void PCM::propagateCavityGradients(const ScalarField& A_shape, ScalarField& A_nCavity, ScalarFieldTilde& A_rhoExplicitTilde, bool electricOnly) const
{ if(fsp.pcmVariant == PCM_SGA13)
{ //Propagate gradient w.r.t expanded cavities to nCavity:
((PCM*)this)->A_nc = 0;
const ScalarField* A_shapeEx[2] = { &A_shape, &Acavity_shapeVdw };
for(int i=0; i<2; i++)
{ //First compute derivative w.r.t expanded electron density:
ScalarField A_nCavityEx;
ShapeFunction::propagateGradient(nCavityEx[i], *(A_shapeEx[i]), A_nCavityEx, fsp.nc, fsp.sigma);
((PCM*)this)->A_nc += (-1./fsp.nc) * integral(A_nCavityEx*nCavityEx[i]);
//then propagate to original electron density:
ScalarField nCavityExUnused; //unused return value below
ShapeFunction::expandDensity(wExpand[i], Rex[i], nCavity, nCavityExUnused, &A_nCavityEx, &A_nCavity);
}
}
else if(fsp.pcmVariant == PCM_CANDLE)
{ ScalarField A_nCavityEx;
ScalarFieldTilde A_phiExt;
double A_pCavity=0.;
ShapeFunction::propagateGradient(nCavityEx[0], coulomb(Sf[0]*rhoExplicitTilde), I(wExpand[0]*J(A_shape)) + Acavity_shapeVdw,
A_nCavityEx, A_phiExt, A_pCavity, fsp.nc, fsp.sigma, fsp.pCavity);
A_nCavity += fsp.Ztot * I(Sf[0] * J(A_nCavityEx));
if(!electricOnly) A_rhoExplicitTilde += coulomb(Sf[0]*A_phiExt);
((PCM*)this)->A_nc = (-1./fsp.nc) * integral(A_nCavityEx*nCavityEx[0]);
((PCM*)this)->A_eta_wDiel = integral(A_shape * I(wExpand[1]*J(shapeVdw)));
((PCM*)this)->A_pCavity = A_pCavity;
}
else if(isPCM_SCCS(fsp.pcmVariant))
{ //Electrostatic and volumetric combinations via shape:
ShapeFunctionSCCS::propagateGradient(nCavity, A_shape - fsp.cavityPressure, A_nCavity, fsp.rhoMin, fsp.rhoMax, epsBulk);
//Add surface contributions:
ScalarField shapePlus, shapeMinus;
ShapeFunctionSCCS::compute(nCavity+(0.5*fsp.rhoDelta), shapePlus, fsp.rhoMin, fsp.rhoMax, epsBulk);
ShapeFunctionSCCS::compute(nCavity-(0.5*fsp.rhoDelta), shapeMinus, fsp.rhoMin, fsp.rhoMax, epsBulk);
VectorField Dn = gradient(nCavity);
ScalarField DnLength = sqrt(lengthSquared(Dn));
ScalarField A_shapeMinus = (fsp.cavityTension/fsp.rhoDelta) * DnLength;
ScalarField A_DnLength = (fsp.cavityTension/fsp.rhoDelta) * (shapeMinus - shapePlus);
A_nCavity -= divergence(Dn * (inv(DnLength) * A_DnLength));
ShapeFunctionSCCS::propagateGradient(nCavity+(0.5*fsp.rhoDelta), -A_shapeMinus, A_nCavity, fsp.rhoMin, fsp.rhoMax, epsBulk);
ShapeFunctionSCCS::propagateGradient(nCavity-(0.5*fsp.rhoDelta), A_shapeMinus, A_nCavity, fsp.rhoMin, fsp.rhoMax, epsBulk);
}
else //All gradients are w.r.t the same shape function - propagate them to nCavity (which is defined as a density product for SaLSA)
{ ShapeFunction::propagateGradient(nCavity, A_shape + Acavity_shape, A_nCavity, fsp.nc, fsp.sigma);
((PCM*)this)->A_nc = (-1./fsp.nc) * integral(A_nCavity*nCavity);
}
}
double SaLSA::get_Adiel_and_grad_internal(ScalarFieldTilde& Adiel_rhoExplicitTilde, ScalarFieldTilde& Adiel_nCavityTilde, IonicGradient* extraForces, bool electricOnly) const
{
EnergyComponents& Adiel = ((SaLSA*)this)->Adiel;
const ScalarFieldTilde& phi = state; // that's what we solved for in minimize
//First-order correct estimate of electrostatic energy:
ScalarFieldTilde phiExt = coulomb(rhoExplicitTilde);
Adiel["Electrostatic"] = -0.5*dot(phi, O(hessian(phi))) + dot(phi - 0.5*phiExt, O(rhoExplicitTilde));
//Gradient w.r.t rhoExplicitTilde:
Adiel_rhoExplicitTilde = phi - phiExt;
//The "cavity" gradient is computed by chain rule via the gradient w.r.t to the shape function:
const auto& solvent = fsp.solvents[0];
ScalarField Adiel_shape; ScalarFieldArray Adiel_siteShape(solvent->molecule.sites.size());
