void TestMain()
{
boost::shared_ptr<A> spA(new A);
boost::shared_ptr<B> spB(new B);
spA->m_spB = spB;
spB->m_spA = spA;
}
/** create Input Analytic function
*
* \xmlonly
* <jastrow name="Jne"
* type="Two-Body|One-Body|Polarization|Three-Body-Geminal"
* function="pade|pade2|no-cusp"
* transform="no|yes" spin="no|yes"
* source="ionic system">
* <grid/>
* <correlation speciesA="sourceSpecies" speciesB="targetSpecies" type="pade|pade2|no-cusp">
* <parameter name=" ">value<parameter>
* </correlation>
* </jastrow>
* \endxmlonly
*/
bool NJABBuilder::putInFunc(xmlNodePtr cur) {
string corr_tag("correlation");
string jastfunction("pade");
int ng=1;
const xmlChar *ftype = xmlGetProp(cur, (const xmlChar *)"function");
if(ftype != NULL) jastfunction = (const char*) ftype;
const xmlChar* s=xmlGetProp(cur,(const xmlChar*)"source");
if(s != NULL) {
map<string,ParticleSet*>::iterator pa_it(ptclPool.find((const char*)s));
if(pa_it == ptclPool.end()) return false;
sourcePtcl = (*pa_it).second;
ng=sourcePtcl->getSpeciesSet().getTotalNum();
}
int ia=0, ib=0, iab=0;
cur = cur->children;
while(cur != NULL) {
string cname((const char*)(cur->name));
if(cname == "grid") {
gridPtr=cur; //save the pointer
} else if(cname == dtable_tag) {
string source_name((const char*)(xmlGetProp(cur,(const xmlChar *)"source")));
map<string,ParticleSet*>::iterator pa_it(ptclPool.find(source_name));
if(pa_it == ptclPool.end()) return false;
sourcePtcl=(*pa_it).second;
ng = sourcePtcl->getSpeciesSet().getTotalNum();
XMLReport("Number of sources " << ng)
InFunc.resize(ng,0);
} else if(cname ==corr_tag) {
if(sourcePtcl==0) return false;
string jfunctype(jastfunction);
string spA((const char*)(xmlGetProp(cur,(const xmlChar *)"speciesA")));
ftype = xmlGetProp(cur, (const xmlChar *)"type");
if(ftype) {
jfunctype=(const char*)ftype;
}
ia = sourcePtcl->getSpeciesSet().findSpecies(spA);
if(!(InFunc[ia])) {
InFuncType *j1=createInFunc(jfunctype);
InFunc[ia]= j1;
app_log() <<" Added Jastrow Correlation ("<<jfunctype
<< ") between " <<spA<<" and "<<targetPtcl.getName() << endl;
}
InFunc[ia]->put(cur);
InFunc[ia]->addOptimizables(targetPsi.VarList);
}
cur = cur->next;
} // while cur
return true;
}
bool NJAABuilder::putInFunc(xmlNodePtr cur) {
string corr_tag("correlation");
string jastfunction("pade");
const xmlChar *ftype = xmlGetProp(cur, (const xmlChar *)"function");
if(ftype) jastfunction = (const char*) ftype;
int ng = targetPtcl.groups();
///happends only once
if(InFunc.size() != ng*ng) {
InFunc.resize(ng*ng,0);
}
int ia=0, ib=0, iab=0;
cur = cur->children;
while(cur != NULL) {
string cname((const char*)(cur->name));
if(cname == "grid") {
gridPtr=cur; //save the pointer
} else if(cname ==corr_tag) {
string spA((const char*)(xmlGetProp(cur,(const xmlChar *)"speciesA")));
string spB((const char*)(xmlGetProp(cur,(const xmlChar *)"speciesB")));
const xmlChar* refptr=xmlGetProp(cur,(const xmlChar *)"ref");
const xmlChar* idptr=xmlGetProp(cur,(const xmlChar *)"id");
if(!IgnoreSpin) { //get the species
ia = targetPtcl.getSpeciesSet().findSpecies(spA);
ib = targetPtcl.getSpeciesSet().findSpecies(spB);
iab = ia*ng+ib;
}
if(!(InFunc[ia*ng+ib])) {
InFuncType *j2=createInFunc(jastfunction,ia,ib);
