/*!\fn int DistanceTable::add(const ParticleSet& s,const ParticleSet& t, const char* aname)
*\param s source particle set
*\param s target particle set
*\param aname of a new DistanceTableData
*\return index of the distance table with the name
*\brief Adding AsymmetricDTD to the list, e.g., el-nuclei distance table
*/
int
DistanceTable::add(const ParticleSet& s, const ParticleSet& t,
const char* aname) {
string newname;
if(aname) {
newname = aname;
} else {
newname = s.getName();
newname.append(t.getName());
}
LOGMSG("Creating a distance table with " << newname)
map<string,int>::iterator it = TableMap.find(newname);
///the named pair does not exist, add a new asymmetric metrics
if(it == TableMap.end()) {
int n = TableList.size();
TableList.push_back(new AsymmetricDTD<NoBConds<double,3> > (s,t));
TableMap[newname] = n;
VisitorID.push_back(t.tag());
return n;
} else {
return (*it).second;
}
}
ParticleSet::ParticleSet(const ParticleSet& p)
: UseBoundBox(p.UseBoundBox), UseSphereUpdate(p.UseSphereUpdate),IsGrouped(p.IsGrouped)
, ThreadID(0), mySpecies(p.getSpeciesSet()),SK(0), ParentTag(p.tag())
{
initBase();
initParticleSet();
assign(p); //obly the base is copied, assumes that other properties are not assignable
//need explicit copy:
Mass=p.Mass;
Z=p.Z;
ostringstream o;
o<<p.getName()<<ObjectTag;
this->setName(o.str());
app_log() << " Copying a particle set " << p.getName() << " to " << this->getName() << " groups=" << groups() << endl;
PropertyList.Names=p.PropertyList.Names;
PropertyList.Values=p.PropertyList.Values;
PropertyHistory=p.PropertyHistory;
Collectables=p.Collectables;
//construct the distance tables with the same order
//first is always for this-this paier
for (int i=1; i<p.DistTables.size(); ++i)
addTable(p.DistTables[i]->origin());
if(p.SK)
{
R.InUnit=p.R.InUnit;
createSK();
SK->DoUpdate=p.SK->DoUpdate;
}
if (p.Sphere.size())
resizeSphere(p.Sphere.size());
add_p_timer(myTimers);
myTwist=p.myTwist;
}
StressPBCAA::StressPBCAA(ParticleSet& ref, bool active) :
AA(0), myGrid(0), rVs(0), FirstTime(true), myConst(0.0), ForceBase(ref,ref), Ps(ref), is_active(active)
{
ReportEngine PRE("StressPBCAA","StressPBCAA");
//save source tag
SourceID=ref.tag();
//create a distance table: just to get the table name
DistanceTableData *d_aa = DistanceTable::add(ref);
PtclRefName=d_aa->Name;
initBreakup(ref);
prefix="S_"+PtclRefName;
app_log() << " Maximum K shell " << AA->MaxKshell << endl;
app_log() << " Number of k vectors " << AA->Fk.size() << endl;
if(!is_active)
{
d_aa->evaluate(ref);
update_source(ref);
app_log()<<"Evaluating Stress SymTensor::Long Range\n";
sLR=evalLR(ref);
app_log()<<"Short Range...\n";
sSR=evalSR(ref);
stress=sLR+sSR+myConst;
//RealType eL(0.0), eS(0.0);
//if (computeForces)
//{
// forces = 0.0;
// eS=evalSRwithForces(ref);
// // 1.3978248322
// eL=evalLRwithForces(ref);
// // 2.130267378
//}
//else
//{
// eL=evalLR(ref);
// eS=evalSR(ref);
//}
//NewValue=Value = eL+eS+myConst;
//app_log() << " Fixed Coulomb potential for " << ref.getName();
//app_log() << "\n e-e Madelung Const. =" << MC0
// << "\n Vtot =" << Value << endl;
}
app_log() << " Stress SymTensor components for " << ref.getName();
app_log() << "\n e-e Madelung Const. =\n" << MC0
<< "\n Stot =\n" << stress
<< "\n S_SR =\n" << sSR
<< "\n S_LR =\n" << sLR
<< "\n S_Const =\n" << myConst<<endl;
}
/** process an xml element
* @param cur current xmlNodePtr
* @return true, if successful.
*
* Creating MCWalkerConfiguration for all the ParticleSet
* objects.