for(int r=rStart; r<rStop; r++)
{ const MultipoleResponse& resp = *response[r];
ScalarField& Adiel_s = resp.iSite<0 ? Adiel_shape : Adiel_siteShape[resp.iSite];
if(resp.l>6) die("Angular momenta l > 6 not supported.\n");
double prefac = 0.5 * 4*M_PI/(2*resp.l+1);
ScalarFieldArray IlGradVphi = I(lGradient(resp.V * phi, resp.l));
for(int lpm=0; lpm<(2*resp.l+1); lpm++)
Adiel_s -= prefac * (IlGradVphi[lpm]*IlGradVphi[lpm]);
}
for(unsigned iSite=0; iSite<solvent->molecule.sites.size(); iSite++)
if(Adiel_siteShape[iSite])
Adiel_shape += I(Sf[iSite] * J(Adiel_siteShape[iSite]));
nullToZero(Adiel_shape, gInfo); Adiel_shape->allReduce(MPIUtil::ReduceSum);
//Propagate shape gradients to A_nCavity:
ScalarField Adiel_nCavity;
propagateCavityGradients(Adiel_shape, Adiel_nCavity, Adiel_rhoExplicitTilde, electricOnly);
Adiel_nCavityTilde = nFluid * J(Adiel_nCavity);
setExtraForces(extraForces, Adiel_nCavityTilde);
return Adiel;
}
// elementary charge
inline quantity e() { return Rep( 1.602176462e-19L ) * coulomb(); }
double FluidMixture::operator()(const ScalarFieldArray& indep, ScalarFieldArray& Phi_indep, Outputs outputs) const
{ static StopWatch watch("FluidMixture::operator()"); watch.start();
//logPrintf("indep.size: %d nIndep: %d\n",indep.size(),nIndep);
myassert(indep.size()==get_nIndep());
//---------- Compute site densities from the independent variables ---------
ScalarFieldTildeArray Ntilde(nDensities); //site densities (in reciprocal space)
std::vector< vector3<> > P0(component.size()); //polarization densities G=0
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
ScalarFieldArray N(c.molecule.sites.size());
c.idealGas->getDensities(&indep[c.offsetIndep], &N[0], P0[ic]);
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{ //Replace negative densities with 0:
double Nmin, Nmax;
callPref(eblas_capMinMax)(gInfo.nr, N[i]->dataPref(), Nmin, Nmax, 0.);
//store site densities in fourier space
Ntilde[c.offsetDensity+i] = J(N[i]);
N[i] = 0; //Really skimp on memory!
}
}
//----------- Handle density constraints ------------
std::vector<double> Nscale(component.size(), 1.0); //density scale factor that satisfies the constraint
std::vector<double> Ntot_c; //vector of total number of molecules for each component
std::vector<double> Nscale_Qfixed(component.size(), 0.); //derivative of Nscale w.r.t the fixed charge
std::vector<std::vector<double> > Nscale_N0(component.size(), std::vector<double>(component.size(),0.0)); //jacobian of Nscale w.r.t the uncorrected molecule counts
std::vector<string> names; //list of molecule names
//Find fixed N and charged species:
double Qfixed = 0.0;
if(rhoExternal) Qfixed += integral(rhoExternal);
std::vector<std::pair<double,double> > N0Q;
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
double Qmolecule = c.molecule.getCharge();
if(c.Nnorm>0 || Qmolecule)
{ double N0 = integral(Ntilde[c.offsetDensity])/c.molecule.sites[0]->positions.size();
if(c.Nnorm>0)
{ Nscale[ic] = c.Nnorm/N0;
Nscale_N0[ic][ic] = -c.Nnorm/pow(N0,2);
Qfixed += Qmolecule*c.Nnorm;
}
else
{ N0Q.push_back(std::make_pair(N0, Qmolecule));
names.push_back(c.molecule.name);
}
}
}
//Find the betaV (see Qtot()) that makes the unit cell neutral
if(N0Q.size()==0)
{ if(fabs(Qfixed)>fabs(Qtol))
die("Unit cell has a fixed net charge %le,"
"and there are no free charged species to neutralize it.\n", Qfixed);
}
else
{ double Qprime, Qcell, betaV=0.0;
if(Qfixed+Qtot(-HUGE_VAL,Qprime,N0Q)<0)
die("Unit cell will always have a net negative charge (no free positive charges).\n")
if(Qfixed+Qtot(+HUGE_VAL,Qprime,N0Q)>0)
