Disposable<Array> FdmExtOUJumpOp::integro(const Array& r) const {
Array integral(r.size());
const boost::shared_ptr<FdmLinearOpLayout> layout = mesher_->layout();
const Size extraDims=layout->size()/(layout->dim()[0]*layout->dim()[1]);
std::vector<Array> y(extraDims, Array(layout->dim()[1]));
std::vector<Matrix> f(extraDims,
Matrix(layout->dim()[1], layout->dim()[0]));
const FdmLinearOpIterator endIter = layout->end();
for (FdmLinearOpIterator iter = layout->begin(); iter != endIter;
++iter) {
const Size i = iter.coordinates()[0];
const Size j = iter.coordinates()[1];
const Size k = iter.index() / (layout->dim()[0]*layout->dim()[1]);
y[k][j] = mesher_->location(iter, 1);
f[k][j][i] = r[iter.index()];
}
std::vector<std::vector<boost::shared_ptr<LinearInterpolation> > >
interpl(extraDims, std::vector<
boost::shared_ptr<LinearInterpolation> >(f[0].columns()));
for (Size k=0; k < extraDims; ++k) {
for (Size i=0; i < f[k].columns(); ++i) {
interpl[k][i] = boost::shared_ptr<LinearInterpolation>(
new LinearInterpolation(y[k].begin(), y[k].end(),
f[k].column_begin(i)));
}
}
const Real eta = process_->eta();
for (FdmLinearOpIterator iter=layout->begin(); iter!=endIter; ++iter) {
const Size i = iter.coordinates()[0];
const Size j = iter.coordinates()[1];
const Size k = iter.index() / (layout->dim()[0]*layout->dim()[1]);
integral[iter.index()] = gaussLaguerreIntegration_(
IntegroIntegrand(interpl[k][i], bcSet_, y[k][j], eta));
}
return process_->jumpIntensity()*(integral-r);
}
Disposable<Array> FdmBatesOp::integro(const Array& r) const {
const shared_ptr<FdmLinearOpLayout> layout = mesher_->layout();
QL_REQUIRE(layout->dim().size() == 2, "invalid layout dimension");
Array x(layout->dim()[0]);
Matrix f(layout->dim()[1], layout->dim()[0]);
const FdmLinearOpIterator endIter = layout->end();
for (FdmLinearOpIterator iter = layout->begin(); iter != endIter;
++iter) {
const Size i = iter.coordinates()[0];
const Size j = iter.coordinates()[1];
x[i] = mesher_->location(iter, 0);
f[j][i] = r[iter.index()];
}
std::vector<shared_ptr<LinearInterpolation> > interpl(f.rows());
for (Size i=0; i < f.rows(); ++i) {
interpl[i] = shared_ptr<LinearInterpolation>(
new LinearInterpolation(x.begin(), x.end(), f.row_begin(i)));
}
Array integral(r.size());
for (FdmLinearOpIterator iter=layout->begin(); iter!=endIter; ++iter) {
const Size i = iter.coordinates()[0];
const Size j = iter.coordinates()[1];
integral[iter.index()] = M_1_SQRTPI*
gaussHermiteIntegration_(
IntegroIntegrand(interpl[j], bcSet_, x[i], delta_, nu_));
}
return lambda_*(integral-r);
}
bool CDelphiFastSOR::isFocusBndy(delphi_real *** phimap)
{
char toblbl[20],label[10],title[60],botlbl[16];
delphi_real fScale1,goff,gmid,goff1;
SGrid<delphi_real> fgBoxCenter1,fgXYZ,fcXYZ,fgTemp;
delphi_integer iGrid1,isgrid;
int i,ix,iy,iz,iout,flag_s,flag_f;//flag_s: start; flag_f: finish.
