void runDelphi(shared_ptr<SPrime> param)
{
#ifdef DELPHI_OUTPUT
string delphi_ntime = "delphi_run_" + to_string(param->ntimes) + ".log";
#endif
#ifndef DELPHI_OUTPUT
string delphi_ntime = "delphi_run_" + to_string(param->ntimes) + ".log";
#endif
ofstream logFile(delphi_ntime);
StreamRedirector redirect_cout(cout,logFile.rdbuf());
StreamRedirector redirect_cerr(cerr,logFile.rdbuf());
cout << boolalpha;
cerr << boolalpha;
try
{
CTimer * pTester = new CTimer; // record execution time
pTester->start();
shared_ptr<CTimer> pTimer( new CTimer); // record execution time
shared_ptr<IDataContainer> pDataContainer( new CDelphiData(param,pTimer) );
// pDataContainer->showMap("showmap_atbegin.dat");
int& inhomo(pDataContainer->getKey_Ref<int>("inhomo"));
const int& iGaussian(pDataContainer->getKey_constRef<int>("gaussian"));
bool& logs (pDataContainer->getKey_Ref<bool>("logs"));
bool& logg (pDataContainer->getKey_Ref<bool>("logg"));
inhomo=0;
if( iGaussian==1 && logs )
{
logg=true; //for gaussian
inhomo=1;
}
//********************************************************************************//
// //
// realize an object of CDelphiSpace class to construct molecular surfaces //
// //
//********************************************************************************//
unique_ptr<IAbstractModule> pSpace( new CDelphiSpace(pDataContainer,pTimer) );
pSpace->run();
pSpace.reset();
// pDataContainer->showMap("showmap_aftersuf.dat");
if( !(iGaussian==1&&inhomo==0&&logs) )
{
cout << " number of atom coordinates read :" << right << setw(10) << pDataContainer->getKey_constRef<delphi_integer>("natom") << endl;
}
if (pDataContainer->getKey_constRef<bool>("isolv"))
{
if( !(iGaussian==1&&inhomo==0&&logs) )
{
cout << " total number of assigned charges :" << right << setw(10) << pDataContainer->getKey_constRef<delphi_integer>("nqass") << endl;
cout << " net assigned charge :" << right << setw(10) << pDataContainer->getKey_constRef<delphi_real>("qnet") << endl;
cout << " assigned positive charge :" << right << setw(10) << pDataContainer->getKey_constRef<delphi_real>("qplus") << endl;
cout << " centred at (gu) :" << right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqplus").nX << " "
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqplus").nY << " "
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqplus").nZ << endl;
cout << " assigned negative charge :" << right << setw(10) << pDataContainer->getKey_constRef<delphi_real>("qmin") << endl;
cout << " centred at (gu) :" << right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqmin").nX << " "
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqmin").nY << " "
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<delphi_real> >("cqmin").nZ << endl;
cout << "\nnumber of dielectric boundary points" << right << setw(10) << pDataContainer->getKey_constRef<delphi_integer>("ibnum") << endl;
}
if (pDataContainer->getKey_constRef<bool>("iexun") && 0 == pDataContainer->getKey_constRef<delphi_integer>("ibnum"))
throw CNoBndyAndDielec(pTimer);
//********************************************************************************//
// //
// realize an object of CDelphiFastSOR class to calculate potentials on grids //
// //
//********************************************************************************//
unique_ptr<CDelphiFastSOR> pSolver( new CDelphiFastSOR(pDataContainer,pTimer) );
if (param->bndcon == 3) {
pSolver->getPRIME(param);
}