die("Unit cell will always have a net positive charge (no free negative charges).\n")
for(int iter=0; iter<10; iter++) //while(1)
{ Qcell = Qfixed+Qtot(betaV,Qprime,N0Q,&names,&gInfo,verboseLog);
if(verboseLog) logPrintf("betaV = %le, Qcell = %le, Qprime = %le\n", betaV, Qcell, Qprime);
if(fabs(Qcell)<fabs(Qtol)) break;
if(std::isnan(Qcell))
{ betaV=0.0; break;}
betaV -= Qcell/Qprime; //Newton-Raphson update
}
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& ci = *component[ic];
double Qi = ci.molecule.getCharge();
if(Qi && ci.Nnorm<=0)
{ Nscale[ic] = exp(-Qi*betaV);
Nscale_Qfixed[ic] = exp(-Qi*betaV) * Qi / Qprime;
for(unsigned jc=0; jc<component.size(); jc++)
{ const FluidComponent& cj = *component[jc];
double Qj = cj.molecule.getCharge();
if(Qj && cj.Nnorm<=0)
Nscale_N0[ic][jc] += Qi*Qj*exp(-(Qi+Qj)*betaV)/Qprime;
}
}
}
}
std::vector<double> Phi_Nscale(component.size(), 0.0); //accumulate explicit derivatives w.r.t Nscale here
//Apply the scale factors to the site densities
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
for(unsigned i=0; i<c.molecule.sites.size(); i++)
Ntilde[c.offsetDensity+i] *= Nscale[ic];
P0[ic] *= Nscale[ic];
Ntot_c.push_back(integral(Ntilde[c.offsetDensity]));
}
EnergyComponents Phi; //the grand free energy (with component information)
ScalarFieldTildeArray Phi_Ntilde(nDensities); //gradients (functional derivative) w.r.t reciprocal space site densities
nullToZero(Phi_Ntilde,gInfo);
std::vector< vector3<> > Phi_P0(component.size()); //functional derivative w.r.t polarization density G=0
VectorFieldTilde Phi_epsMF; //functional derivative w.r.t mean field electric field
//G=0 fix for mismatch in fluid-fluid vs. fluid-electron charge kernels
//We do this AFTER we have applied the appropriate scale factors
if( N0Q.size() && (!useMFKernel)) //if we have charged species in our fluid, and are using mismatched charge kernels
{
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{
const Molecule::Site& s = *(c.molecule.sites[i]);
Phi["Gzero"] += Qfixed*(Ntot_c[ic]/gInfo.detR-c.idealGas->Nbulk)*s.positions.size()*s.deltaS;
Phi_Ntilde[c.offsetDensity+i]->data()[0] += (1.0/gInfo.dV) * (Qfixed*s.deltaS);
}
}
}
//--------- Compute the (scaled) mean field coulomb interaction --------
{ ScalarFieldTilde rho; //total charge density
ScalarFieldTilde rhoMF; //effective charge density for mean-field term
bool needRho = rhoExternal || outputs.Phi_rhoExternal;
VectorFieldTilde epsMF = polarizable ? J(VectorField(&indep[nIndepIdgas])) : 0; //mean field electric field
vector3<> P0tot;
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{ const Molecule::Site& s = *(c.molecule.sites[i]);
if(s.chargeKernel)
{ if(needRho) rho += s.chargeKernel * Ntilde[c.offsetDensity+i];
rhoMF += s.chargeKernel(0) * (c.molecule.mfKernel * Ntilde[c.offsetDensity+i]);
}
//Polarization contributions:
if(polarizable && s.polKernel)
{
#define Polarization_Compute_Pi_Ni \
VectorField Pi = (Cpol*s.alpha) * I(c.molecule.mfKernel*epsMF - (rhoExternal ? gradient(s.polKernel*coulomb(rhoExternal)) : 0)); \
ScalarField Ni = I(Ntilde[c.offsetDensity+i]);
Polarization_Compute_Pi_Ni
ScalarField Phi_Ni = (0.5/(Cpol*s.alpha))*lengthSquared(Pi);
Phi["Apol"] += gInfo.dV * dot(Ni, Phi_Ni);
//Derivative contribution to site densities:
Phi_Ntilde[c.offsetDensity+i] += Idag(Phi_Ni); Phi_Ni=0;
//Update contributions to bound charge:
VectorFieldTilde NPtilde = J(Ni * Pi); Pi=0; Ni=0;
ScalarFieldTilde divNPbar;
if(needRho) rho -= s.polKernel*divergence(NPtilde);
VectorFieldTilde NPbarMF = c.molecule.mfKernel*NPtilde; NPtilde=0;
rhoMF -= divergence(NPbarMF);