delphi_real *** phimap_pre;
string strLine,strSubLine;
SGrid<delphi_real> oldmid_1;
#if !defined(MCCE) && !defined(PRIME)
if(debug_solver)cout << "#### in isFocusBndy: phiintype: " << phiintype << endl;
if(phiintype==0)
{
ifstream ifPhiiFileStream;
ifPhiiFileStream.open(strPhiiFile.c_str());
if (!ifPhiiFileStream.is_open())
{
throw CUnknownPhiiFile(strPhiiFile);
return false;
}
cout << "\n";
cout << "focussing boundary condition\n";
cout << "read from file\n";
cout << strPhiiFile << endl << endl;
ifPhiiFileStream.read(toblbl,21);
ifPhiiFileStream.read(label ,10);
ifPhiiFileStream.read(title ,54);
//cout << "###title: " << title << endl;
for (iz = 0; iz < iGrid; iz++)
{
for (iy = 0; iy < iGrid; iy++)
{
for (ix = 0; ix < iGrid; ix++)
{
ifPhiiFileStream.read(reinterpret_cast<char*>(&phimap[iz][iy][ix]),sizeof(delphi_real));
//cout << "iz,iy,iz,phi: " << iz << iy << ix << phimap[iz][iy][ix] << endl;
}
}
}
ifPhiiFileStream.read(botlbl,16);
ifPhiiFileStream.read(reinterpret_cast<char*>(&fScale1),sizeof(fScale1));
ifPhiiFileStream.read(reinterpret_cast<char*>(&fgBoxCenter1),sizeof(fgBoxCenter1));
ifPhiiFileStream.read(reinterpret_cast<char*>(&iGrid1),sizeof(iGrid1));
ifPhiiFileStream.close();
}
else if(phiintype==1) // cube format
{
ifstream ifPhiiFileStream;
ifPhiiFileStream.open(strPhiiFile.c_str());
if (!ifPhiiFileStream.is_open())
{
throw CUnknownPhiiFile(strPhiiFile);
return false;
}
cout << "\n";
cout << "focussing boundary condition\n";
cout << "read from file\n";
cout << strPhiiFile << endl << endl;
getline(ifPhiiFileStream,strLine);
//cout << strLine << endl;
strSubLine = strLine.substr(0,9);
//cout << strSubLine << endl;
//exit(0);
fScale1 = atof( strSubLine.c_str() );
strSubLine = strLine.substr(10,15);
iGrid1=atoi( strSubLine.c_str() );
strSubLine = strLine.substr(16,25);
oldmid_1.nX = atof( strSubLine.c_str() );
strSubLine = strLine.substr(26,35);
oldmid_1.nY = atof( strSubLine.c_str() );
strSubLine = strLine.substr(36,45);
oldmid_1.nZ = atof( strSubLine.c_str() );
fgBoxCenter1=oldmid_1;
cout << fScale1 << " " << iGrid1 << " " << oldmid_1.nX << " " << oldmid_1.nY << " " << oldmid_1.nZ<< endl;
cout << fScale << " " << iGrid << " " << fgBoxCenter.nX << " " << fgBoxCenter.nY << " " << fgBoxCenter.nZ<< endl;
//--------- allocate memory for previous phimap -------
phimap_pre_v.assign(iGrid1*iGrid1*iGrid1,0.0);
phimap_pre = pdc->getKey_Ptr<delphi_real>("phimap_pre",iGrid1,iGrid1,iGrid1); // pointer to 3D phimap
for(i=1; i<=6; i++)
{
getline(ifPhiiFileStream,strLine);
cout << strLine << endl;
}
flag_s=0;
for (iz = 0; iz < iGrid1; iz++)
{
for (iy = 0; iy < iGrid1; iy++)
{
flag_s=0;
while (flag_s<iGrid1)
{
getline(ifPhiiFileStream,strLine);
if(ifPhiiFileStream.eof()) break;
if(flag_s+5 > iGrid1-1)
{
flag_f=iGrid1-1;
}
else
{
flag_f=flag_s+5;
}
i=0;//for ith number in a line
for(ix=flag_s; ix<=flag_f; ix++)
{
strSubLine = strLine.substr(13*i,13);
i++; //for ith number in a line
//cout << "strSubLine: " << strSubLine << endl;
//phimap_pre_v[iz*iGrid1*iGrid1+iy*iGrid1+ix] = atof( strSubLine.c_str() );
phimap_pre[iz][iy][ix] = atof( strSubLine.c_str() );
//cout << phimap_pre_v[iz*iGrid1*iGrid1+iy*iGrid1+ix] << " ";
}
flag_s=flag_s+6;
//cout << endl;
}
}
}
ifPhiiFileStream.close();
}
else
{
cout << "Focusing is not CUBE or PHI" << endl;
exit(0);
}
#endif
#ifdef MCCE
phimap_pre_v = pmcce->phimap;
fScale1 = pmcce->scale1;
fgBoxCenter1 = pmcce->oldmid1;
iGrid1 = pmcce->igrid1;
phimap_pre = pdc->getKey_Ptr<delphi_real>("phimap_pre",iGrid1,iGrid1,iGrid1);
#endif
#ifdef PRIME
phimap_pre_v = pPrime->phimap;
fScale1 = pPrime->scale1;
fgBoxCenter1 = pPrime->oldmid1;
iGrid1 = pPrime->igrid1;
phimap_pre = pdc->getKey_Ptr<delphi_real>("phimap_pre",iGrid1,iGrid1,iGrid1);
#endif
if (fZero > abs(fScale1-fScale))
{
cout << "scales are the same.\n";
cout << "therefore assuming this to be a continuence\n";
}
else
{
cout << "\n";
cout << " focussing potential map:\n";
if (debug_solver) cout << title << endl;
cout << "original scale (grids/A) : " << fScale1 << endl;
cout << "object centre at (A) : " << fgBoxCenter1.nX << " "
