bool QDwfBuilder::put(xmlNodePtr cur)
{
typedef DiracDeterminant<SPOSet_t> DDet_t;
typedef SlaterDeterminant<SPOSet_t> SDet_t;
map<string,QDwf*> qdwfs;
int nbasis=0;
SDet_t* sdet = new SDet_t;
cur = cur->xmlChildrenNode; /// cur->name = DeterminantSet
while(cur!=NULL)
{
string cname((const char*)(cur->name));
if(cname =="SlaterDeterminant")
{
int first = 0;
xmlNodePtr tcur = cur->xmlChildrenNode;
while(tcur != NULL)
{
string cname2((const char*)(tcur->name));
if(cname2 == "Determinant")
{
SPOSet_t* swfs = new SPOSet_t;
int norb
=atoi((const char*)(xmlGetProp(tcur, (const xmlChar *)"orbitals"))) ;
XMLReport("The number of orbitals for a Dirac Determinant " << norb)
xmlNodePtr t = tcur->xmlChildrenNode;
while(t != NULL)
{
string oname((const char*)(t->name));
if(oname == "Orbital")
{
string
orbname((const char*)(xmlGetProp(t, (const xmlChar *)"name")));
map<string,QDwf*>::iterator it = qdwfs.find(orbname);
if(it == qdwfs.end())
{
XMLReport("Adding a new orbital " << orbname)
QDwf *neworb = new QDwf();
neworb->put(t,wfs_ref.VarList);
swfs->add(neworb);
qdwfs[oname] = neworb;
}
else
{
XMLReport("Using an existing " << orbname)
swfs->add((*it).second);
}
}
t = t->next;
}
XMLReport("The number of basis functions " << swfs->size())
DDet_t* ddet = new DDet_t(*swfs,first);
ddet->set(first,swfs->size());
XMLReport("Adding a determinant to the SlaterDeterminant of size "
<< swfs->size() << " begining with orbital " << first)
first += swfs->size();
sdet->add(ddet);
} //dirac-determinant
tcur = tcur->next;
}
}//slater-determinant
cur = cur->next;
}
wfs_ref.add(sdet);
return true;
}
void GamesXmlParser::getGaussianCenters(vector<xmlNodePtr>& bPtrList) {
//if(bPtrList.size() != aPtrList.size())
gBound.push_back(0);
int offset=0;
double zeta,c;
SizeOfBasisSet=0;
for(int i=0; i<bPtrList.size(); i++) {
string p;
int ng_tot=0,ng;
xmlNodePtr cur=bPtrList[i]->children;
while(cur != NULL) {
string cname((const char*)cur->name);
if(cname == "PSHELL") {
ng_tot++;
xmlNodePtr cur1=cur->children;
int gshellType=1;
while(cur1!= NULL) {
string tname((const char*)cur1->name);
if(tname == "PTYPE") {
putContent(p,cur1);
if(p == "S") {
gshellType=1;
SizeOfBasisSet+=1;
} else if(p == "P") {
gshellType=3;
SizeOfBasisSet+=3;
} else if(p == "D") {
gshellType=4;
SizeOfBasisSet+=5;
}
gShell.push_back(gshellType);
} else if(tname == "PNGAUSS") {
putContent(ng,cur1);
gNumber.push_back(ng);
// ng_tot+=ng;
} else if(tname == "PGAUSSIAN") {
xmlNodePtr cur2=cur1->children;
while(cur2 != NULL) {
string cname2((const char*)cur2->name);
if(cname2 == "PZETA") {
putContent(zeta,cur2);
gExp.push_back(zeta);
} else if(cname2 == "PCONE") {
putContent(c,cur2);
gC0.push_back(c);
}
cur2=cur2->next;
}
cout << "zeta,c " << zeta << " " << c << endl;
}
cur1=cur1->next;
}
}
cur=cur->next;
}
offset+=ng_tot;
gBound.push_back(offset);
}
cout << "Bound of gauassians " << endl;
std::copy(gBound.begin(), gBound.end(),ostream_iterator<int>(cout, " "));