Phi_epsMF += gInfo.nr * NPbarMF;
P0tot += getGzero(NPbarMF);
}
}
P0tot += P0[ic];
}
if(rhoMF)
{ //External charge interaction:
ScalarFieldTilde Phi_rho;
ScalarFieldTilde Phi_rhoMF;
if(needRho)
{ if(rhoExternal)
{
ScalarFieldTilde OdExternal = O(coulomb(rhoExternal));
if (!useMFKernel)
{
Phi["ExtCoulomb"] += dot(rho, OdExternal);
Phi_rho += OdExternal;
}
if (useMFKernel)
{
Phi["ExtCoulomb"] += dot(rhoMF, OdExternal);
Phi_rhoMF += OdExternal;
}
}
if(outputs.Phi_rhoExternal)
{
if (!useMFKernel) *outputs.Phi_rhoExternal = coulomb(rho);
if (useMFKernel) *outputs.Phi_rhoExternal = coulomb(rhoMF);
}
}
//Mean field contributions:
{ ScalarFieldTilde OdMF = O(coulomb(rhoMF)); //mean-field electrostatic potential
Phi["Coulomb"] += 0.5*dot(rhoMF, OdMF);
Phi_rhoMF += OdMF;
}
//Polarization density interactions:
if(outputs.electricP) *outputs.electricP = P0tot * gInfo.detR;
//--- corrections for net dipole in cell:
vector3<> Phi_P0tot = (4*M_PI*gInfo.detR) * P0tot;
Phi["PsqCell"] += 0.5 * dot(Phi_P0tot, P0tot);
//--- external electric field interactions:
Phi["ExtCoulomb"] -= gInfo.detR * dot(Eexternal, P0tot);
Phi_P0tot -= gInfo.detR * Eexternal;
//Propagate gradients:
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{ const Molecule::Site& s = *(c.molecule.sites[i]);
if(s.chargeKernel)
{ if(Phi_rho) Phi_Ntilde[c.offsetDensity+i] += (1./gInfo.dV) * (s.chargeKernel * Phi_rho);
Phi_Ntilde[c.offsetDensity+i] += (s.chargeKernel(0)/gInfo.dV) * (c.molecule.mfKernel * Phi_rhoMF);
}
//Polarization contributions:
if(polarizable && s.polKernel)
{ VectorFieldTilde Phi_NPtilde = gradient(c.molecule.mfKernel*Phi_rhoMF + (needRho ? s.polKernel*Phi_rho : 0));
setGzero(Phi_NPtilde, getGzero(Phi_NPtilde) + Phi_P0tot);
VectorField Phi_NP = Jdag(Phi_NPtilde); Phi_NPtilde=0;
//propagate gradients from NP to N, epsMF and rhoExternal:
Polarization_Compute_Pi_Ni
#undef Polarization_Compute_Pi_Ni
// --> via Ni
ScalarField Phi_Ni; for(int k=0; k<3; k++) Phi_Ni += Phi_NP[k]*Pi[k];
Phi_Ntilde[c.offsetDensity+i] += (1./gInfo.dV) * Idag(Phi_Ni); Phi_Ni=0;
// --> via Pi
VectorFieldTilde Phi_PiTilde = Idag(Phi_NP * Ni); Phi_NP=0;
Phi_epsMF += (Cpol*s.alpha/gInfo.dV)*(c.molecule.mfKernel*Phi_PiTilde);
}
}
Phi_P0[ic] += (1./gInfo.detR) * Phi_P0tot; //convert to functional derivative
}
}
}
//--------- Hard sphere mixture and bonding -------------
{ //Compute the FMT weighted densities:
ScalarFieldTilde n0tilde, n1tilde, n2tilde, n3tilde, n1vTilde, n2mTilde;
std::vector<ScalarField> n0mol(component.size(), 0); //partial n0 for molecules that need bonding corrections
std::vector<int> n0mult(component.size(), 0); //number of sites which contribute to n0 for each molecule
std::vector<std::map<double,int> > bond(component.size()); //sets of bonds for each molecule
bool bondsPresent = false; //whether bonds are present for any molecule
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
bond[ic] = c.molecule.getBonds();
ScalarFieldTilde n0molTilde;
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{ const Molecule::Site& s = *(c.molecule.sites[i]);
if(s.Rhs)
{ const ScalarFieldTilde& Nsite = Ntilde[c.offsetDensity+i];
n0mult[ic] += s.positions.size();
n0molTilde += s.w0 * Nsite;
n1tilde += s.w1 * Nsite;
n2tilde += s.w2 * Nsite;
n3tilde += s.w3 * Nsite;
n1vTilde += s.w1v * Nsite;
n2mTilde += s.w2m * Nsite;
}
}
if(n0molTilde) n0tilde += n0molTilde;
if(bond[ic].size())
{ n0mol[ic] = I(n0molTilde);
bondsPresent = true;
}
}
if(n0tilde) //at least one sphere in the mixture
{ ScalarField n0 = I(n0tilde); n0tilde=0;
ScalarField n1 = I(n1tilde); n1tilde=0;