<< fgBoxCenter1.nY << " " << fgBoxCenter1.nZ << endl;
//----- check to see that new grid lies within old one that is going to provide bc's
iout = 0;
goff = (iGrid+1.0)/2.0;
goff1 = (iGrid1+1.0)/2.0;
for (iz = 0; iz < iGrid; iz += iGrid-1)
{
for (iy = 0; iy < iGrid; iy += iGrid-1)
{
for (ix = 0; ix < iGrid; ix += iGrid-1)
{
fgXYZ.nX = (delphi_real)(ix+1);
fgXYZ.nY = (delphi_real)(iy+1);
fgXYZ.nZ = (delphi_real)(iz+1);
//for each new grid corner, calculate old grid coords
fcXYZ = (fgXYZ-goff)/fScale+fgBoxCenter;
fgTemp = (fcXYZ-fgBoxCenter1)*fScale1+goff1;
if (optORLE<delphi_real>(fgTemp,1.0) || optORGE<delphi_real>(fgTemp,(delphi_real)iGrid1)) iout = 1;
}
}
}
if (0 != iout) throw COutsideFocus(fScale1,fgBoxCenter1,fScale,fgBoxCenter);
/*
* for each boundary point
* convert to delphi_real coordinates
* convert to old grid coordinates
* interpolate potential
* note that can use same potential array for boundaries since old potentials at boundary are not used for new ones
*/
//----- save new grid size, and set temporarily to 65
isgrid = iGrid;
iGrid = iGrid1;
gmid = (isgrid+1.0)/2.0;
cout << "pulling boundary values out of old potential map...\n";
// cout << "phimap_pre[0]: " << phimap_pre[0][0][0] << endl;
// cout << "phimap_pre[1][1][2]: " << phimap_pre[0][0][1] << endl;
for (iz = 0; iz < isgrid; iz++)
{
for (iy = 0; iy < isgrid; iy++)
{
for (ix = 0; ix < isgrid; ix += isgrid-1)
{
fgXYZ.nX = (delphi_real)(ix+1);
fgXYZ.nY = (delphi_real)(iy+1);
fgXYZ.nZ = (delphi_real)(iz+1);
fcXYZ = (fgXYZ-gmid)/fScale+fgBoxCenter;
fgTemp = (fcXYZ-fgBoxCenter1)*fScale1+goff1;
//for each new grid side, calculate old grid coords find potential
//phimap[iz][iy][ix] = interpl(iGrid,phimap_pre,fgTemp);
phimap[ix][iy][iz] = interpl(iGrid,phimap_pre,fgTemp);
}
}
}
for (iz = 0; iz < isgrid; iz++)
{
for (iy = 0; iy < isgrid; iy += isgrid-1)
{
for (ix = 0; ix < isgrid; ix++)
{
fgXYZ.nX = (delphi_real)(ix+1);
fgXYZ.nY = (delphi_real)(iy+1);
fgXYZ.nZ = (delphi_real)(iz+1);
fcXYZ = (fgXYZ-gmid)/fScale+fgBoxCenter;
fgTemp = (fcXYZ-fgBoxCenter1)*fScale1+goff1;
//for each new grid side, calculate old grid coords find potential
//phimap[iz][iy][ix] = interpl(iGrid,phimap_pre,fgTemp);
phimap[ix][iy][iz] = interpl(iGrid,phimap_pre,fgTemp);
}
}
}
for (iz = 0; iz < isgrid; iz += isgrid-1)
{
for (iy = 0; iy < isgrid; iy++)
{
for (ix = 0; ix < isgrid; ix++)
{
fgXYZ.nX = (delphi_real)(ix+1);
fgXYZ.nY = (delphi_real)(iy+1);
fgXYZ.nZ = (delphi_real)(iz+1);
fcXYZ = (fgXYZ-gmid)/fScale+fgBoxCenter;
fgTemp = (fcXYZ-fgBoxCenter1)*fScale1+goff1;
//for each new grid side, calculate old grid coords find potential
//phimap[iz][iy][ix] = interpl(iGrid,phimap_pre,fgTemp);
phimap[ix][iy][iz] = interpl(iGrid,phimap_pre,fgTemp);
}
}
}
iGrid = isgrid;
}
if (debug_solver)
{
cout << "phimap[0][0][0]: " << phimap[0][0][0]<< endl;
cout << "phimap[1][1][1]: " << phimap[1][1][1]<< endl;
cout << "phimap[1][1][0]: " << phimap[1][1][0]<< endl;
cout << "phimap[1][0][0]: " << phimap[1][0][0]<< endl;
cout << "iGrid: " << iGrid << endl;
cout << "phimap[iGrid-1][iGrid-1][iGrid-1]: " << phimap[iGrid-1][iGrid-1][iGrid-1]<< endl;
cout << "phimap[1][1][1]: " << phimap[1][1][1]<< endl;
cout << "phimap[1][1][iGrid-1]: " << phimap[1][1][iGrid-1]<< endl;
cout << "phimap[1][iGrid-1][iGrid-1]: " << phimap[1][iGrid-1][iGrid-1]<< endl;
}
/** remove phimap_pre pointers*/
for(int i = 0; i != iGrid1; ++i)
{
delete[] phimap_pre[i];
}
delete[] phimap_pre;
//exit(0);
return true;
}
void CSite::writeSite(const int& iisitsf)
{
//---------------------------------------------------------------------------------------------//
bool isita = bAtomInSite, isiti = bSaltInSite, isitmd = bMDInSite, isitpot = bPotentialInSite,
isitx = bAtomCoordInSite, isitq = bCrgInSite, isitf = bFieldInSite, isitp = bGridPotentialInSite,
isitr = bReactPotentialInSite, isitc = bCoulombPotentialInSite, isitap = bAtomPotentialInSite, isitdeb = bDebyeFractionInSite,
isitsf = bSurfCrgInSite, isittf = bTotalForceInSite, isitrf = bReactForceInSite, isitt = bTotalPotentialInSite,
isitcf = bCoulombForceInSite, iself = bPDB2FRCInSite;
