilename[64];
sprintf(allFitStatFilename, "S%dall.fit", seed());
QFile allFitStatData(allFitStatFilename);
openOk = false;
if (gn == 0)
{
openOk = allFitStatData.open(QIODevice::WriteOnly);
}
else
{
openOk = allFitStatData.open(QIODevice::Append);
}
if (openOk)
{
QTextStream allFitStat(&allFitStatData);
saveFitStats(fit, allFitStat);
allFitStatData.close();
}
}
// Save the best genotype
sprintf(bestOutFilename, "S%dB%d.gen", seed(), 0);
QFile bestOutData(bestOutFilename);
bool operation = false;
if (gn == 0)
{
// Open the QFile in write mode
operation = bestOutData.open(QIODevice::WriteOnly);
}
else
{
// Open the QFile in append mode
operation = bestOutData.open(QFile::Append);
}
if (operation)
{
QTextStream bestOut(&bestOutData);
GenotypeInt* ind = dynamic_cast<GenotypeInt*>(m_population[0]);
ind->saveGen(bestOut);
bestOutData.close();
}
// Save all the genotypes
sprintf(outFilename, "S%dG%d.gen", seed(), (gn + 1));
QFile outData(outFilename);
if (outData.open(QIODevice::WriteOnly))
{
QTextStream out(&outData);
// Save the population
for (int i = 0; i < m_popSize; i++)
{
GenotypeInt* ind = dynamic_cast<GenotypeInt*>(m_population[i]);
ind->saveGen(out);
}
outData.close();
}
// Decrease the mutation rate (until it becomes equal to the lower bound)
if (m_mutRate > finalMutRate)
{
m_mutRate -= m_mutDecay;
}
else
{
m_mutRate = finalMutRate;
}
// Check the best generation
if (fit[indices[0]] > bestFitness)
{
bestFitness = fit[indices[0]];
bestGeneration = gn;
}
m_gae->endGeneration(gn);
}
// Save the information about the best generation
char bestGenFileName[64];
sprintf(bestGenFileName, "S%dbest.fit", seed());
QFile bestGenData(bestGenFileName);
// Open the QFile in write mode
if (bestGenData.open(QIODevice::WriteOnly))
{
QTextStream bestGenOut(&bestGenData);
QString outStr;
//! Write the best generation index
outStr = QString::number(bestGeneration);
bestGenOut << outStr;
//! Write the fitness of the best generation
outStr = QString::number(bestFitness);
bestGenOut << " " << outStr;
bestGenOut << endl;
bestGenData.close();
}
}