ScalarField n2 = I(n2tilde); n2tilde=0;
ScalarField Phi_n0, Phi_n1, Phi_n2; ScalarFieldTilde Phi_n3tilde, Phi_n1vTilde, Phi_n2mTilde;
//Compute the sphere mixture free energy:
Phi["MixedFMT"] += T * PhiFMT(n0, n1, n2, n3tilde, n1vTilde, n2mTilde,
Phi_n0, Phi_n1, Phi_n2, Phi_n3tilde, Phi_n1vTilde, Phi_n2mTilde);
//Bonding corrections if required
if(bondsPresent)
{ for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
ScalarField Phi_n0mol;
for(const auto& b: bond[ic])
Phi["Bonding"] += T * PhiBond(b.first, b.second*1./n0mult[ic],
n0mol[ic], n2, n3tilde, Phi_n0mol, Phi_n2, Phi_n3tilde);
if(Phi_n0mol)
{ //Propagate gradient w.r.t n0mol[ic] to the site densities:
ScalarFieldTilde Phi_n0molTilde = Idag(Phi_n0mol);
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{ const Molecule::Site& s = *(c.molecule.sites[i]);
if(s.Rhs)
Phi_Ntilde[c.offsetDensity+i] += T * (s.w0 * Phi_n0molTilde);
}
}
}
}
//Accumulate gradients w.r.t weighted densities to site densities:
ScalarFieldTilde Phi_n0tilde = Idag(Phi_n0); Phi_n0=0;
ScalarFieldTilde Phi_n1tilde = Idag(Phi_n1); Phi_n1=0;
ScalarFieldTilde Phi_n2tilde = Idag(Phi_n2); Phi_n2=0;
for(const FluidComponent* c: component)
{ for(unsigned i=0; i<c->molecule.sites.size(); i++)
{ const Molecule::Site& s = *(c->molecule.sites[i]);
if(s.Rhs)
{ ScalarFieldTilde& Phi_Nsite = Phi_Ntilde[c->offsetDensity+i];
Phi_Nsite += T * (s.w0 * Phi_n0tilde);
Phi_Nsite += T * (s.w1 * Phi_n1tilde);
Phi_Nsite += T * (s.w2 * Phi_n2tilde);
Phi_Nsite += T * (s.w3 * Phi_n3tilde);
Phi_Nsite += T * (s.w1v * Phi_n1vTilde);
Phi_Nsite += T * (s.w2m * Phi_n2mTilde);
}
}
}
}
}
//---------- Excess functionals --------------
for(const FluidComponent* c: component) if(c->fex)
Phi["Fex("+c->molecule.name+")"] += c->fex->compute(Ñ[c->offsetDensity], &Phi_Ntilde[c->offsetDensity]);
//--------- Mixing functionals --------------
for(const Fmix* fmix: fmixArr)
Phi["Fmix("+fmix->getName()+")"] += fmix->compute(Ntilde, Phi_Ntilde);
//--------- PhiNI ---------
nullToZero(Phi_Ntilde, gInfo);
if(outputs.N) outputs.N->resize(nDensities);
//Put the site densities and gradients back in real space
ScalarFieldArray N(nDensities);
ScalarFieldArray Phi_N(nDensities);
for(unsigned i=0; i<nDensities; i++)
{ N[i] = I(Ntilde[i]); Ntilde[i]=0;
Phi_N[i] = Jdag(Phi_Ntilde[i]); Phi_Ntilde[i] = 0;
if(outputs.N) (*outputs.N)[i] = N[i]; //Link site-density to return pointer if necessary
}
//Estimate psiEff based on gradients, if requested
if(outputs.psiEff)
{ outputs.psiEff->resize(nDensities);
for(const FluidComponent* c: component)
for(unsigned i=0; i<c->molecule.sites.size(); i++)
{ ScalarField& psiCur = outputs.psiEff->at(c->offsetDensity+i);
psiCur = Phi_N[c->offsetDensity+i] + c->idealGas->V[i];
if(i==0) psiCur -= c->idealGas->mu / c->molecule.sites[0]->positions.size();
psiCur *= (-1./T);
}
}
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
Phi["PhiNI("+c.molecule.name+")"] +=
c.idealGas->compute(&indep[c.offsetIndep], &N[c.offsetDensity], &Phi_N[c.offsetDensity], Nscale[ic], Phi_Nscale[ic]);
//Fixed N correction to entropy:
if(Nscale[ic]!=1.0)
{ double deltaTs = T*log(Nscale[ic]) / c.molecule.sites[0]->positions.size();
Phi_N[c.offsetDensity] += deltaTs;
Phi["PhiNI("+c.molecule.name+")"] += integral(N[c.offsetDensity])*deltaTs;
}
}
//Add in the implicit contributions to Phi_Nscale
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& ci = *component[ic];
bool anyNonzero=false;
for(unsigned jc=0; jc<component.size(); jc++)
if(Nscale_N0[ic][jc])
anyNonzero=true;
if(anyNonzero)
{ Phi_Nscale[ic] += gInfo.detR*dot(P0[ic], Phi_P0[ic])/ Nscale[ic];
