int CXXSurface::assignAtom (mmdb::PManager allAtomsManager_in, int selHnd){
void **pointerBuffer;
mmdb::PPAtom selAtom;
int nSelAtoms;
double minDistSq;
allAtomsManager_in->GetSelIndex(selHnd, selAtom, nSelAtoms);
pointerBuffer = new void* [vertices.size()];
// Loop over all vertices
for (int i=0; i< int(vertices.size()); i++){
const CXXCoord &vertex = coordRef(vectors["vertices"], i);
int j;
for (j = 0, minDistSq=1e30; j<nSelAtoms; j++){
CXXCoord atom (selAtom[j]->x, selAtom[j]->y, selAtom[j]->z);
CXXCoord diff = atom - vertex;
double dxsq = diff.x() * diff.x();
if (dxsq<minDistSq){
double dysq = diff.y() * diff.y();
if (dysq<minDistSq){
double dzsq = diff.z() * diff.z();
if (dzsq<minDistSq){
if (dxsq + dysq + dzsq < minDistSq){
pointerBuffer[i] = (void *) selAtom[j];
minDistSq = dxsq + dysq + dzsq;
}
}
}
}
}
}
addPerVertexPointer ("atom", pointerBuffer);
delete [] pointerBuffer;
return 0;
}
int CXXSurface::getCoord(const int type, const int iVertex, double *buffer)
{
if (type>=0 && type <= int(vectors.size())){
const CXXCoord &theCoord = coordRef(type, iVertex);
for (int i=0; i<4; i++){
buffer[i] = theCoord.element(i);
}
return 0;
}
else return 1;
}
std::string CXXSurface::report(){
double area = 0.;
double pMin, pMax, pMean;
int i;
CXXCoord AB, AC, ABxAC;
std::ostringstream output;
output << "This surface has " << vertices.size() << " vertices and " << nTriangles
<< " triangles\n";
if (vectors.find("vertices") != vectors.end()){
for (i=0, area = 0.; i<nTriangles; i++){
const CXXCoord &coordA = coordRef(vectors["vertices"], i, 0);
const CXXCoord &coordB = coordRef(vectors["vertices"], i, 1);
const CXXCoord &coordC = coordRef(vectors["vertices"], i, 2);
AB = coordA - coordB;
AC = coordC - coordB;
ABxAC = AB ^ AC;
area += 0.5 * fabs(ABxAC.get3DLength());
}
output << "The Molecular surface area is " << area << endl;
}
if (vectors.find("accessibles") != vectors.end()){
for (i=0, area = 0.; i<nTriangles; i++){
const CXXCoord &coordA = coordRef(vectors["accessibles"], i, 0);
const CXXCoord &coordB = coordRef(vectors["accessibles"], i, 1);
const CXXCoord &coordC = coordRef(vectors["accessibles"], i, 2);
AB = coordA - coordB;
AC = coordC - coordB;
ABxAC = AB ^ AC;
area += 0.5 * fabs(ABxAC.get3DLength());
}
output << "The Solvent Accessible surface area is " << area << endl;
}
map<string, int>::iterator scalar;
int j;
for (scalar = scalars.begin(), j=0; scalar != scalars.end(); ++scalar, j++){
double potential;
for (i=0, pMin = 1e30, pMax = -1e30, pMean = 0.; i<int(vertices.size()); i++){
potential = vertices[i].scalar(scalars[scalar->first]);
pMin = (potential<pMin?potential:pMin);
pMax = (potential>pMax?potential:pMax);
pMean += potential;
}
pMean /= vertices.size();
output << "Property Number " << scalar->second //<< " name " << scalar->first
<< " Range " << pMin << " to " << pMax << " mean " << pMean << endl;
}
return output.str();
}
void NineFourNodeQuadUP::globalShapeFunction(double *dvol, double *w, int nint, int nen, int mode)
{
static double coord[2][9], xs[2][2], det, temp;
int i, j, k, m;
for (i=0; i<3; i++) {
for (j=0; j<nen; j++) {
for (k=0; k<nint; k++) {
if (mode==0) shgu[i][j][k] = shlu[i][j][k];
if (mode==1) shgp[i][j][k] = shlp[i][j][k];
if (mode==2) shgq[i][j][k] = shlq[i][j][k];
}
}
}
for (i=0; i<nen; i++) {
const Vector &coordRef = theNodes[i]->getCrds();
coord[0][i] = coordRef(0);
coord[1][i] = coordRef(1);
}
for (m=0; m<nint; m++) {
for (i=0; i<2; i++) {
for (j=0; j<2; j++) {
xs[i][j] = 0.0;
for (k=0; k<nen; k++) {
if (mode==0) xs[i][j] += coord[j][k]*shgu[i][k][m];
if (mode==1) xs[i][j] += coord[j][k]*shgp[i][k][m];
if (mode==2) xs[i][j] += coord[j][k]*shgq[i][k][m];
}
}
}
det = xs[0][0]*xs[1][1] - xs[0][1]*xs[1][0];
if (det < 0.0) {
opserr << "WARNING NineFourNodeQuadUP: Determinant<=0 in tag "
<< this->getTag();
exit(-1);
}
for (i=0; i<nen; i++) {
if (mode==0) {
temp = (shgu[0][i][m]*xs[1][1] - shgu[1][i][m]*xs[0][1])/det;
shgu[1][i][m] = (-shgu[0][i][m]*xs[1][0] + shgu[1][i][m]*xs[0][0])/det;
shgu[0][i][m] = temp;
}
if (mode==1) {
temp = (shgp[0][i][m]*xs[1][1] - shgp[1][i][m]*xs[0][1])/det;
shgp[1][i][m] = (-shgp[0][i][m]*xs[1][0] + shgp[1][i][m]*xs[0][0])/det;
shgp[0][i][m] = temp;
}
if (mode==2) {
temp = (shgq[0][i][m]*xs[1][1] - shgq[1][i][m]*xs[0][1])/det;
shgq[1][i][m] = (-shgq[0][i][m]*xs[1][0] + shgq[1][i][m]*xs[0][0])/det;
shgq[0][i][m] = temp;
}
}
dvol[m] = w[m]*thickness*det;
} //end of m loop
}