j2->put(cur,targetPsi.VarList);
InFunc[ia*ng+ib]= j2;
XMLReport("Added Jastrow Correlation between "<<spA<<" and "<<spB)
} else {
int main(int argc, char **argv)
{
if(argc != 4) {
std::cout<<"No enough arugments\n";
exit(0);
}
double alpha = 0.15;
int maxIter = 50;
int n_threads;
std::string meta_file, data_file;
n_threads = atoi(argv[1]);
meta_file = argv[2];
data_file = argv[3];
int row, col, size;
//reading the meta file
std::ifstream fmeta(meta_file.c_str());
fmeta >> row >> col >> size;
double *R = new double[col];
for(int i=0; i<col; i++) {
R[i] = (double)1/col;
}
double *Y = new double[col]();
double *pM = new double[col]();
//create a sparse matrix
pr_spMatrix spA(n_threads, data_file);
spA.getpM(pM, alpha);
spA.initNodes(R, Y);
spA.initEdges(pM);
spA.initV(alpha, col);
//--------timing--------------------
Galois::StatTimer T;
T.start();
for(size_t i=0; i<maxIter; i++) {
spA.pagerank_multiply();
}
T.stop();
int maxTop = 10;
spA.getR(R);
int* idx = new int[col];
sort_idx(R, idx, col);
for(int i=0; i<maxTop; i++) {
printf("rank: %d | %d | %0.15f\n", i+1, idx[i], R[idx[i]]);
}
printf("total running time: %f seconds\n", double(T.get())/1000);
delete[] idx;
delete[] pM;
delete[] Y;
delete[] R;
}
/** Create a two-body Jatrow function with a template
*@param cur the current xmlNode
*@param dummy null pointer used to identify FN
*
*The template class JeeType is a functor which handles the
*evaluation of the function value, gradients and laplacians using
*distance tables. This is a specialized builder function for
*spin-dependent Jastrow function,e.g., for electrons, two functions
*are created for uu(dd) and ud(du).
*/
template <class FN> TwoBodyJastrowOrbital<FN>* JAABuilder::createJAA(xmlNodePtr cur, const string& jname)
{
string corr_tag("correlation");
int ng = targetPtcl.groups();
int ia=0, ib=0, iab=0;
xmlNodePtr gridPtr=NULL;
cur = cur->children;
const SpeciesSet& species(targetPtcl.getSpeciesSet());
typedef TwoBodyJastrowOrbital<FN> JeeType;
JeeType *J2 = new JeeType(targetPtcl,targetPsi.is_manager());
typedef DiffTwoBodyJastrowOrbital<FN> dJ2Type;
dJ2Type *dJ2 = new dJ2Type(targetPtcl);
RealType rc=targetPtcl.Lattice.WignerSeitzRadius;
int pairs=0;
while (cur != NULL)
{
string cname((const char*)(cur->name));
if (cname == corr_tag)
{
string spA("u");
string spB("u");
OhmmsAttributeSet rAttrib;
rAttrib.add(spA, "speciesA");
rAttrib.add(spA, "species1");
rAttrib.add(spB, "speciesB");
rAttrib.add(spB, "species2");
rAttrib.put(cur);
if (spA==targetPsi.getName()) //could have used the particle name
{
spA=species.speciesName[0];
spB=species.speciesName[0];
}
int ia = species.findSpecies(spA);
int ib = species.findSpecies(spB);
if (ia==species.size() || ia == species.size())
{
APP_ABORT("JAABuilder::createJAA is trying to use invalid species");
}
string pairID=spA+spB;
FN *j= new FN;
j->cutoff_radius=rc;
j->put(cur);
J2->addFunc(pairID,ia,ib,j);
dJ2->addFunc(pairID,ia,ib,j);
++pairs;
}
cur = cur->next;
} // while cur
if (pairs)
{
J2->dPsi=dJ2;
string j2name="J2_"+jname;
targetPsi.addOrbital(J2,j2name);
return J2;
}
else
{//clean up and delete the twobody orbitals