for(unsigned i=0; i<ci.molecule.sites.size(); i++)
Phi_Nscale[ic] += gInfo.dV*dot(N[ci.offsetDensity+i], Phi_N[ci.offsetDensity+i])/ Nscale[ic];
}
}
//Propagate gradients from Nscale to N:
for(unsigned jc=0; jc<component.size(); jc++)
{ const FluidComponent& cj = *component[jc];
double Phi_Ncontrib = 0.0;
for(unsigned ic=0; ic<component.size(); ic++)
if(Nscale_N0[ic][jc])
Phi_Ncontrib += Phi_Nscale[ic] * Nscale_N0[ic][jc];
if(Phi_Ncontrib)
Phi_N[cj.offsetDensity] += Phi_Ncontrib / (Nscale[jc] * cj.molecule.sites[0]->positions.size());
}
//Propagate gradients from Phi_N and Phi_P to Phi_indep
Phi_indep.resize(get_nIndep());
for(unsigned ic=0; ic<component.size(); ic++)
{ const FluidComponent& c = *component[ic];
c.idealGas->convertGradients(&indep[c.offsetIndep], &N[c.offsetDensity],
&Phi_N[c.offsetDensity], Phi_P0[ic], &Phi_indep[c.offsetIndep], Nscale[ic]);
}
for(unsigned k=nIndepIdgas; k<get_nIndep(); k++) Phi_indep[k] = Jdag(Phi_epsMF[k-nIndepIdgas]);
//Propagate gradients from Nscale to Qfixed / rhoExternal (Natural G=0 solution)
if(outputs.Phi_rhoExternal)
{ double Phi_Qfixed = 0.;
for(unsigned ic=0; ic<component.size(); ic++)
{
Phi_Qfixed += Phi_Nscale[ic] * Nscale_Qfixed[ic];
if (N0Q.size() && (!useMFKernel))
{
const FluidComponent& c = *component[ic];
for(unsigned i=0; i<c.molecule.sites.size(); i++)
{
//Correction to lambda from charge kernel mismatch
const Molecule::Site& s = *(c.molecule.sites[i]);
double lambda_s = (Ntot_c[ic]/gInfo.detR-c.idealGas->Nbulk)*s.deltaS*s.positions.size();
if(verboseLog) logPrintf("Charge kernel mismatch correction for site %s of molecule %s: %lg\n",
s.name.c_str(),c.molecule.name.c_str(),lambda_s);
Phi_Qfixed += lambda_s;
}
if(verboseLog) logPrintf("Total number of molecules of type %s: %lg\n",c.molecule.name.c_str(),Ntot_c[ic]);
}
}
nullToZero(*outputs.Phi_rhoExternal, gInfo);
(*outputs.Phi_rhoExternal)->setGzero(Phi_Qfixed);
}
Phi["+pV"] += p * gInfo.detR; //background correction
if(verboseLog) Phi.print(globalLog, true, "\t\t\t\t%15s = %25.16lf\n");
if(outputs.Phi) *(outputs.Phi) = Phi;
Phi_indep *= gInfo.dV; //convert functional derivative to partial derivative
watch.stop();
return Phi;
}
float coulomb_conf(int ires, int iconf, int jres, int jconf, PROT prot)
{
float e = 0.0;
int iatom, jatom;
ATOM *connect13[MAX_CONNECTED2], *connect14[MAX_CONNECTED3];
ATOM *iatom_p, *jatom_p;
int connect13_res[MAX_CONNECTED2], connect14_res[MAX_CONNECTED3];
int iconnect, jconnect, kconnect, n_connect13, n_connect14;
if (ires<0 || ires>prot.n_res-1) printf(" Error! coulomb_conf(): residue index out of range in protein\n"),exit(-1);
if (jres<0 || jres>prot.n_res-1) printf(" Error! coulomb_conf(): residue index out of range in protein\n"),exit(-1);
if (iconf<0 || iconf>prot.res[ires].n_conf-1) printf(" Error! coulomb_conf(): conformer index out of range in protein\n"),exit(-1);
if (jconf<0 || jconf>prot.res[jres].n_conf-1) printf(" Error! coulomb_conf(): conformer index out of range in protein\n"),exit(-1);
for (iatom=0; iatom<prot.res[ires].conf[iconf].n_atom; iatom++) {
iatom_p = &prot.res[ires].conf[iconf].atom[iatom];
if (!iatom_p->on) continue;
n_connect13 = 0;
n_connect14 = 0;
memset(connect13, 0,MAX_CONNECTED2*sizeof(void *));
memset(connect13_res,0,MAX_CONNECTED2*sizeof(int));
memset(connect14, 0,MAX_CONNECTED3*sizeof(void *));
memset(connect14_res,0,MAX_CONNECTED3*sizeof(int));
for (iconnect = 0; iconnect < MAX_CONNECTED; iconnect++) {
if (!iatom_p->connect12[iconnect]) break;
n_connect13++;
connect13[n_connect13-1] = iatom_p->connect12[iconnect];