*/
bool ParticleSetPool::put(xmlNodePtr cur)
{
ReportEngine PRE("ParticleSetPool","put");
//const ParticleSet::ParticleLayout_t* sc=DistanceTable::getSimulationCell();
//ParticleSet::ParticleLayout_t* sc=0;
string id("e"), role("none");
OhmmsAttributeSet pAttrib;
pAttrib.add(id,"id"); pAttrib.add(id,"name");
pAttrib.add(role,"role");
pAttrib.put(cur);
//backward compatibility
if(id == "e" && role=="none") role="MC";
ParticleSet* pTemp = getParticleSet(id);
if(pTemp == 0)
{
app_log() << " Creating " << id << " particleset" << endl;
pTemp = new MCWalkerConfiguration;
//if(role == "MC")
// pTemp = new MCWalkerConfiguration;
//else
// pTemp = new ParticleSet;
if(SimulationCell)
{
app_log() << " Initializing the lattice of " << id << " by the global supercell" << endl;
pTemp->Lattice.copy(*SimulationCell);
}
myPool[id] = pTemp;
XMLParticleParser pread(*pTemp,TileMatrix);
bool success = pread.put(cur);
pTemp->setName(id);
app_log() << pTemp->getName() <<endl;
return success;
} else {
app_warning() << "particleset " << id << " is already created. Ignore this" << endl;
}
return true;
}
int main(int argc, char **argv) {
using namespace ohmmsqmc;
xmlDocPtr m_doc;
xmlNodePtr m_root;
xmlXPathContextPtr m_context;
enum {SourceIndex = DistanceTableData::SourceIndex};
OHMMS::Controller->initialize(argc,argv);
OhmmsInfo welcome(argc,argv,OHMMS::Controller->mycontext());
///project description
OHMMS::ProjectData myProject;
///random number controller
OHMMS::RandomNumberControl myRandomControl;
if(argc>1) {
// build an XML tree from a the file;
LOGMSG("Opening file " << argv[1])
m_doc = xmlParseFile(argv[1]);
if (m_doc == NULL) {
ERRORMSG("File " << argv[1] << " is invalid")
xmlFreeDoc(m_doc);
return 1;
}
// Check the document is of the right kind
m_root = xmlDocGetRootElement(m_doc);
if (m_root == NULL) {
ERRORMSG("Empty document");
xmlFreeDoc(m_doc);
return 1;
}
} else {
WARNMSG("No argument is given. Assume that does not need an input file")
}
m_context = xmlXPathNewContext(m_doc);
xmlXPathObjectPtr result
= xmlXPathEvalExpression((const xmlChar*)"//project",m_context);
if(xmlXPathNodeSetIsEmpty(result->nodesetval)) {
WARNMSG("Project is not defined")
myProject.reset();
} else {
myProject.put(result->nodesetval->nodeTab[0]);
}
xmlXPathFreeObject(result);
//initialize the random number generator
xmlNodePtr rptr = myRandomControl.initialize(m_context);
if(rptr) {
xmlAddChild(m_root,rptr);
}
///the ions
ParticleSet ion;
MCWalkerConfiguration el;
el.setName("e");
int iu = el.Species.addSpecies("u");
int id = el.Species.addSpecies("d");
int icharge = el.Species.addAttribute("charge");
el.Species(icharge,iu) = -1;
el.Species(icharge,id) = -1;
bool init_els = determineNumOfElectrons(el,m_context);
result
= xmlXPathEvalExpression((const xmlChar*)"//particleset",m_context);
xmlNodePtr el_ptr=NULL, ion_ptr=NULL;
for(int i=0; i<result->nodesetval->nodeNr; i++) {
xmlNodePtr cur=result->nodesetval->nodeTab[i];
xmlChar* aname= xmlGetProp(cur,(const xmlChar*)"name");
if(aname) {
char fc = aname[0];
if(fc == 'e') {
el_ptr=cur;
}
else if(fc == 'i') {
ion_ptr=cur;
}
}
}
bool donotresize = false;
if(init_els) {
el.setName("e");
XMLReport("The configuration for electrons is already determined by the wave function")
donotresize = true;
}
if(el_ptr) {
XMLParticleParser pread(el,donotresize);
pread.put(el_ptr);
}
if(ion_ptr) {
XMLParticleParser pread(ion);
pread.put(ion_ptr);
}
xmlXPathFreeObject(result);
if(!ion.getTotalNum()) {
ion.setName("i");
ion.create(1);
ion.R[0] = 0.0;
}
//The ion-ion distance-table
DistanceTableData* d_ii = DistanceTable::getTable(DistanceTable::add(ion));