//----- ifrm is true if ANY of the flags for special output have been set
bool ifrm = isita || isitq || isitp || isitf || isitr || isitt || isitc || isitx || isiti || isitrf || isitcf || isitap ||
isittf || isitdeb;
bool isitmp1 = ifrm; ifrm = ifrm || isitsf;
bool ofrm = true;
if (isitmd || isitpot) {iFrcFormatOut = -1; ofrm = false;}
if (!ifrm && (0 == iFrcFormatOut || 3 == iFrcFormatOut))
{
isitx = true; isitq = true; isitf = true; isitp = true;
}
switch (iFrcFormatOut)
{
case 1: isitx = true; isitq = true; isitr = true; isitc = true; break;
case 2: isitx = true; isitq = true; isitr = true; break;
case 3: ofrm = false; break;
}
string vrow(80,' '),datum(65,' '); int j = 0, k = 0;
if (isita)
{
vrow.replace(j,15,"ATOM DESCRIPTOR"); datum.replace(k,5,"ATOM ");
j += 20; k += 5;
}
if (isitx)
{
vrow.replace(j+4,24,"ATOM COORDINATES (X,Y,Z)"); datum.replace(k,12,"COORDINATES ");
j += 30; k += 12;
}
if (isitq)
{
vrow.replace(j+3,6,"CHARGE"); datum.replace(k,7,"CHARGE ");
j += 10; k += 7;
}
if (isitp)
{
vrow.replace(j+2,8,"GRID PT."); datum.replace(k,11,"POTENTIALS ");
j += 10; k += 11;
}
if (isiti)
{
vrow.replace(j+1,8,"SALT CON"); datum.replace(k,5,"SALT ");
j += 10; k += 5;
}
if (80 <= j)
{
isitr = false; isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitr)
{
vrow.replace(j,10," REAC. PT."); datum.replace(k,9,"REACTION ");
j += 10; k += 9;
}
if (80 <= j)
{
isitc = false; isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitc)
{
vrow.replace(j,10," COUL. POT"); datum.replace(k,10,"COULOMBIC ");
j += 10; k += 10;
}
if (80 <= j)
{
isitap = false; isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitap)
{
vrow.replace(j+2,8,"ATOM PT."); datum.replace(k,11,"ATOMIC PT. ");
j += 10; k += 11;
}
if (80 <= j)
{
isitdeb = false; isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitdeb)
{
vrow.replace(j+3,11,"DEBFRACTION"); datum.replace(k,12,"DEBFRACTION ");
j += 14; k += 12;
}
if (60 <= j)
{
isitf = false;
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitf)
{
vrow.replace(j+4,25,"GRID FIELDS: (Ex, Ey, Ez)"); datum.replace(k,7,"FIELDS ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitrf = false; isitcf = false; isitt = false;
}
if (isitrf)
{
vrow.replace(j+4,25,"REAC. FORCE: (Rx, Ry, Rz)"); datum.replace(k,7,"RFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitcf = false; isitt = false;
}
if (isitcf)
{
vrow.replace(j+4,25,"COUL. FORCE: (Cx, Cy, Cz)"); datum.replace(k,7,"CFORCE ");
j += 30;
}
if (60 <= j)
{
isitsf = false; isittf = false; isitt = false;
}
if (isittf)
{
vrow.replace(j+4,25,"TOTAL FORCE: (Tx, Ty, Tz)"); datum.replace(k,7,"TFORCE ");
j += 30;
}
if (70 <= j)
{
isitt = false;
}
if (isitt)
{
vrow.replace(j+4,6," TOTAL"); datum.replace(k,6,"TOTAL ");
j += 10;
}
if (50 <= j) isitsf = false;
if (isitsf)
{
vrow.replace(j+4,65,"sCharge, x y z urf.E°n,surf. E[kT/(qA)]");
datum.replace(k,35,"SCh, x, y, z, surf En, surf. E");
j += 50;
}
//---------------------------------------------------------------------------------------------//
/*
* if site potentials required and unformatted read/write, skip during formatted frc file read/write can write unformatted frc.pdb
*/
bool ifrm2 = false, iqass = true;
ifstream ifFileStream;
vector<bool> residsf(iResidueNum,false);
if (!(isitmd || isitpot)) cout << "\nwriting potentials at given sites...\n";
if (iself)
{
cout << "using the current pdb file\n";
ifrm2 = true; iqass = false;
}
else
{
if (!isitpot)
{
ifFileStream.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
ifFileStream.close();
return;
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
ifrm2 = checkFileFormat(strFrciFile);
}
ifFileStream.close();
}
}
//----- if unformatted may not contain all the info needed for all options, i.e atom info
if (!ifrm2 && isita)
{
CNoAtomInfo warning(strFrciFile);
isita = false; iqass = false;
}
if (!ifrm2) iqass = false;
if (!iself && !isitpot)
{
if (ifrm2) ifFileStream.open(strFrciFile.c_str());
else ifFileStream.open(strFrciFile.c_str(),ios::binary);
if (!ifFileStream.is_open()) CUnknownInFrcFile warning(strFrciFile);
}
if (isitsf) //----- isitsf assumes ifrm2=.true.
