void ERMSD::setReference(const vector<Vector> & reference, const std::vector<unsigned> & pairs_vec, double mycutoff) {
natoms = reference.size();
nresidues = natoms/3;
unsigned npairs = pairs_vec.size()/2;
pairs.resize(npairs);
//for(unsigned i=0;i<2*npairs;++i) {
// std::cout << "CCC " << pairs_vec[i] << " ";
//}
for(unsigned i=0; i<npairs; ++i) {
pairs[i].first = pairs_vec[2*i];
pairs[i].second = pairs_vec[2*i+1];
}
cutoff = mycutoff;
std::vector<TensorGeneric<4,3> > deri;
deri.resize(natoms*natoms);
reference_mat.resize(nresidues*nresidues);
Pbc fake_pbc;
calcMat(reference,fake_pbc,reference_mat,deri);
}
void critfunc(double *grad, int *nPar, int *nD, double *probs, int *M,
double *design, double *n2, double *nold,
double *A, double *tol, double *MEDgrad, int *type,
int *stand, double *res){
// grad - contains gradient vectors (4 cells reserved for each model)
// nPar - number of parameters (dim A)
// nD - number of dose-levels
// design - design
// type - 1: MED, 2: Dopt, 3: MED&Dopt
int m,incgrad=0,incb=0;
double resM=0,resD=0,fracp=0;
// variables for SVD decomposition, initialize to max possible dimension
double work[30]={0.0};
double s[4]={0.0};
double VT[16]={0.0};
double U[16]={0.0};
*res = 0.0;
// calculate weight vector
getAllocs(design, n2, nold, nD);
for(m=0;m<*M;m++){
if(m > 0){
incgrad+=*nD*nPar[m-1];
incb+=nPar[m-1];
}
setzero(A, 16);resM = 0.0;
// calulate matrix
calcMat(grad, &nPar[m], design, nD, A, &incgrad);
// calculate det and/or MP-Inverse
calcDetGinv(A, &nPar[m], work, s, VT, U,
tol, type, &resD);
if(*type == 1){ // calculate quadratic form (for MED designs)
calcQuadform(MEDgrad, A, &nPar[m], &resM, &incb);
*res += probs[m]*log(resM);
}
if(*type == 2){
if(*stand == 1){
fracp = (double) nPar[m];
*res += probs[m]*(-log(resD)/fracp);
} else {
*res += probs[m]*(-log(resD));
}
}
if(*type == 3){ // calculate quadratic form (for MED designs)
calcQuadform(MEDgrad, A, &nPar[m], &resM, &incb);
if(*stand == 1){
fracp = (double) nPar[m];
*res += probs[m]*(-0.5*log(resD)/fracp+0.5*log(resM));
} else {
*res += probs[m]*(-0.5*log(resD)+0.5*log(resM));
}
}
}
}
double ERMSD::calculate(const std::vector<Vector> & positions,const Pbc& pbc,\
std::vector<Vector> &derivatives, Tensor& virial) {
double ermsd=0.;
std::vector<Vector4d> mat;
mat.resize(nresidues*nresidues);
std::vector<TensorGeneric<4,3> > Gderi;
Gderi.resize(natoms*natoms);
calcMat(positions,pbc,mat,Gderi);
unsigned idx1 = 0;
for(unsigned i=0; i<nresidues; i++) {
for(unsigned j=0; j<nresidues; j++) {
unsigned ii = i*nresidues + j;
Vector4d dd = delta(reference_mat[ii],mat[ii]);
double val = dd.modulo2();
//std::cout << "AAA " << i << " " << j << " " << ii << " "<< val << "\n";
if(val>0.0 && i!=j) {
for(unsigned k=0; k<3; k++) {
idx1 = i*nresidues*6 + j*6 + k;
derivatives[3*i+k] += matmul(dd,Gderi[idx1]);
derivatives[3*j+k] += matmul(dd,Gderi[idx1+3]);
}
ermsd += val;
}
}
}
//std::cout << ermsd << " ";
//if(pairs.size()!=0) nresidues=pairs.size();
//std::cout << ermsd << " " << nresidues;
ermsd = sqrt(ermsd/nresidues);
double iermsd = 1.0/(ermsd*nresidues);
for(unsigned i=0; i<natoms; ++i) {derivatives[i] *= iermsd;}
return ermsd;
}
