mirror of https://github.com/QMCPACK/qmcpack.git
Final Test version of Converter for Pyscf. Works with all molecular systems and stores correctly MO for solids with Kpoints. Fixed MO order in Cartesian and Spherical.
This commit is contained in:
Anouar Benali
parent
94149ba6fe
commit
d4f698ab62
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@ -71,7 +71,6 @@ void PyscfParser::parse(const std::string& fname)
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multideterminant=false;
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std::cout <<"Multideterminant: " <<(multideterminant?("yes"):("no")) << std::endl;
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hin.read(SpinRestricted,"SpinResticted");
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if(SpinRestricted)
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@ -119,7 +119,7 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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GroupBasisSet.create_dataset("NbElements",(1,),dtype="i4",data=NbSpecies)
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LCAOName=GroupBasisSet.create_dataset("name",(1,),dtype="S8")
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LCAOName[0:]="LCAOBset"
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LCAOName[0:]="LCAOBSet"
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#atomicBasisSets Group
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for x in range(NbSpecies):
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@ -204,10 +204,22 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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break
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atomicBasisSetGroup.create_dataset("NbBasisGroups",(1,),dtype="i4",data=NbShellIndex)
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Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype="S9")
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Angular[0:]="cartesian"
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if cell.cart==True:
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Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype="S9")
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ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype="S6")
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Angular[0:]="cartesian"
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ExpandYLM[0:]="Gamess"
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else:
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Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype="S9")
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ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype="S5")
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Angular[0:]="spherical"
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ExpandYLM[0:]="pyscf"
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mylen="S"+str(len(uniq_atoms[x][0]))
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elemtype=atomicBasisSetGroup.create_dataset("elementType",(1,),dtype=mylen)
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elemtype[0:]=uniq_atoms[x][0]
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atomicBasisSetGroup.create_dataset("grid_npts",(1,),dtype="i4",data=1001)
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atomicBasisSetGroup.create_dataset("grid_rf",(1,),dtype="i4",data=100)
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@ -231,6 +243,82 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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GroupDet=H5_qmcpack.create_group("determinant")
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if cell.cart==True:
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d_gms_order ={ 0:["s"],
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1:[ "x", "y", "z" ],
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2:[ "xx", "yy", "zz", "xy", "xz", "yz" ],
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3:[ "xxx", "yyy", "zzz", "xxy", "xxz", "yyx", "yyz", "zzx", "zzy", "xyz"],
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4: ["xxxx", "yyyy", "zzzz", "xxxy", "xxxz", "yyyx", "yyyz", "zzzx", "zzzy", "xxyy", "xxzz", "yyzz", "xxyz", "yyxz", "zzxy", "xxxx", "yyyy", "zzzz", "xxxy", "xxxz", "yyyx", "yyyz", "zzzx", "zzzy", "xxyy", "xxzz", "yyzz", "xxyz", "yyxz","zzxy"] }
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d_l = {'s':0,'p':1, 'd':2, 'f':3,'g':4}
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def n_orbital(n):
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if n==0:
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return 1
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elif n==1:
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return 3
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else:
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return 2*n_orbital(n-1)-n_orbital(n-2)+1
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def compare_gamess_style(item1, item2):
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# Warning:
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# - d_gms_order is a global variable
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n1,n2 = map(len,(item1,item2))
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assert (n1 == n2)
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try:
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l = d_gms_order[n1]
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except KeyError:
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return 0
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else:
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a = l.index(item1)
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b = l.index(item2)
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return cmp( a, b )
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ao_label = cell.ao_labels(False)
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# Create a list of shell
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l_l = []
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for label, name, t, l in ao_label:
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# Change yyx -> xyy "
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q = "".join(sorted(l, key=l.count, reverse=True))
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l_l.append(q)
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# Pyscf ordering of shell
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l_order = list(range(len(l_l)))
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# Shell ordering indexed
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n = 1
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l_order_new = []
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for i,(label, name, t, l) in enumerate(ao_label):
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r = d_l[t[-1]]
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# print r,n_orbital(r)
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if n != 1:
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n-=1
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else:
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n = n_orbital(r)
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unordered_l = l_l[i:i+n]
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unordered = l_order[i:i+n]
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#print i,n,unordered
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ordered = [x for _,x in sorted(zip(unordered_l,unordered),key=lambda p: p[0], cmp=compare_gamess_style)]
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l_order_new.extend(ordered)
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def order_mo_coef(ll):
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# Order a list of transposed mo_coeff (Ao,Mo) -> (Mo,Ao) ordered
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# Warning:
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# - l_order_new is used as global variable