pSolver->run();
pSolver.reset();
// pDataContainer->showMap("showmap_afteritr.dat");
//********************************************************************************//
// //
// realize an object of CDelphiEnergy class to calculate energies //
// //
//********************************************************************************//
unique_ptr<IAbstractModule> pEnergy( new CDelphiEnergy(pDataContainer,pTimer) );
pEnergy->run();
pEnergy.reset();
// pDataContainer->showMap("showmap_aftereng.dat");
if(iGaussian==1&&inhomo==1&&logs) //second run for Gaussian
{
inhomo=0;
unique_ptr<IAbstractModule> pSpace( new CDelphiSpace(pDataContainer,pTimer) );
pSpace->run();
pSpace.reset();
unique_ptr<IAbstractModule> pSolver( new CDelphiFastSOR(pDataContainer,pTimer) );
pSolver->run();
pSolver.reset();
unique_ptr<IAbstractModule> pEnergy( new CDelphiEnergy(pDataContainer,pTimer) );
pEnergy->run();
pEnergy.reset();
}
//********************************************************************************//
// //
// realize an object of CSite class to write site info //
// //
//********************************************************************************//
unique_ptr<CSite> pSite( new CSite(pDataContainer,pTimer) );
if (pDataContainer->getKey_constRef<bool>("isite"))
{
int iisitsf = 0;
if (pDataContainer->getKey_Ref<bool>("isitsf")) iisitsf = 1;
pSite->writeSite(iisitsf);
}
if (pDataContainer->getKey_constRef<bool>("phiwrt")) pSite->writePhi();
// pDataContainer->showMap("showmap_aftersite.dat");
/*
* equivalent to out(frc,file="filename") in the parameter file
if (0 == pSite->prime_grdphiv.size())
{
pSite.reset();
pTimer->exit(); pTimer.reset();
}
*/
param->strAtomDes = pSite->prime_atomdes;
param->vecGridPot = pSite->prime_grdphiv;
param->vecSiteCrg = pSite->prime_crhgv;
#ifdef PRIME
pSite->clearIO();
#endif
pSite.reset();
}
//********************************************************************************//
// //
// retrieve the solvation energy and grid energy from data container //
// //
//********************************************************************************//
param->ergs = pDataContainer->getKey_Val<delphi_real>("ergs");
param->ergg = pDataContainer->getKey_Val<delphi_real>("ergg");
if(pDataContainer->getKey_constRef<int>("ibctyp") == 2)
{
param->igrid1 = pDataContainer->getKey_constRef<delphi_integer>("igrid");
param->scale1 = pDataContainer->getKey_constRef<delphi_real>("scale");
param->oldmid1 = pDataContainer->getKey_constRef<SGrid<delphi_real> >("oldmid");
param->phimap = pDataContainer->getKey_constRef<vector<delphi_real> >("phimap");
// pDataContainer->showMap("test_phimap");
}
pDataContainer.reset();
pTimer->exit(); pTimer.reset();
delete pTester;
#ifdef DELPHI_OUTPUT
param->ntimes++;
#endif
remove(&delphi_ntime[0]);
} // ---------- end of try block
catch (CException&)
{
cerr << "\n\n ......... PROGRAM ABORTS WITH AN EXCEPTION AND " << CWarning::iWarningNum << " WARNING(S) ........\n\n";
}
cout << "\n\n ......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL " << CWarning::iWarningNum << " WARNING(S) ........\n\n";
cout.unsetf(ios_base::floatfield); // return to cout default notation
}
/**
* single delphi run, the same as app_delphi.cpp
*/
bool runDelphi(SMCCE * mcce_data)
{
/*
* bool values are inserted/extracted by their textual representation: either true or false, instead of integral values.
* This flag can be unset with the noboolalpha manipulator.