d_ii->create(1);
d_ii->evaluate(ion);
vector<double> Cut, Core;
int Centers = ion.getTotalNum();
//attribute id for cut
int icut = ion.Species.addAttribute("cut");
//store the max distance from atom
Cut.resize(Centers);
for(int iat=0; iat<Centers; iat++) {
int id = ion.GroupID[iat];
Cut[iat] = ion.Species(icut,id);
}
int icore = ion.Species.addAttribute("core");
//store the max distance from atom
Core.resize(Centers);
for(int iat=0; iat<Centers; iat++) {
Core[iat]=ion.Species(icore,ion.GroupID[iat]);
}
//3N-dimensional Gaussian
ParticleSet::ParticlePos_t chi(el.getTotalNum());
makeGaussRandom(chi);
//determine if odd or even number of particles
int irem = el.getTotalNum()%2;
int ihalf = el.getTotalNum()/2;
//assign the core
int ncore(0);
for(int iat=0; iat<Centers; iat++) {
double sep=0.8*Cut[iat];
for(int iel=0; iel<Core[iat]/2; iel++,ncore++) {
el.R[ncore]=ion.R[iat]+sep*chi[ncore];
el.R[ncore+ihalf]=ion.R[iat]+sep*chi[ncore+ihalf];
}
}
int ipart = ncore;
int isave_iat=0;
for(int iat=0; iat<Centers; iat++) {
for(int nn=d_ii->M[iat]; nn<d_ii->M[iat+1]; nn++) {
double bondlength = d_ii->r(nn);
int jat = d_ii->J[nn];
//only assign if the half bond-length < cutoff
if(bondlength < Cut[iat]+Cut[jat]) {
if(ipart < ihalf) {
XMLReport("Assigning particles = " << ipart << " and " << ipart+ihalf)
/*place 2 electrons (an up and a down) at half
the bond-length plus a random number multiplied
by 10% of the bond-length*/
el.R[ipart] = ion.R[iat]+0.5*d_ii->dr(nn)+0.1*bondlength*chi[ipart];
el.R[ipart+ihalf] = ion.R[iat]+0.5*d_ii->dr(nn)+0.1*bondlength*chi[ipart+ihalf];
ipart++;
isave_iat = iat;
}
}
}
}
//assign the last particle (if odd number of particles)
int flag = 1;
ipart = el.getTotalNum()-1;
if(irem) {
XMLReport("Assigning last particle.")
for(int iat = isave_iat+1; iat<Centers; iat++) {
for(int nn=d_ii->M[iat]; nn<d_ii->M[iat+1]; nn++) {
double bondlength = d_ii->r(nn);
if((0.5*bondlength < Cut[iat]) && flag) {
XMLReport("Assigning particle = " << ipart)
el.R[ipart] = ion.R[iat]+0.5*d_ii->dr(nn)+0.1*bondlength*chi[ipart];
flag = 0;
}
}
}
}
cout << "Ionic configuration : " << ion.getName() << endl;
ion.get(cout);
cout << "Electronic configuration : " << el.getName() << endl;
el.get(cout);
string newxml(myProject.CurrentRoot());
newxml.append(".ptcl.xml");
ofstream ptcl_out(newxml.c_str());
/*
ofstream molmol("assign.xyz");
molmol << Centers+el.getTotalNum() << endl;
molmol << endl;
for(int iat=0; iat<Centers; iat++)
molmol << ion.Species.speciesName[ion.GroupID[iat]] << 0.5292*ion.R[iat] << endl;
for(int ipart=0; ipart<el.getTotalNum(); ipart++)
molmol << "He" << 0.5292*el.R[ipart] << endl;
molmol.close();
*/
xmlXPathFreeContext(m_context);
xmlFreeDoc(m_doc);
int nup = el.last(0);
int ndown = el.last(1)-el.last(0);
ptcl_out << "<?xml version=\"1.0\"?>" << endl;
ptcl_out << "<particleset name=\"e\">" << endl;
ptcl_out << "<group name=\"u\" size=\"" << nup << "\">" << endl;
ptcl_out << "<parameter name=\"charge\">-1</parameter>" << endl;
ptcl_out << "<attrib name=\"position\" datatype=\"posArray\">" << endl;
for (int ipart=0; ipart<nup; ++ipart)
ptcl_out << el.R[ipart] << endl;
ptcl_out << "</attrib>" << endl;
ptcl_out << "</group>" << endl;
ptcl_out << "<group name=\"d\" size=\"" << ndown << "\">" << endl;
ptcl_out << "<parameter name=\"charge\">-1</parameter>" << endl;
ptcl_out << "<attrib name=\"position\" datatype=\"posArray\">" << endl;
for (int ipart=nup; ipart<el.getTotalNum(); ++ipart)
ptcl_out << el.R[ipart] << endl;
ptcl_out << "</attrib>" << endl;
ptcl_out << "</group>" << endl;
ptcl_out << "</particleset>" << endl;
OHMMS::Controller->finalize();
return 0;
}