cout << endl;
cout << "Number of shell type " << endl;
std::copy(gShell.begin(), gShell.end(),ostream_iterator<int>(cout, " "));
cout << endl;
cout << "Number of gaussians per shell " << endl;
std::copy(gNumber.begin(), gNumber.end(),ostream_iterator<int>(cout, " "));
cout << endl;
gC1.resize(gC0.size(),0.0);
}
void GamesXmlParser::parse(const std::string& fname) {
xmlDocPtr m_doc = xmlParseFile(fname.c_str());
if (m_doc == NULL) {
ERRORMSG("File " << fname << " is invalid")
xmlFreeDoc(m_doc);
return;
}
xmlNodePtr cur = xmlDocGetRootElement(m_doc);
if(!xmlStrEqual(cur->name,(const xmlChar*)"GAMESS")) {
ERRORMSG("File " << fname << " does not have GAMESS as its root. Invalid")
xmlFreeDoc(m_doc);
return;
}
//xmlNodePtr for atoms
vector<xmlNodePtr> aPtrList;
//xmlNodePtr for eigvectors
vector<xmlNodePtr> ePtrList;
//xmlNodePtr for gaussian basis
vector<xmlNodePtr> bPtrList;
cur=cur->children;
while(cur != NULL) {
string cname((const char*)cur->name);
if(cname == "IN") {
xmlNodePtr cur1=cur->children;
while(cur1 != NULL) {
string cname1((const char*)cur1->name);
if(cname1 == "RUN_TITLE") {
string atitle;
putContent(atitle,cur1);
string::size_type wh=atitle.find("...");
if(wh<atitle.size()) atitle.erase(wh,atitle.size()-wh);
Title = atitle;
} else if(cname1 == "CONTRL") {
getControlParameters(cur1);
}
cur1=cur1->next;
}//everything within IN
} else if(cname == "OUT") {
xmlNodePtr cur1=cur->children;
while(cur1 != NULL) {
string cname1((const char*)cur1->name);
if(cname1 == "SYSTEM_STATE") {
//Unit needs to be generalized!!
string unitL((const char*)xmlGetProp(cur1,(const xmlChar*)"UNITS"));
if(unitL == "ANGS") BohrUnit=false;
xmlNodePtr cur2 = cur1->children;
while(cur2 != NULL) {
string cname2((const char*)cur2->name);
if(cname2 == "ATOM") {
aPtrList.push_back(cur2);
} else if(cname2 == "VEC") {
ePtrList.push_back(cur2);
}
cur2=cur2->next;
}
} else if(cname1 == "PDATA") {
xmlNodePtr cur2 = cur1->children;
while(cur2 != NULL) {
string cname2((const char*)cur2->name);
if(cname2 == "PATOMIC_BASIS_SET") {
bPtrList.push_back(cur2);
}
cur2=cur2->next;
}
}
cur1=cur1->next;
}//everything within OUT
}
cur=cur->next;
}
//xmlXPathContextPtr m_context = xmlXPathNewContext(m_doc);
getGeometry(aPtrList);
getGaussianCenters(bPtrList);
getEigVectors(ePtrList);
//xmlXPathFreeContext(m_context);
xmlFreeDoc(m_doc);
}
ParticleSet* ParticleSetPool::createESParticleSet(xmlNodePtr cur, const string& target)
{
TinyVector<int,OHMMS_DIM> tilefactor;
Tensor<int,OHMMS_DIM> tilematrix(1,0,0,0,1,0,0,0,1);
double lr_cut=10;
string h5name;
string source("i");
string bc("p p p");
OhmmsAttributeSet attribs;
attribs.add(h5name, "href");
attribs.add(tilefactor, "tile");
attribs.add(tilematrix, "tilematrix");
attribs.add(source, "source");
attribs.add(bc, "bconds");
attribs.add(lr_cut, "LR_dim_cutoff");
attribs.put(cur);
ParticleSet* ions=getParticleSet(source);
if(ions==0)
{
ions=new MCWalkerConfiguration;