{
ifstream ifFileStream15;
string strLine,strHead;
int iresnum;
ifFileStream15.open(strFrciFile.c_str()); // just inquire whether the file exists or not
if (!ifFileStream15.is_open())
{
CUnknownInFrcFile warning(strFrciFile);
}
else
{
cout << "coordinates, etc for potential output read from file " << strFrciFile << endl;
while (!ifFileStream15.eof()) // loop D302
{
getline(ifFileStream15,strLine);
strHead = strLine.substr(0,6);
if (0 != strHead.compare(" ")) strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
iresnum = atoi(strLine.substr(23,4).c_str());
residsf[iresnum-1] = true;
}
}
ifFileStream15.close();
}
//---------------------------------------------------------------------------------------------//
ofstream ofFileStream;
if (ofrm) ofFileStream.open(strFrcFile.c_str());
if(!(ofrm || isitmd || isitpot)) ofFileStream.open(strFrcFile.c_str(),ios::binary);
if (!isitmd && !isitpot) cout << "potentials written to file " << strFrcFile << endl << endl;
if (ofrm)
{
ofFileStream << "DELPHI SITE POTENTIAL FILE\n";
ofFileStream << "grid size,percent fill: " << iGrid << " " << fPercentageFill << endl;
ofFileStream << "outer diel. and first one assigned : " << fExDielec << " " << vctfMediaEps[1]*fEPKT << endl;
ofFileStream << "ionic strength (M): " << fIonStrength << endl;
ofFileStream << "ion excl., probe radii: " << fIonRadius << " " << rgfProbeRadius[0] << " " << rgfProbeRadius[1] << endl;
ofFileStream << "linear, nolinear iterations: " << iLinIterateNum << " " << iNonIterateNum << endl;
ofFileStream << "boundary condition: " << iBndyType << endl;
ofFileStream << "Data Output: " << datum << endl;
ofFileStream << "title: " << rgcFileMap << endl;
ofFileStream << "\n\n";
ofFileStream << vrow << endl;
}
if (!ofrm && (!(isitmd || isitpot)))
{
ofFileStream << fixed << setprecision(4);
string strLine;
strLine = "DELPHI FRC FILE"; ofFileStream << strLine << endl;
strLine = "FORMAT NUMBER=1"; ofFileStream << strLine << endl;
strLine = "DATA="; strLine.append(datum); ofFileStream << strLine << endl;
ofFileStream << setw(5) << right << iGrid << setw(10) << right << fPercentageFill << setw(10) << right << fExDielec
<< setw(10) << right << fIonStrength << endl;
for (int i = 1; i <= iMediaNum; i++)
ofFileStream << "dielectric in medium nr. " << i << ": " << vctfMediaEps[i]*fEPKT << endl;
ofFileStream << setw(10) << right << fIonRadius << setw(10) << right << rgfProbeRadius[0] << setw(10) << right << rgfProbeRadius[1]
<< setw(5) << right << iLinIterateNum << setw(5) << right << iNonIterateNum << setw(5) << right << iBndyType << endl;
ofFileStream.unsetf(ios_base::floatfield);
}
if (!iself && (isitrf || isitmd || isittf))
{
CCalcReactForceError warning;
isitrf = false; isittf = false; isitmd = false;
}
vector< SGrid<real> > rfield;
if (isitrf || isitmd || isittf)
{
if (1 == iMediaNum && fZero > abs(vctfMediaEps[1]*fEPKT-1.0))
rfield = rforceeps1();
else
rfield = rforce();
}
//---------------------------------------------------------------------------------------------//
integer nnatom,inum,ncrgs;
SGrid<real> cxyz = {0.0,0.0,0.0},xo,xn,fu,fl,xo2,fxyz,vtemp,xu2,xu,rxyz;
real chrgv,radu,goff,vphi,aphi,etot,phiv,temp,phii,debyefraction,phirt,phict,phir,phias,tcrgs,dist,phirtt,crgs,phiat,phic,phiac,eps,phiact,phit;
real sdist,ff,fn;
string atm,res,rnum,chn,crdstr,atnum,atdes(16,' '),strLine,strHead;
bool isitmp;
int iFound,iresnum,idist,ncrg,jtmp;
vector<bool> atmsf(iAtomNum*iisitsf,false);
vector<real> sold,scomp;
char otemp[10];
string oline(80,' ');
nnatom = 0; chrgv = 0.0; goff = ((real)iGrid+1.0)/2.0; etot = 0.0; phirt = 0.0; phict =0.0;
if (isitpot)
{
CSitePhiError warning;
}
else
{
do // beginning of the big loop on natom
{
if(iself)
{
if (iAtomNum == nnatom) break;
xo = prgfgAtomCoordA[nnatom];
chrgv = vctapAtomPdb[nnatom].getCharge();
radu = vctapAtomPdb[nnatom].getRadius()*fScale;
atm = vctapAtomPdb[nnatom].getAtInf().substr(0,4);
res = vctapAtomPdb[nnatom].getAtInf().substr(6,3);
rnum = vctapAtomPdb[nnatom].getAtInf().substr(11,4);
chn = vctapAtomPdb[nnatom].getAtInf().substr(10,1);
}