APP_ABORT("JAABuilder::put Failed to create Two-Body with "+jname);
return 0;
}
}
bool
JastrowBuilder::createTwoBodySpin(xmlNodePtr cur, JeeType* J2) {
/**\typedef The type of a simple function,e.g., PadeJastrow<double> */
typedef typename JeeType::FuncType FuncType;
int cur_var = targetPsi.VarList.size();
DistanceTableData* d_table = DistanceTable::getTable(DistanceTable::add(targetPtcl));
int ng = targetPtcl.groups();
map<string,FuncType*> jastrowMap;
vector<FuncType*> jastrow(ng*ng);
for(int i=0; i<ng*ng; i++) jastrow[i]=0;
int nj = 0;
cur = cur->children;
while(cur != NULL) {
string cname((const char*)(cur->name));
//if(cname == dtable_tag) {
// string source_name((const char*)(xmlGetProp(cur,(const xmlChar *)"source")));
// //int iptcl = 0;
// map<string,ParticleSet*>::iterator pit(ptclPool.find(source_name));
// if(pit == ptclPool.end()) return false;
// ParticleSet* a = (*pit).second;
// d_table = DistanceTable::getTable(DistanceTable::add(*a));
// ng = a->groups();
// //create a Jastrow function for each pair type
// //for spin 1/2 particles (up-up, down-up = up-down,
// //down-down)
// for(int i=0; i<ng*ng; i++) jastrow.push_back(NULL);
//} else if(cname ==corr_tag) {
if(cname ==corr_tag) {
string spA((const char*)(xmlGetProp(cur,(const xmlChar *)"speciesA")));
string spB((const char*)(xmlGetProp(cur,(const xmlChar *)"speciesB")));
const xmlChar* refptr=xmlGetProp(cur,(const xmlChar *)"ref");
const xmlChar* idptr=xmlGetProp(cur,(const xmlChar *)"id");
int ia = targetPtcl.getSpeciesSet().findSpecies(spA);
int ib = targetPtcl.getSpeciesSet().findSpecies(spB);
int iab = ia*ng+ib;
if(!(jastrow[iab])) {
//create the new Jastrow function
FuncType *j2=NULL;
if(refptr == NULL) {
j2 = new FuncType;
} else {
typename map<string,FuncType*>::iterator it(jastrowMap.find((const char*)refptr));
if(it != jastrowMap.end()) {
j2 = new FuncType((*it).second);
} else {
j2 = new FuncType;
}
}
if(idptr == NULL) {
ostringstream idassigned; idassigned << "j2"<<iab;
jastrowMap[idassigned.str()]=j2;
} else {
jastrowMap[(const char*)idptr]=j2;
}
//initialize
j2->put(cur,targetPsi.VarList);
jastrow[iab]= j2;
if(ia != ib) {//up-down-type pair, treat down-up the same way
jastrow[ib*ng+ia] = j2;
} else {
for(int iaa=0; iaa<ng; iaa++) if(iaa != ia) jastrow[iaa*ng+iaa] = j2;
}
XMLReport("Added Jastrow Correlation between "<<spA<<" and "<<spB)
nj++;
} else {
ERRORMSG("Using an existing Jastrow Correlation "<<spA<<" and "<<spB)
}
}
cur = cur->next;
} // while cur
bool BsplineJastrowBuilder::put(xmlNodePtr cur)
{
ReportEngine PRE(ClassName,"put(xmlNodePtr)");
bool PrintTables=false;
typedef BsplineFunctor<RealType> RadFuncType;
// Create a one-body Jastrow
if (sourcePtcl)
{
string j1spin("no");
OhmmsAttributeSet jAttrib;
jAttrib.add(j1spin,"spin");
jAttrib.put(cur);
#ifdef QMC_CUDA
return createOneBodyJastrow<OneBodyJastrowOrbitalBspline,DiffOneBodySpinJastrowOrbital<RadFuncType> >(cur);
#else
//if(sourcePtcl->IsGrouped)
//{
// app_log() << "Creating OneBodySpinJastrowOrbital<T> " << endl;
// return createOneBodyJastrow<OneBodySpinJastrowOrbital<RadFuncType>,DiffOneBodySpinJastrowOrbital<RadFuncType> >(cur);
//}
//else
//{
// app_log() << "Creating OneBodyJastrowOrbital<T> " << endl;
