bool OrbitalConstraintsBase::getVariables(xmlNodePtr cur)
{
xmlChar* prnode=xmlGetProp(cur,(const xmlChar*)"print");
if(prnode != NULL)
{
PrintTables = xmlStrEqual(prnode,(const xmlChar*)"yes");
}
//save the xml node
myNode=cur;
cur = cur->children;
while(cur != NULL) {
string cname((const char*)(cur->name));
if(cname == "correlation") {
xmlNodePtr cur1=cur->children;
while(cur1 != NULL) {
string cname1((const char*)(cur1->name));
if(cname1 == "parameter") {
getParam(cur1);
}
cur1=cur1->next;
}
} else if(cname == "parameter") {
getParam(cur);
}
cur = cur->next;
} // while cur
return true;
}
void PolyConstraints::addSingleBasisPerSpecies(xmlNodePtr cur)
{
RealType rcut=10.0;
int npts=101;
RealType step=-1.0;
if(myGrid) {
rcut=myGrid->rmax();
npts = myGrid->size();
}
OhmmsAttributeSet gAttrib;
gAttrib.add(rcut,"rf");
BasisGroupType* curBG=0;
cur=cur->children;
while(cur != NULL)
{
string cname((const char*)(cur->name));
string elementType("e");
OhmmsAttributeSet aAttrib;
aAttrib.add(elementType,"elementType");
aAttrib.put(cur);
if(cname == "atomicBasisSet")
{
xmlNodePtr cur1=cur->children;
while(cur1 != NULL)
{
string cname1((const char*)(cur1->name));
if(cname1 == "basisGroup")
{
createBasisGroup(cur1,elementType,rcut);
}
else if(cname1 == "grid")
{
gAttrib.put(cur1);
}
cur1=cur1->next;
}
}
else if(cname == "basisGroup")
{
createBasisGroup(cur,elementType,rcut);
}
else if(cname == "grid")
gAttrib.put(cur);
cur=cur->next;
}
}
void ECPComponentBuilder::addSemiLocal(xmlNodePtr cur)
{
GridType* grid_semilocal=0;
RealType rmax= pp_nonloc->Rmax;
cur=cur->children;
while(cur != NULL)
{
string cname((const char*)cur->name);
if(cname == "grid")
{
grid_semilocal=createGrid(cur);
rmax=grid_semilocal->rmax();
}
else
if(cname == "vps")
{
//should be able to overwrite rmax
int l=angMon[(const char*)xmlGetProp(cur,(const xmlChar*)"l")];
Lmax = std::max(l,Lmax);
xmlNodePtr cur1=cur->children;
while(cur1 != NULL)
{
string cname1((const char*)cur1->name);
if(cname1 == "basisGroup")
{
pp_nonloc->add(l,createVrWithBasisGroup(cur1,grid_semilocal));
}
//else if(cname1 == "data")
//{
// pp_nonloc->add(l,createVrWithData(cur1,grid_semilocal));
//}
cur1=cur1->next;
}
NumNonLocal++;
}
cur=cur->next;
}
pp_nonloc->lmax=Lmax;
pp_nonloc->Rmax=rmax;
}
GridMolecularOrbitals::BasisSetType*
GridMolecularOrbitals::addBasisSet(xmlNodePtr cur)
{
if(!BasisSet)
BasisSet = new BasisSetType(IonSys.getSpeciesSet().getTotalNum());
QuantumNumberType nlms;
string rnl;
//current number of centers
int ncenters = CenterID.size();
int activeCenter;
int gridmode = -1;
bool addsignforM = false;
string sph("default"), Morder("gaussian");
//go thru the tree
cur = cur->xmlChildrenNode;
map<string,RGFBuilderBase*> rbuilderlist;
while(cur!=NULL)
{
string cname((const char*)(cur->name));
if(cname == basis_tag || cname == "atomicBasisSet")
{
int expandlm = GAUSSIAN_EXPAND;
string abasis("invalid"), btype("Numerical");
//Register valid attributes attributes
OhmmsAttributeSet aAttrib;
aAttrib.add(abasis,"elementType");
aAttrib.add(abasis,"species");
aAttrib.add(btype,"type");
aAttrib.add(sph,"angular");
aAttrib.add(addsignforM,"expM");