ions->setName(source);
}
//set the boundary condition
ions->Lattice.LR_dim_cutoff=lr_cut;
std::istringstream is(bc);
char c;
int idim=0;
while(!is.eof() && idim<OHMMS_DIM)
{
if(is>>c) ions->Lattice.BoxBConds[idim++]=(c=='p');
}
//initialize ions from hdf5
hid_t h5=-1;
if(myComm->rank()==0)
h5 = H5Fopen(h5name.c_str(),H5F_ACC_RDONLY,H5P_DEFAULT);
ESHDFIonsParser ap(*ions,h5,myComm);
ap.put(cur);
ap.expand(tilematrix);
if(h5>-1) H5Fclose(h5);
//failed to initialize the ions
if(ions->getTotalNum() == 0) return 0;
typedef ParticleSet::SingleParticleIndex_t SingleParticleIndex_t;
vector<SingleParticleIndex_t> grid(OHMMS_DIM,SingleParticleIndex_t(1));
ions->Lattice.reset();
ions->Lattice.makeGrid(grid);
if(SimulationCell==0)
{
SimulationCell = new ParticleSet::ParticleLayout_t(ions->Lattice);
}
//create the electrons
MCWalkerConfiguration* qp = new MCWalkerConfiguration;
qp->setName(target);
qp->Lattice.copy(ions->Lattice);
//qp->Lattice.reset();
//qp->Lattice.makeGrid(grid);
app_log() << " Simulation cell radius = " << qp->Lattice.SimulationCellRadius << endl;
app_log() << " Wigner-Seitz radius = " << qp->Lattice.WignerSeitzRadius << endl;
SimulationCell->print(app_log());
myPool[target]=qp;
myPool[source]=ions;
//addParticleSet(qp);
//addParticleSet(ions);
{//get the number of electrons per spin
vector<int> num_spin;
xmlNodePtr cur1=cur->children;
while(cur1!=NULL)
{
string cname1((const char*)cur1->name);
if(cname1 == OrbitalBuilderBase::sd_tag)
{
num_spin.clear();
xmlNodePtr cur2=cur1->children;
while(cur2!=NULL)
{
string cname2((const char*)cur2->name);
if(cname2 == OrbitalBuilderBase::det_tag)
{
int n=0;
OhmmsAttributeSet a;
a.add(n,"size");
a.put(cur2);
if(num_spin.size()<2) num_spin.push_back(n);
}
cur2=cur2->next;
}
}
cur1=cur1->next;
}
//create species
SpeciesSet& species=qp->getSpeciesSet();
//add up and down
species.addSpecies("u");
if(num_spin.size()>1) species.addSpecies("d");
int chid=species.addAttribute("charge");
for(int i=0; i<num_spin.size(); ++i) species(chid,i)=-1.0;
int mid=species.addAttribute("membersize");
for(int i=0; i<num_spin.size(); ++i) species(mid,i)=num_spin[i];
mid=species.addAttribute("mass");
for(int i=0; i<num_spin.size(); ++i) species(mid,i)=1.0;
qp->create(num_spin);
}
//name it with the target
qp->setName(target);
//assign non-trivial positions for the quanmtum particles
if(qp->Lattice.SuperCellEnum)
{
makeUniformRandom(qp->R);
qp->R.setUnit(PosUnit::LatticeUnit);
qp->convert2Cart(qp->R);
qp->createSK();
}
else
{
InitMolecularSystem mole(this);
if(ions->getTotalNum()>1)
mole.initMolecule(ions,qp);
else
mole.initAtom(ions,qp);
}
//for(int i=0; i<qp->getTotalNum(); ++i)
// cout << qp->GroupID[i] << " " << qp->R[i] << endl;
if(qp->getTotalNum() == 0 || ions->getTotalNum() == 0)
{
delete qp;
delete ions;
APP_ABORT("ParticleSetPool failed to create particlesets for the electron structure calculation");
return 0;
}
return qp;
}