connect13_res[n_connect13-1] = iatom_p->connect12_res[iconnect];
for (jconnect = 0; jconnect < MAX_CONNECTED; jconnect++) {
if (!iatom_p->connect12[iconnect]->connect12[jconnect]) break;
n_connect13++;
connect13[n_connect13-1] = iatom_p->connect12[iconnect]->connect12[jconnect];
connect13_res[n_connect13-1] = iatom_p->connect12[iconnect]->connect12_res[jconnect];
for (kconnect = 0; kconnect < MAX_CONNECTED; kconnect++) {
if (!iatom_p->connect12[iconnect]->connect12[jconnect]->connect12[kconnect]) break;
n_connect14++;
connect14[n_connect14-1] = iatom_p->connect12[iconnect]->connect12[jconnect]->connect12[kconnect];
connect14_res[n_connect14-1] = iatom_p->connect12[iconnect]->connect12[jconnect]->connect12_res[kconnect];
}
}
}
for (jatom=0; jatom<prot.res[jres].conf[jconf].n_atom; jatom++) {
jatom_p = &prot.res[jres].conf[jconf].atom[jatom];
if (!jatom_p->on) continue;
for (iconnect = 0; iconnect < n_connect13; iconnect++) {
if (jres == connect13_res[iconnect] && !strcmp(jatom_p->name,connect13[iconnect]->name)) break;
}
if (iconnect < n_connect13) continue;
for (iconnect = 0; iconnect < n_connect14; iconnect++) {
if (jres == connect14_res[iconnect] && !strcmp(jatom_p->name,connect14[iconnect]->name)) break;
}
if (iconnect < n_connect13) {
e += coulomb(*iatom_p, *jatom_p) * env.factor_14lj;
continue;
}
e += coulomb(*iatom_p, *jatom_p);
//printf("iatom %d,jatom %d\n",iatom,jatom);
}
}
return e;
}
void TransformerSPRINGEMBEDDER::SpringEmbed(Graph& G, vector<float> dimension_limits, IntermediateStepHandler* intermediatestephandler)
{
vector<VectorND> tractions;
int dimensions = dimension_limits.size();
unstressed_spring_length = dimension_limits[0];
for(int i = 1; i < dimensions; i++)
unstressed_spring_length *= dimension_limits[i];
unstressed_spring_length /= G.NumberOfVertices();
unstressed_spring_length = pow(unstressed_spring_length, 1.0f/dimensions) / (dimensions * 2);
// init
srand ( time(NULL) );
for(VertexIterator a = G.BeginVertices(); a != G.EndVertices(); a++)
{
Coordinates coordinates;
for(int i = 0; i < dimensions; i++)
coordinates.push_back(fmod(rand(), dimension_limits[i]));
(*a)->SetCoordinates(coordinates);
// should make sure that no two vertices have the same position
tractions.push_back(VectorND(dimensions));
}
float max_movement;
iteration = 0;
do
{
// compute movement
max_movement = 0;
int i = 0;
for(VertexIterator a = G.BeginVertices(); a != G.EndVertices(); a++, i++)
{
VectorND traction = tractions[i] * friction;
// compute forces on a by the other vertices
VectorND aCoordinates((*a)->GetCoordinates(0));
for(VertexIterator b = G.BeginVertices(); b != G.EndVertices(); b++)
{
if(b==a)
continue;
// force on a by vertex b
VectorND bCoordinates((*b)->GetCoordinates(0));
traction += coulomb(aCoordinates, bCoordinates);
if((*a)->Adjacent(*b))
traction += hooke(aCoordinates, bCoordinates);
}
tractions[i] = traction;
}
// execute movement
VertexIterator a = G.BeginVertices();
for(int i = 0; a != G.EndVertices(); a++, i++)
{
Coordinates OldCoordinates = (*a)->GetCoordinates(0);
Coordinates NewCoordinates(dimensions);
for(int j = 0; j < dimensions; j++)
NewCoordinates[j] = max(0.0f,min(dimension_limits[j], OldCoordinates[j] + delta * tractions[i][j] ));
(*a)->SetCoordinates( NewCoordinates );
// for the loop-condition
float current_movement = 0.0f;
for(int j = 0; j < dimensions; j++)
current_movement += (OldCoordinates[j] - NewCoordinates[j]) * (OldCoordinates[j] - NewCoordinates[j]);
if(sqrt(current_movement) > max_movement)
max_movement = sqrt(current_movement);
}
if(intermediatestephandler != NULL)