aAttrib.add(Morder,"expandYlm");
aAttrib.put(cur);
if(abasis == "invalid")
continue;
if(sph == "spherical")
addsignforM=1; //include (-1)^m
if(Morder == "gaussian")
{
expandlm = GAUSSIAN_EXPAND;
}
else
if(Morder == "natural")
{
expandlm = NATURAL_EXPAND;
}
else
if(Morder == "no")
{
expandlm = DONOT_EXPAND;
}
if(addsignforM)
LOGMSG("Spherical Harmonics contain (-1)^m factor")
else
LOGMSG("Spherical Harmonics DO NOT contain (-1)^m factor")
//search the species name
map<string,int>::iterator it = CenterID.find(abasis);
if(it == CenterID.end())
//add the name to the map CenterID
{
if(btype == "Numerical" || btype == "NG" || btype == "HFNG")
{
rbuilder = new NumericalRGFBuilder(cur);
}
else
{
rbuilder = new Any2GridBuilder(cur);
}
//CenterID[abasis] = activeCenter = ncenters++;
CenterID[abasis]=activeCenter=IonSys.getSpeciesSet().findSpecies(abasis);
int Lmax(0); //maxmimum angular momentum of this center
int num(0);//the number of localized basis functions of this center
//process the basic property: maximun angular momentum, the number of basis functions to be added
vector<xmlNodePtr> radGroup;
xmlNodePtr cur1 = cur->xmlChildrenNode;
xmlNodePtr gptr=0;
while(cur1 != NULL)
{
string cname1((const char*)(cur1->name));
if(cname1 == basisfunc_tag || cname1 == "basisGroup")
{
radGroup.push_back(cur1);
int l=atoi((const char*)(xmlGetProp(cur1, (const xmlChar *)"l")));
Lmax = max(Lmax,l);
//expect that only Rnl is given
if(expandlm)
num += 2*l+1;
else
num++;
}
else
if(cname1 == "grid")
{
gptr = cur1;
}
cur1 = cur1->next;
}
XMLReport("Adding a center " << abasis << " centerid "<< CenterID[abasis])
XMLReport("Maximum angular momentum = " << Lmax)
XMLReport("Number of centered orbitals = " << num)
//create a new set of atomic orbitals sharing a center with (Lmax, num)
//if(addsignforM) the basis function has (-1)^m sqrt(2)Re(Ylm)
CenteredOrbitalType* aos = new CenteredOrbitalType(Lmax,addsignforM);
aos->LM.resize(num);
aos->NL.resize(num);
//Now, add distinct Radial Orbitals and (l,m) channels
num=0;
rbuilder->setOrbitalSet(aos,abasis); //assign radial orbitals for the new center
rbuilder->addGrid(gptr); //assign a radial grid for the new center
vector<xmlNodePtr>::iterator it(radGroup.begin());
vector<xmlNodePtr>::iterator it_end(radGroup.end());
while(it != it_end)
{
cur1 = (*it);
xmlAttrPtr att = cur1->properties;
while(att != NULL)
{
string aname((const char*)(att->name));
if(aname == "rid" || aname == "id")
//accept id/rid
{
rnl = (const char*)(att->children->content);
}
else
{
map<string,int>::iterator iit = nlms_id.find(aname);
if(iit != nlms_id.end())
//valid for n,l,m,s
{
nlms[(*iit).second] = atoi((const char*)(att->children->content));
}
}
att = att->next;
}
XMLReport("\n(n,l,m,s) " << nlms[0] << " " << nlms[1] << " " << nlms[2] << " " << nlms[3])
//add Ylm channels
num = expandYlm(rnl,nlms,num,aos,cur1,expandlm);
++it;
}
//add the new atomic basis to the basis set
BasisSet->add(aos,activeCenter);
#if !defined(HAVE_MPI)
rbuilder->print(abasis,1);
#endif
if(rbuilder)
{
delete rbuilder;
rbuilder=0;
}
}
else
{
WARNMSG("Species " << abasis << " is already initialized. Ignore the input.")