else
{
//if (!ifFileStream.is_open()) break;
if(ifrm2) // formatted reading
{
getline(ifFileStream,strLine);
if (ifFileStream.eof()) break;
strHead = strLine.substr(0,6); strHead = toUpperCase(strHead);
if (0 != strHead.compare("ATOM ") && 0 != strHead.compare("HETATM")) continue;
crdstr = strLine.substr(30,24);
atnum = strLine.substr(6,5);
xo.nX = atof(crdstr.substr(0,8).c_str()); xo.nY = atof(crdstr.substr(8,8).c_str()); xo.nZ = atof(crdstr.substr(16,8).c_str());
inum = atoi(atnum.c_str());
}
else // unformatted (binary) reading
{
ifFileStream.read( reinterpret_cast<char*>(&xo.nX),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nY),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&xo.nZ),sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&radu), sizeof(real) );
ifFileStream.read( reinterpret_cast<char*>(&chrgv),sizeof(real) );
}
} //----- end of atom reading
nnatom++;
isitmp = (isitq && iqass) || isitap || isitp;
if((isita || isitmp) && !iself)
{
atm = strLine.substr(11,5);
res = strLine.substr(17,3);
rnum = strLine.substr(22,4);
chn = strLine.substr(21,1);
if (0 != atm.compare(" ")) {atm = removeSpace(atm); atm = toUpperCase(atm);}
if (0 != res.compare(" ")) {res = removeSpace(res); res = toUpperCase(res);}
if (0 != rnum.compare(" ")) {rnum = removeSpace(rnum); rnum = toUpperCase(rnum);}
if (0 != chn.compare(" ")) {chn = removeSpace(chn); chn = toUpperCase(chn);}
}
xn = (xo-fgBoxCenter)*fScale+goff; // scale atoms to grid space
if (isita)
{
atdes.assign(16,' ');
atdes.replace( 0,atm.size(),atm);
atdes.replace( 5,res.size(),res);
atdes.replace( 9,chn.size(),chn);
atdes.replace(11,rnum.size(),rnum);
}
/*
* assign charge to atom, searching for decreasingly specific specification
* note if no charge record found, is assumed to be 0.0
*/
if(!iself && ifrm2 && isitmp)
{
chrgv = 0.0;
iFound = FindRecord(atm,res,rnum,chn,CHARGEFILE,chrgv);
if(isitap) iFound = FindRecord(atm,res,rnum,chn,SIZEFILE,radu);
radu = radu*fScale;
}
if (isitsf)
{
iresnum = atoi(rnum.c_str());
atmsf[nnatom-1] = false;
if (residsf[iresnum-1]) atmsf[nnatom-1] = true;
}
if(isitap && fZero < abs(chrgv))
{
real rads = min(radu,fPotentialUpperBond*fScale);
SGrid<real> xt;
xt = xn; xt.nX += rads;
vphi = interpl(iGrid,phimap,xt);
aphi = vphi;
xt = xn; xt.nX -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nY -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ += rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
xt = xn; xt.nZ -= rads;
vphi = interpl(iGrid,phimap,xt);
aphi += vphi;
aphi = aphi/6.0;
}
if (isitp || isiti || (isitap && fZero > abs(chrgv)))
{
vphi = interpl(iGrid,phimap,xn);
if (isitap && fZero > abs(chrgv)) aphi = vphi;
if (isitp) { etot += chrgv*vphi; phiv = vphi; }
if (isiti)
{
CNoIDebMap warning;
/*
* we have changed the iconc action so that the phimap has NOT been converted to salt concentrations. therefore
*/
if (0 != iNonIterateNum)
{
temp = vphi*fTaylorCoeff5+fTaylorCoeff4; temp = vphi*temp+fTaylorCoeff3;
temp = vphi*temp+fTaylorCoeff2; temp = vphi*temp+fTaylorCoeff1;
phii = vphi*temp;
}
else
phii = -fIonStrength*2.0*vphi;
}
} //----- end if isitp or isiti, salt and or potentials
if (isitdeb) // it calculates the fraction of closest grid points that are in solution
{
cout << "Calculating Debye Fraction\n";
debyefraction = boolinterpl(iGrid,prgbDielecMap,xn);
}
if (isitf)
{
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fl.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fl.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fl.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = (fl-fu)*0.5*fScale; // the electric field is opposite the potential gradient so I change the sign
}
/*
* check if this point is within the box.
*/
if (isitt)
{
SExtrema<real> bedge;
bedge.nMin = fgBoxCenter-0.5*(iGrid-1)/fScale; bedge.nMax = fgBoxCenter+0.5*(iGrid-1)/fScale;
int it = 0;
if ( optORLT<real>(xo,bedge.nMin) || optORGT<real>(xo,bedge.nMax) ) it = 1;
if (0 == it)
{
xo2 = (xo-fgBoxCenter)*fScale+goff;
/*
* first find reaction field from surface elements inside of the box..