intermediatestephandler->Handle(&G);
if(++iteration > nextincrease)
{
movement_threshold += 0.01f;
nextincrease *= 4;
}
if(iteration > max_iterations)
break;
}
while(max_movement > movement_threshold*unstressed_spring_length);
}
void PCM::updateCavity()
{
//Cavities from expanded densities for SGA13 variant:
if(fsp.pcmVariant == PCM_SGA13)
{ ScalarField* shapeEx[2] = { &shape, &shapeVdw };
for(int i=0; i<2; i++)
{ ShapeFunction::expandDensity(wExpand[i], Rex[i], nCavity, nCavityEx[i]);
ShapeFunction::compute(nCavityEx[i], *(shapeEx[i]), fsp.nc, fsp.sigma);
}
}
else if(fsp.pcmVariant == PCM_CANDLE)
{ nCavityEx[0] = fsp.Ztot * I(Sf[0] * J(nCavity));
ShapeFunction::compute(nCavityEx[0], coulomb(Sf[0]*rhoExplicitTilde), shapeVdw,
fsp.nc, fsp.sigma, fsp.pCavity); //vdW cavity
shape = I(wExpand[0] * J(shapeVdw)); //dielectric cavity
}
else if(isPCM_SCCS(fsp.pcmVariant))
ShapeFunctionSCCS::compute(nCavity, shape, fsp.rhoMin, fsp.rhoMax, epsBulk);
else //Compute directly from nCavity (which is a density product for SaLSA):
ShapeFunction::compute(nCavity, shape, fsp.nc, fsp.sigma);
//Compute and cache cavitation energy and gradients:
const auto& solvent = fsp.solvents[0];
switch(fsp.pcmVariant)
{
case PCM_SaLSA:
case PCM_CANDLE:
case PCM_SGA13:
{ //Select relevant shape function:
const ScalarFieldTilde sTilde = J(fsp.pcmVariant==PCM_SaLSA ? shape : shapeVdw);
ScalarFieldTilde A_sTilde;
//Cavitation:
const double nlT = solvent->Nbulk * fsp.T;
const double Gamma = log(nlT/solvent->Pvap) - 1.;
const double Cp = 15. * (solvent->sigmaBulk/(2*solvent->Rvdw * nlT) - (1+Gamma)/6);
const double coeff2 = 1. + Cp - 2.*Gamma;
const double coeff3 = Gamma - 1. -2.*Cp;
ScalarField sbar = I(wCavity*sTilde);
Adiel["Cavitation"] = nlT * integral(sbar*(Gamma + sbar*(coeff2 + sbar*(coeff3 + sbar*Cp))));
A_sTilde += wCavity*Idag(nlT * (Gamma + sbar*(2.*coeff2 + sbar*(3.*coeff3 + sbar*(4.*Cp)))));
//Dispersion:
ScalarFieldTildeArray Ntilde(Sf.size()), A_Ntilde(Sf.size()); //effective nuclear densities in spherical-averaged ansatz
for(unsigned i=0; i<Sf.size(); i++)
Ntilde[i] = solvent->Nbulk * (Sf[i] * sTilde);
const double vdwScaleEff = (fsp.pcmVariant==PCM_CANDLE) ? fsp.sqrtC6eff : fsp.vdwScale;
Adiel["Dispersion"] = e.vanDerWaals->energyAndGrad(atpos, Ntilde, atomicNumbers, vdwScaleEff, &A_Ntilde);
A_vdwScale = Adiel["Dispersion"]/vdwScaleEff;
for(unsigned i=0; i<Sf.size(); i++)
if(A_Ntilde[i])
A_sTilde += solvent->Nbulk * (Sf[i] * A_Ntilde[i]);
//Propagate gradients to appropriate shape function:
(fsp.pcmVariant==PCM_SaLSA ? Acavity_shape : Acavity_shapeVdw) = Jdag(A_sTilde);
break;
}
case PCM_GLSSA13:
{ VectorField Dshape = gradient(shape);
ScalarField surfaceDensity = sqrt(lengthSquared(Dshape));
ScalarField invSurfaceDensity = inv(surfaceDensity);
A_tension = integral(surfaceDensity);
Adiel["CavityTension"] = A_tension * fsp.cavityTension;
Acavity_shape = (-fsp.cavityTension)*divergence(Dshape*invSurfaceDensity);
break;
}
case PCM_LA12:
case PCM_PRA05:
break; //no contribution
case_PCM_SCCS_any:
{ //Volume contribution:
Adiel["CavityPressure"] = fsp.cavityPressure * (gInfo.detR - integral(shape));
//Surface contribution:
ScalarField shapePlus, shapeMinus;
ShapeFunctionSCCS::compute(nCavity+(0.5*fsp.rhoDelta), shapePlus, fsp.rhoMin, fsp.rhoMax, epsBulk);
ShapeFunctionSCCS::compute(nCavity-(0.5*fsp.rhoDelta), shapeMinus, fsp.rhoMin, fsp.rhoMax, epsBulk);
ScalarField DnLength = sqrt(lengthSquared(gradient(nCavity)));
Adiel["CavityTension"] = (fsp.cavityTension/fsp.rhoDelta) * integral(DnLength * (shapeMinus - shapePlus));
break;
}
}
}