}
}
cur = cur->next;
}
GTOMolecularOrbitals::BasisSetType*
GTOMolecularOrbitals::addBasisSet(xmlNodePtr cur) {
if(!BasisSet)
BasisSet = new BasisSetType(IonSys.getSpeciesSet().getTotalNum());
QuantumNumberType nlms;
string rnl;
//current number of centers
int ncenters = CenterID.size();
int activeCenter;
int gridmode = -1;
bool addsignforM = true;
string sph("spherical"), Morder("gaussian");
//go thru the tree
cur = cur->xmlChildrenNode;
while(cur!=NULL) {
string cname((const char*)(cur->name));
if(cname == basis_tag || cname == "atomicBasisSet") {
int expandlm = GAUSSIAN_EXPAND;
string abasis("invalid"), norm("no");
//Register valid attributes attributes
OhmmsAttributeSet aAttrib;
aAttrib.add(abasis,"elementType"); aAttrib.add(abasis,"species");
aAttrib.add(sph,"angular"); aAttrib.add(addsignforM,"expM");
aAttrib.add(Morder,"expandYlm");
aAttrib.add(norm,"normalized");
aAttrib.put(cur);
if(norm == "yes") Normalized=true;
else Normalized=false;
if(abasis == "invalid") continue;
if(sph == "spherical") addsignforM=true; //include (-1)^m
if(sph == "cartesian") addsignforM=false;
if(Morder == "gaussian") {
expandlm = GAUSSIAN_EXPAND;
} else if(Morder == "natural"){
expandlm = NATURAL_EXPAND;
} else if(Morder == "no") {
expandlm = DONOT_EXPAND;
}
if(addsignforM)
LOGMSG("Spherical Harmonics contain (-1)^m factor")
else
LOGMSG("Spherical Harmonics DO NOT contain (-1)^m factor")
map<string,int>::iterator it = CenterID.find(abasis); //search the species name
if(it == CenterID.end()) {//add the name to the map CenterID
//CenterID[abasis] = activeCenter = ncenters++;
CenterID[abasis]=activeCenter=IonSys.getSpeciesSet().findSpecies(abasis);
int Lmax(0); //maxmimum angular momentum of this center
int num(0);//the number of localized basis functions of this center
//process the basic property: maximun angular momentum, the number of basis functions to be added
vector<xmlNodePtr> radGroup;
xmlNodePtr cur1 = cur->xmlChildrenNode;
xmlNodePtr gptr=0;
while(cur1 != NULL) {
string cname1((const char*)(cur1->name));
if(cname1 == basisfunc_tag || cname1 == "basisGroup") {
radGroup.push_back(cur1);
int l=atoi((const char*)(xmlGetProp(cur1, (const xmlChar *)"l")));
Lmax = max(Lmax,l);
if(expandlm)
num += 2*l+1;
else
num++;
}
cur1 = cur1->next;
}
LOGMSG("Adding a center " << abasis << " centerid "<< CenterID[abasis])
LOGMSG("Maximum angular momentum = " << Lmax)
LOGMSG("Number of centered orbitals = " << num)
//create a new set of atomic orbitals sharing a center with (Lmax, num)
//if(addsignforM) the basis function has (-1)^m sqrt(2)Re(Ylm)
CenteredOrbitalType* aos = new CenteredOrbitalType(Lmax,addsignforM);
aos->LM.resize(num);
aos->NL.resize(num);
//Now, add distinct Radial Orbitals and (l,m) channels
num=0;
vector<xmlNodePtr>::iterator it(radGroup.begin());
vector<xmlNodePtr>::iterator it_end(radGroup.end());
while(it != it_end) {
cur1 = (*it);
xmlAttrPtr att = cur1->properties;
while(att != NULL) {
string aname((const char*)(att->name));
if(aname == "rid" || aname == "id") { //accept id/rid
rnl = (const char*)(att->children->content);
} else {
map<string,int>::iterator iit = nlms_id.find(aname);
if(iit != nlms_id.end()) { //valid for n,l,m,s
nlms[(*iit).second] = atoi((const char*)(att->children->content));
}
}
att = att->next;
}
LOGMSG("\n(n,l,m,s) " << nlms[0] << " " << nlms[1] << " " << nlms[2] << " " << nlms[3])
//add Ylm channels
num = expandYlm(rnl,nlms,num,aos,cur1,expandlm);
++it;
}
LOGMSG("Checking the order of angular momentum ")
std::copy(aos->LM.begin(), aos->LM.end(), ostream_iterator<int>(app_log()," "));
app_log() << endl;
//add the new atomic basis to the basis set
BasisSet->add(aos,activeCenter);
}else {
WARNMSG("Species " << abasis << " is already initialized. Ignore the input.")
}
}
cur = cur->next;
}
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;
}
