void AsymmetricUnit::SetSpaceGroup(const SpaceGroup &spg)
{
VFN_DEBUG_MESSAGE("AsymmetricUnit::SetSpaceGroup(SpGroup)",5)
tmp_C_Numeric_locale tmploc;
# if 0
TAU_PROFILE("(AsymmetricUnit::SetSpaceGroup)","void (SpaceGroup)",TAU_DEFAULT);
mXmin=0.;
mYmin=0.;
mZmin=0.;
mXmax=1.;
mYmax=1.;
mZmax=1.;
if(1==spg.GetSpaceGroupNumber()) return;//no need to search an asymmetric unit
// Test points=reular grid of points inside the unit cell
// All points must be or have at least a symmetric in the asymmetric unit
const long nbPoints=13;
CrystMatrix_REAL testPoints(nbPoints*nbPoints*nbPoints,3);
{
long l=0;
for(long i=0;i<nbPoints;i++)
for(long j=0;j<nbPoints;j++)
for(long k=0;k<nbPoints;k++)
{
testPoints(l ,0)=i/(REAL)nbPoints;
testPoints(l ,1)=j/(REAL)nbPoints;
testPoints(l++,2)=k/(REAL)nbPoints;
}
}
testPoints += 0.01;
CrystVector_REAL vert(8);//vertices limits
vert(0)=1/8.; vert(1)=1/6.; vert(2)=1/4.; vert(3)=1/3.;
vert(4)=1/2.; vert(5)=2/3.; vert(6)=3/4.; vert(7)=1.;
const int NbStep=vert.numElements();
CrystMatrix_REAL coords;
double junk;
REAL minVolume=1.;
bool allPtsInAsym,tmp;
for(long nx=0;nx<NbStep;nx++)
for(long ny=0;ny<NbStep;ny++)
for(long nz=0;nz<NbStep;nz++)
{
if(minVolume<(vert(nx)*vert(ny)*vert(nz)-.0001)) break;
allPtsInAsym=true;
for(int i=0;i<testPoints.rows();i++)
{
coords=spg.GetAllSymmetrics(testPoints(i,0),testPoints(i,1),testPoints(i,2));
for(long j=0;j<coords.numElements();j++) coords(j)=modf(coords(j)+10.,&junk) ;
tmp=false;
for(long j=0;j<coords.rows();j++)
{//Test if at least one of the symmetrics is in the parallelepiped
if( (coords(j,0) < vert(nx))
&&(coords(j,1) < vert(ny))
&&(coords(j,2) < vert(nz)))
{
//cout << modf(coords(j,0)+10.,junk) << " "
// << modf(coords(j,1)+10.,junk) << " "
// << modf(coords(j,2)+10.,junk) << endl;
tmp=true;
break;
}
}
if(false==tmp)
{
//cout << " Rejected:"<<vert(nx)<<" "<<vert(ny)<<" "<<vert(nz)<<" "<<i<<endl;
//cout << coords <<endl;
allPtsInAsym=false;
break;
}
}
if( (true==allPtsInAsym))
{
mXmax=vert(nx);
mYmax=vert(ny);
mZmax=vert(nz);
VFN_DEBUG_MESSAGE("->ACCEPTED:" << mXmax <<" "<< mYmax <<" "<< mZmax <<endl,2)
//cout << "->ACCEPTED:" << mXmax <<" "<< mYmax <<" "<< mZmax <<endl;
minVolume=vert(nx)*vert(ny)*vert(nz);
break;//no need to grow any more along z
}
}
cout<<"->Finished Generating (pseudo) Asymmetric Unit, with:"<<endl
<<" 0 <= x <= "<< mXmax<<endl
<<" 0 <= y <= "<< mYmax<<endl
<<" 0 <= z <= "<< mZmax<<endl<<endl;
#else
const cctbx::sgtbx::brick b(spg.GetCCTbxSpg().type());
#ifdef __DEBUG__
cout<<"->>Parallelepipedic Asymmetric Unit, from cctbx::sgtbx::brick:"<<endl
<<b.as_string()<<endl;
#endif
mXmin=boost::rational_cast<REAL,int>(b(0,0).value());
mYmin=boost::rational_cast<REAL,int>(b(1,0).value());
mZmin=boost::rational_cast<REAL,int>(b(2,0).value());
mXmax=boost::rational_cast<REAL,int>(b(0,1).value());
mYmax=boost::rational_cast<REAL,int>(b(1,1).value());
mZmax=boost::rational_cast<REAL,int>(b(2,1).value());
#endif
}
void CIFData::ExtractSpacegroup(const bool verbose)
{
map<ci_string,string>::const_iterator positem;
bool found = false;
positem=mvItem.find("_space_group_IT_number");
if(positem!=mvItem.end())
{
mSpacegroupNumberIT=CIFNumeric2Int(positem->second);
found = true;
if(verbose) cout<<"Found spacegroup IT number:"<<mSpacegroupNumberIT<<endl;
}
else
{
positem=mvItem.find("_symmetry_Int_Tables_number");
if(positem!=mvItem.end())
{
mSpacegroupNumberIT=CIFNumeric2Int(positem->second);
found = true;
if(verbose) cout<<"Found spacegroup IT number (with OBSOLETE CIF #1.0 TAG):"<<mSpacegroupNumberIT<<endl;
}
else
mSpacegroupNumberIT=0;
}
positem=mvItem.find("_space_group_name_Hall");
if(positem!=mvItem.end())
{
mSpacegroupSymbolHall=positem->second;
found = true;
if(verbose) cout<<"Found spacegroup Hall symbol:"<<mSpacegroupSymbolHall<<endl;
}
else
{
positem=mvItem.find("_symmetry_space_group_name_Hall");
if(positem!=mvItem.end())
{