// return createOneBodyJastrow<OneBodyJastrowOrbital<RadFuncType>,DiffOneBodyJastrowOrbital<RadFuncType> >(cur);
//}
if(j1spin=="yes")
return createOneBodyJastrow<OneBodySpinJastrowOrbital<RadFuncType>,DiffOneBodySpinJastrowOrbital<RadFuncType> >(cur);
else
return createOneBodyJastrow<OneBodyJastrowOrbital<RadFuncType>,DiffOneBodyJastrowOrbital<RadFuncType> >(cur);
#endif
}
else // Create a two-body Jastrow
{
string init_mode("0");
{
OhmmsAttributeSet hAttrib;
hAttrib.add(init_mode,"init");
hAttrib.put(cur);
}
BsplineInitializer<RealType> j2Initializer;
xmlNodePtr kids = cur->xmlChildrenNode;
#ifdef QMC_CUDA
typedef TwoBodyJastrowOrbitalBspline J2Type;
#else
typedef TwoBodyJastrowOrbital<BsplineFunctor<RealType> > J2Type;
#endif
typedef DiffTwoBodyJastrowOrbital<BsplineFunctor<RealType> > dJ2Type;
int taskid=(targetPsi.is_manager())?targetPsi.getGroupID():-1;
J2Type *J2 = new J2Type(targetPtcl,taskid);
dJ2Type *dJ2 = new dJ2Type(targetPtcl);
SpeciesSet& species(targetPtcl.getSpeciesSet());
int chargeInd=species.addAttribute("charge");
//std::map<std::string,RadFuncType*> functorMap;
bool Opt(false);
while (kids != NULL)
{
std::string kidsname((const char*)kids->name);
if (kidsname == "correlation")
{
OhmmsAttributeSet rAttrib;
RealType cusp=-1e10;
string pairType("0");
string spA(species.speciesName[0]);
string spB(species.speciesName[0]);
rAttrib.add(spA,"speciesA");
rAttrib.add(spB,"speciesB");
rAttrib.add(pairType,"pairType");
rAttrib.add(cusp,"cusp");
rAttrib.put(kids);
if(pairType[0]=='0')
{
pairType=spA+spB;
}
else
{
PRE.warning("pairType is deprecated. Use speciesA/speciesB");
//overwrite the species
spA=pairType[0];
spB=pairType[1];
}
int ia = species.findSpecies(spA);
int ib = species.findSpecies(spB);
if(ia==species.size() || ib == species.size())
{
PRE.error("Failed. Species are incorrect.",true);
}
if(cusp<-1e6)
{
RealType qq=species(chargeInd,ia)*species(chargeInd,ib);
cusp = (ia==ib)? -0.25*qq:-0.5*qq;
}
app_log() << " BsplineJastrowBuilder adds a functor with cusp = " << cusp << endl;
RadFuncType *functor = new RadFuncType(cusp);
functor->cutoff_radius = targetPtcl.Lattice.WignerSeitzRadius;
bool initialized_p=functor->put(kids);
functor->elementType=pairType;
if (functor->cutoff_radius < 1.0e-6)
{
app_log() << " BsplineFunction rcut is currently zero.\n"
<< " Setting to Wigner-Seitz radius = "
<< targetPtcl.Lattice.WignerSeitzRadius << endl;
functor->cutoff_radius = targetPtcl.Lattice.WignerSeitzRadius;
functor->reset();
}
//RPA INIT
if(!initialized_p && init_mode =="rpa")
{
app_log() << " Initializing Two-Body with RPA Jastrow " << endl;
j2Initializer.initWithRPA(targetPtcl,*functor,-cusp/0.5);
}
J2->addFunc(ia,ib,functor);
dJ2->addFunc(ia,ib,functor);
Opt=(!functor->notOpt or Opt);
if(qmc_common.io_node)
{
char fname[32];
if(qmc_common.mpi_groups>1)
sprintf(fname,"J2.%s.g%03d.dat",pairType.c_str(),taskid);
else
sprintf(fname,"J2.%s.dat",pairType.c_str());
functor->setReportLevel(ReportLevel,fname);
functor->print();
}
}
kids = kids->next;
}
//dJ2->initialize();
//J2->setDiffOrbital(dJ2);
J2->dPsi=dJ2;
targetPsi.addOrbital(J2,"J2_bspline");
J2->setOptimizable(Opt);
}
return true;
}