*/
phir=0.0; phias=0.0; ncrgs=0; tcrgs=0.0; sold.assign(30,0.0);
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
//----- first find reaction field from surface elements inside of the box
ncrgs++; tcrgs += prgfSurfCrgE[i]; phirtt = prgfSurfCrgE[i]/dist;
//----- medeps either epsin contain the 561.0 factor....
phirtt = phirtt*fEPKT; phir += phirtt;
xu2.nX = (real)prgigBndyGrid[i].nX; xu2.nY = (real)prgigBndyGrid[i].nY; xu2.nZ = (real)prgigBndyGrid[i].nZ;
crgs = prgfSurfCrgE[i];
//----- took place of repsin because eps is no more included in schrg , surface charge
phiat = tops(xu2,xo2,crgs,1.0,1); phiat = phiat*2.0; phias += phiat;
idist = (int)dist; sold[idist] += phiat - phirtt;
}
temp = 0.0;
cout << "Writing sold(1:30) and temp \n";
for (integer i = 0; i < 30; i++)
{
temp += sold[i];
cout << sold[i] << " " << temp;
}
cout << endl;
/*
* next find the colombic potential for that site from charges within the box
*/
phic = 0.0; phiac = 0.0; ncrg = 0;
for (integer i = 0; i < iCrgGridNum; i++)
{
it = 0;
if (optORLT<real>(prgfgCrgPoseA[i],bedge.nMin) || optORGT<real>(prgfgCrgPoseA[i],bedge.nMax)) it = 1;
if (0 == it)
{
ncrg++;
vtemp = xo - prgfgCrgPoseA[i]; dist = sqrt(optDot(vtemp,vtemp));
if (5.0 > dist)
{
if (fZero < dist) {temp = prggvAtomicCrg[i].nValue/dist; phic += temp/prgfAtomEps[i];}
//----- find analytic potential from this real charge..=phiac
xu = prgfgCrgPoseA[i]; crgs = prggvAtomicCrg[i].nValue;
xu2 = (xu-fgBoxCenter)*fScale+goff;
eps = prgfAtomEps[i]*fEPKT;
phiact = tops(xu2,xo2,crgs,eps,1);
phiac += phiact;
}
}
}
/*
* medeps, either epsin contain the 561.0 factor....
*/
phiac = phiac*2.0;
/*
* find the grid potentials..
*/
phiv = interpl(iGrid,phimap,xn);
string strFileName7 = "extra.dat";
ofstream ofFileSteam7;
ofFileSteam7.open(strFileName7.c_str());
ofFileSteam7 << phic << " " << phir << " " << phiv << " " << phias << " " << phiac << " "<< ncrg << " "
<< ncrgs << " " << tcrgs << endl;
ofFileSteam7.close();
phit = phic + phir + phiv - phias - phiac;
}
else
phit = 0.0;
/*
* phit contains the total corrected potential
*/
}
if (isitr)
{
scomp.assign(30,0.0); sold.assign(30,0.0); phir = 0.0;
for (integer i = 0; i < iDielecBndySum; i++)
{
vtemp = xo - prgfgSurfCrgA[i]; dist = sqrt(optDot(vtemp,vtemp));
idist = (int)dist;
if (30 > idist) sold[idist] += fEPKT*prgfSurfCrgE[i]/dist;
phir += prgfSurfCrgE[i]/dist;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
phir = phir*fEPKT;
for (integer i = 0; i < 30; i++)
{
if (0 == i) scomp[i] = sold[i];
if (0 != i) scomp[i] = scomp[i-1]+sold[i];
}
phirt += phir*chrgv;
}
/*
* medeps either epsin contains the 561.0 factor....
*/
if (isitrf || isitmd || isittf) rxyz = rfield[nnatom-1]*fEPKT;
if(isitcf || isitmd || isittf)
{
cxyz.nX = 0.0; cxyz.nY = 0.0; cxyz.nZ = 0.0;
if (fZero < abs(chrgv))
{
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist)*dist;
temp = prggvAtomicCrg[i].nValue/(prgfAtomEps[i]*sdist);
cxyz = cxyz + vtemp*temp;
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
cxyz = cxyz*chrgv;
}
}
if (isitc)
{
phic = 0.0;
for (integer i = 0; i < iCrgGridNum; i++)
{
vtemp = xo - prgfgCrgPoseA[i]; dist = optDot(vtemp,vtemp);
if (fZero < dist)
{
sdist = sqrt(dist);
temp = prggvAtomicCrg[i].nValue/sdist;
phic += temp/prgfAtomEps[i];
}
}
/*
* atmeps and medeps and epsin contain the 561.0 factor....
*/
phict += phic*chrgv;
}
//---------------------------------------------------------------------------------------//
/*
* write out calculated/assigned charges
*
* need otemp cos can not write into a substring apparently
* otemp needs to be at least 15 long to avoid an error!!