*/
cout << boolalpha;
cerr << boolalpha;
#ifdef DEVELOPER
cout << fixed << setprecision(7); //cout.precision(15)
#else
cout << fixed << setprecision(3); //cout.precision(7)
#endif
shared_ptr<CTimer> pTimer(new CTimer); // record execution time
//---------- a shared_ptr to an object of CDelphiData
shared_ptr<IDataContainer> pDataContainer( new CDelphiData(mcce_data,pTimer) );
pDataContainer->showMap("test_delphicpp_atbeginning.dat");
try
{
//********************************************************************************//
// //
// realize an object of CDelphiSpace class to construct molecular surfaces //
// //
//********************************************************************************//
unique_ptr<IAbstractModule> pSpace( new CDelphiSpace(pDataContainer,pTimer) );
pSpace->run();
pSpace.reset(); // !!! need to be changed to pSpace.reset();
//---------- print out results after constructing molecular surfaces
cout << endl;
cout << " number of atom coordinates read :" << right << setw(10) << pDataContainer->getKey_constRef<integer>("natom") << endl;
if (pDataContainer->getKey_constRef<bool>("isolv"))
{
cout << " total number of assigned charges :" << right << setw(10) << pDataContainer->getKey_constRef<integer>("nqass") << endl;
cout << " net assigned charge :" << right << setw(10) << pDataContainer->getKey_constRef<real>("qnet") << endl;
cout << " assigned positive charge :" << right << setw(10) << pDataContainer->getKey_constRef<real>("qplus") << endl;
cout << " centred at (gu) :" << right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqplus").nX
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqplus").nY
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqplus").nZ << endl;
cout << " assigned negative charge :" << right << setw(10) << pDataContainer->getKey_constRef<real>("qmin") << endl;
cout << " centred at (gu) :" << right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqmin").nX
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqmin").nY
<< right << setw(10) << pDataContainer->getKey_constRef< SGrid<real> >("cqmin").nZ << endl;
cout << "\nnumber of dielectric boundary points" << right << setw(10) << pDataContainer->getKey_constRef<integer>("ibnum") << endl;
if (pDataContainer->getKey_constRef<bool>("iexun") && 0 == pDataContainer->getKey_constRef<integer>("ibnum"))
throw CNoBndyAndDielec(pTimer);
//********************************************************************************//
// //
// realize an object of CDelphiFastSOR class to calculate potentials on grids //
// //
//********************************************************************************//
unique_ptr<CDelphiFastSOR> pSolver( new CDelphiFastSOR(pDataContainer,pTimer) );
if (3 == mcce_data->bndcon) pSolver->getMCCE(mcce_data);
pSolver->run();
pSolver.reset();
//********************************************************************************//
// //
// realize an object of CDelphiEnergy class to calculate energys //
// //
//********************************************************************************//
unique_ptr<IAbstractModule> pEnergy( new CDelphiEnergy(pDataContainer,pTimer) );
pEnergy->run();
pEnergy.reset();
//********************************************************************************//
// //
// realize an object of CSite class to write site info //
// //
//********************************************************************************//
unique_ptr<CSite> pSite( new CSite(pDataContainer,pTimer) );
if (pDataContainer->getKey_constRef<bool>("isite"))
{
int iisitsf = 0;
if (pDataContainer->getKey_Ref<bool>("isitsf")) iisitsf = 1;
pSite->writeSite(iisitsf);
}
if (pDataContainer->getKey_constRef<bool>("phiwrt")) pSite->writePhi();
/*
* equivalent to out(frc,file="filename") in the parameter file
*/
if (0 == pSite->mcce_phiv.size())
{
pSite.reset();
pTimer->exit(); pTimer.reset();
return false;
}
mcce_data->phiv = pSite->mcce_phiv;
pSite.reset();
/*
* equivalent to out(phi,file="filename") in the parameter file
*/
mcce_data->phimap = pDataContainer->getKey_Val< vector<real> >("phimap");
mcce_data->scale1 = pDataContainer->getKey_Val<real>("scale");
mcce_data->oldmid1 = pDataContainer->getKey_Val< SGrid<real> >("oldmid");
mcce_data->igrid1 = pDataContainer->getKey_Val<integer>("igrid");
/*
* equivalent to energy(s) in the parameter file
*/
mcce_data->ergs = pDataContainer->getKey_Val<real>("ergs");
}
pDataContainer.reset();
pTimer->exit(); pTimer.reset();
}
catch (CException&)
{
cerr << "\n\n ......... PROGRAM ABORTS WITH AN EXCEPTION AND " << CWarning::iWarningNum << " WARNING(S) ........\n\n";
return false;
}
cout << "\n\n ......... PROGRAM EXITS SUCCESSFULLY : WITH TOTAL " << CWarning::iWarningNum << " WARNING(S) ........\n\n";
cout.unsetf(ios_base::floatfield); // return to cout default notation
return true;
}