mSpacegroupSymbolHall=positem->second;
found = true;
if(verbose) cout<<"Found spacegroup Hall symbol (with OBSOLETE CIF #1.0 TAG):"<<mSpacegroupSymbolHall<<endl;
}
}
positem=mvItem.find("_space_group_name_H-M_alt");
if(positem!=mvItem.end())
{
mSpacegroupHermannMauguin=positem->second;
found = true;
if(verbose) cout<<"Found spacegroup Hermann-Mauguin symbol:"<<mSpacegroupHermannMauguin<<endl;
}
else
{
positem=mvItem.find("_symmetry_space_group_name_H-M");
if(positem!=mvItem.end())
{
mSpacegroupHermannMauguin=positem->second;
found = true;
if(verbose) cout<<"Found spacegroup Hermann-Mauguin symbol (with OBSOLETE CIF #1.0 TAG):"<<mSpacegroupHermannMauguin<<endl;
}
}
if (mSpacegroupSymbolHall.length() > 0)
mSpaceGroup = SpaceGroup::GetSpaceGroup(mSpacegroupSymbolHall);
else
mSpaceGroup=NULL;
if (!mSpaceGroup && mSpacegroupHermannMauguin.length() > 0)
mSpaceGroup = SpaceGroup::GetSpaceGroup(mSpacegroupHermannMauguin);
if (!mSpaceGroup)
mSpaceGroup = SpaceGroup::GetSpaceGroup(mSpacegroupNumberIT);
SpaceGroup *sg = new SpaceGroup();
if (mSpacegroupSymbolHall.length() > 0)
sg->SetHallName(mSpacegroupSymbolHall);
if (mSpacegroupHermannMauguin.length() > 0)
sg->SetHMName(mSpacegroupHermannMauguin);
if (mSpacegroupNumberIT > 0)
sg->SetId(mSpacegroupNumberIT);
positem=mvItem.find("_symmetry_equiv_pos_as_xyz");
if(positem!=mvItem.end())
{
sg->AddTransform (positem->second);
found = true;
}
else for(map<set<ci_string>,map<ci_string,vector<string> > >::const_iterator loop=mvLoop.begin();
loop!=mvLoop.end();++loop)
{
map<ci_string,vector<string> >::const_iterator pos;
unsigned i, nb;
pos=loop->second.find("_symmetry_equiv_pos_as_xyz");
if (pos!=loop->second.end())
{
nb=pos->second.size();
found = true;
for (i = 0; i < nb; i++)
sg->AddTransform(pos->second[i]);
break; // found the transforms, so we have done with them
}
}
if (found)
mSpaceGroup = SpaceGroup::Find(sg);
delete sg;
if (mSpaceGroup != NULL)
// set the space group name to Hall symbol
mSpacegroupSymbolHall = mSpaceGroup->GetHallName();
}
void testSpaceGroupTransformations()
{
// See https://github.com/openbabel/openbabel/pull/254
SpaceGroup group;
vector<string> trans;
vector<string> trans_exp;
vector<string> trans_got;
// Same transformation
trans_exp.push_back("x,y,z");
trans.push_back("x,y,z");
trans.push_back(" x , y , z ");
trans.push_back("x,y+1,z");
trans.push_back("x,y-1,z-1");
trans.push_back("x,y-1,z");
// Same transformation
trans_exp.push_back("x,-y,z");
trans.push_back("x,-y,z");
trans.push_back("x,1-y,z");
trans.push_back("x,-y+1,z");
// Same transformation
trans_exp.push_back("x,-y,-z");
trans.push_back("x,-y,-z");
trans.push_back("x,1-y,1-z");
trans.push_back("x,-y+1,-z+1");
// Same transformation
trans_exp.push_back("x,-y,-y-z");
trans.push_back("x,-y,-z-y");
trans.push_back("x,1-y,-y+1-z");
trans.push_back("x,-y+1,-y-z+1");
// Same transformation
trans_exp.push_back("x,-y,1/6-y-z");
trans.push_back("x,-y,-z-y+1/6");
trans.push_back("x,-y,-z-y+7/6");
trans.push_back("x,1-y,7/6-y+1-z");
trans.push_back("x,-y+1,-y-z+1+1/6");
trans.push_back("x,-y+1,-y+1/6-z+1");
// Same transformation
trans_exp.push_back("x,3/4-y+z,5/6-y-z");
trans.push_back("x,3/4-y+z,-1/6-z-y");
trans.push_back("x,-y+3/4+z,-z-y-1/6");
trans.push_back("x,z-y+3/4,-z-y-7/6");
trans.push_back("x,1+z+3/4-y,-7/6-y-z");
trans.push_back("X , 3 / 4 - Y + 1 + z , - Y - Z - 1 / 6 ");
trans.push_back("x,z-y+1+3/4,-y-1/6-z+1");
vector<string>::const_iterator i, iend;
iend = trans.end();
for (i = trans.begin(); i != iend; ++i)
group.AddTransform(i->c_str());
// Loop over symmetry operators
transform3dIterator ti;
const transform3d *t = group.BeginTransform(ti);
while(t){
trans_got.push_back(t->DescribeAsString());
//cout << t->DescribeAsString() << "\n";
t = group.NextTransform(ti);
}
OB_ASSERT( trans_exp.size() == trans_got.size() );
OB_ASSERT( equal(trans_exp.begin(), trans_exp.end(), trans_got.begin()) );
}