*/
oline.assign(80,' '); // reset oline
j = 0;
if (isita)
{
oline.replace(j,16,atdes.substr(0,16));
j += 20;
}
if (isitx)
{
sprintf(otemp,"%10.4f",xo.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitq)
{
sprintf(otemp,"%10.4f",chrgv); oline.replace(j,10,otemp); j += 10;
}
if (isitp)
{
sprintf(otemp,"%10.4f",phiv); oline.replace(j,10,otemp); j += 10;
#ifdef MCCE
mcce_phiv.push_back(phiv);
#endif
}
if (isiti)
{
sprintf(otemp,"%10.4f",phii); oline.replace(j,10,otemp); j += 10;
}
if (isitr)
{
sprintf(otemp,"%10.4f",phir); oline.replace(j,10,otemp); j += 10;
}
if (isitc)
{
sprintf(otemp,"%10.4f",phic); oline.replace(j,10,otemp); j += 10;
}
if (isitap)
{
sprintf(otemp,"%10.4f",aphi); oline.replace(j,10,otemp); j += 10;
}
if (isitdeb)
{
sprintf(otemp,"%10.4f",debyefraction); oline.replace(j,10,otemp); j += 10;
}
if (isitf)
{
sprintf(otemp,"%10.4f",fxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",fxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitrf)
{
sprintf(otemp,"%10.4f",rxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",rxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitcf)
{
sprintf(otemp,"%10.4f",cxyz.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",cxyz.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isittf)
{
vtemp = rxyz + cxyz;
sprintf(otemp,"%10.4f",vtemp.nX); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nY); oline.replace(j,10,otemp); j += 10;
sprintf(otemp,"%10.4f",vtemp.nZ); oline.replace(j,10,otemp); j += 10;
}
if (isitmd)
{
vtemp = rxyz + cxyz;
cout << "atom: " << nnatom << " rx= " << rxyz.nX << " cx= " << cxyz.nX << " tx= " << vtemp.nX << endl;
cout << "atom: " << nnatom << " ry= " << rxyz.nY << " cy= " << cxyz.nY << " ty= " << vtemp.nY << endl;
cout << "atom: " << nnatom << " rz= " << rxyz.nZ << " cz= " << cxyz.nZ << " tz= " << vtemp.nZ << endl;
}
if (isitt)
{
sprintf(otemp,"%10.4f",phit); oline.replace(j,10,otemp); j += 10;
}
if (ofrm && isitmp1) ofFileStream << oline << endl;
if (!ofrm && isitmp1)
{
if (isita) ofFileStream << atdes << endl;
if (isitx) ofFileStream << xo << endl;
if (isitq) ofFileStream << chrgv << endl;
if (isitp) ofFileStream << phiv << endl;
if (isiti) ofFileStream << phii << endl;
if (isitr) ofFileStream << phir << endl;
if (isitc) ofFileStream << phic << endl;
if (isitap) ofFileStream << aphi << endl;
if (isitf) ofFileStream << fxyz << endl;
if (isitrf) ofFileStream << rxyz << endl;
if (isitcf) ofFileStream << cxyz << endl;
if (isittf) { vtemp = rxyz + cxyz; ofFileStream << vtemp << endl;}
}
} while(true); // end of the big loop on natom
}
if (isitsf)
{
for (integer jj = 0; jj < iBndyGridNum; jj++)
{
integer i = prgiAtSurf[jj];
if (atmsf[i-1] && (0 < prgiAtNdx[jj]))
{
/*
* if the bgp belongs to the interesting site
* attention: using always radprb(1), in some case might be inappropriate
*/
xo = prgfgSurfCrgA[jj]+rgfProbeRadius[0]*prgfgSurfCrgE[jj];
xn = (xo-fgBoxCenter)*fScale+goff;
xn.nX += 1.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX -= 2.0; fu.nX = interpl(iGrid,phimap,xn);
xn.nX += 1.0; xn.nY += 1.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY -= 2.0; fu.nY = interpl(iGrid,phimap,xn);
xn.nY += 1.0; xn.nZ += 1.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ -= 2.0; fu.nZ = interpl(iGrid,phimap,xn);
xn.nZ += 1.0;
fxyz = fl - fu;
fn = 0.5*fScale*(optDot(fxyz,prgfgSurfCrgE[jj]));
ff = 0.5*fScale*(optDot(fxyz,fxyz));
if (ofrm)
{
jtmp = j;
sprintf(otemp,"%10.4f",prgfSurfCrgE[jj]); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nX); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nY); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",xo.nZ); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",fn); oline.replace(jtmp,10,otemp); jtmp += 10;
sprintf(otemp,"%10.4f",ff); oline.replace(jtmp,10,otemp); jtmp += 10;
ofFileStream << oline << endl;
}
if (!ofrm) ofFileStream << prgfSurfCrgE[jj] << " " << fn << endl;
}
}
}
if(!iself) ifFileStream.close();
#ifdef VERBOSE
cout << "\n number of atom coordinates read : " << nnatom << endl << endl;
#endif
etot = etot/2.0;
if (ofrm)
{
if (0 == iFrcFormatOut)
{
ofFileStream << "total energy = " << etot << " kt\n";
if (isitr) ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (1 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
ofFileStream << "total coulombic energy = " << phict/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
if (2 == iFrcFormatOut)
{
ofFileStream << "corrected reaction field energy= " << phirt/2.0 << " kt\n";
if (isitap) ofFileStream << "Atomic potential for charged atoms is averaged over a spherical surface of less than "
<< fPotentialUpperBond << " A\n";
}
}
/*
* end of formatted frc read/write and unformatted frc write
* end of unformatted frc.pdb read and frc write
*/
if (ofFileStream.is_open()) ofFileStream.close();
#ifdef VERBOSE
cout << "frc stuff now done at "; pTimer->showTime(); cout << endl;
#endif
}