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# - gamess order
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ll_new= []
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for l in zip(*ll):
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ll_new.append([l[i] for i in l_order_new])
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return ll_new
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mo_coeff = mf.mo_coeff
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Complex=is_complex(mo_coeff)
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if Complex:
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@ -246,12 +334,15 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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if UnRestricted==False:
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NbMO=len(mo_coeff)
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NbAO=len(mo_coeff[0])
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eigenset=GroupDet.create_dataset("eigenset_0",(NbMO,NbAO),dtype="f8",data=mo_coeff)
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if cell.cart==True:
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eigenset=GroupDet.create_dataset("eigenset_0",(NbMO,NbAO),dtype="f8",data=order_mo_coef(mo_coeff))
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else:
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eigenset=GroupDet.create_dataset("eigenset_0",(NbMO,NbAO),dtype="f8",data=zip(*mo_coeff))
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else:
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NbMO=len(mo_coeff[0])
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NbAO=len(mo_coeff[0][0])
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eigenset_up=GroupDet.create_dataset("eigenset_0",(NbMO,NbAO),dtype="f8",data=mo_coeff[0])
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eigenset_dn=GroupDet.create_dataset("eigenset_1",(NbMO,NbAO),dtype="f8",data=mo_coeff[1])
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eigenset_up=GroupDet.create_dataset("eigenset_0",(NbMO,NbAO),dtype="f8",data=order_mo_coef(mo_coeff[0]))
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eigenset_dn=GroupDet.create_dataset("eigenset_1",(NbMO,NbAO),dtype="f8",data=order_mo_coef(mo_coeff[1]))
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else:
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#Cell Parameters
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GroupCell=H5_qmcpack.create_group("Cell")
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@ -259,7 +350,7 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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Nbkpts=len(kpts)
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GroupDet.create_dataset("Nb_Kpoints",(1,),dtype="i4",data=Nbkpts)
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if UnRestricted==False:
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if not UnRestricted:
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NbMO=len(mo_coeff[0])
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NbAO=len(mo_coeff[0][0])
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else:
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@ -270,12 +361,19 @@ def savetoqmcpack(cell,mf,title="Default",kpts=0):
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GroupKpts.create_dataset("Coord",(1,3),dtype="f8",data=kpts[i])
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GroupSpin=GroupKpts.create_group("spin_Up")
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if not UnRestricted:
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=mo_coeff[i])
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if cell.cart==True:
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=order_mo_coef(mo_coeff[i]))
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else:
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=zip(*mo_coeff[i]))
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GroupSpin.create_dataset("MO_EIGENVALUES",(1,NbMO),dtype="f8",data=mf.mo_energy[i])
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else:
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GroupSpindn=GroupKpts.create_group("spin_Dn")
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=mo_coeff[0][i])
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GroupSpindn.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=mo_coeff[1][i])
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if cell.cart==True:
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=order_mo_coef(mo_coeff[0][i]))
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GroupSpindn.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=order_mo_coef(mo_coeff[1][i]))
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else:
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GroupSpin.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=zip(*mo_coeff[0][i]))
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GroupSpindn.create_dataset("MO_Coeff",(NbMO,NbAO),dtype=mytype,data=zip(*mo_coeff[1][i]))
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GroupSpin.create_dataset("MO_EIGENVALUES",(1,NbMO),dtype="f8",data=mf.mo_energy[0][i])
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GroupSpindn.create_dataset("MO_EIGENVALUES",(1,NbMO),dtype="f8",data=mf.mo_energy[1][i])
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@ -127,14 +127,14 @@ bool AtomicBasisBuilder<RFB>::put(xmlNodePtr cur)
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template<class RFB>
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bool AtomicBasisBuilder<RFB>::putH5(hdf_archive &hin)
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{
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std::string CenterID, Normalized, basisName;
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//TO BE EXPANDED TO OTHER FORMATS
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Morder="Gamess";
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if(myComm->rank()==0){
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hin.read(sph,"angular");
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hin.read(CenterID,"elementType");
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hin.read(Normalized,"normalized");
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hin.read(Morder,"expandYlm");
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hin.read(basisName,"name");
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}
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myComm->bcast(sph);
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@ -580,7 +580,28 @@ int AtomicBasisBuilder<RFB>::expandYlmH5(const std::string& rnl, const QuantumNu
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}
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else
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{
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APP_ABORT(" NON CARTESIAN EXPAND OF BASIS SET NOT IMPLEMENTED WITH HDF5");
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//assign the index for real Spherical Harmonic with (l,m)
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aos->LM[num] = aos->Ylm.index(nlms[q_l],nlms[q_m]);
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//radial orbitals: add only distinct orbitals
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std::map<std::string,int>::iterator rnl_it = RnlID.find(rnl);
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if(rnl_it == RnlID.end())
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{
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int nl = aos->Rnl.size();
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if(radFuncBuilder.addRadialOrbitalH5(hin,nlms))
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//assign the index for radial orbital with (n,l)
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{
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aos->NL[num] = nl;
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RnlID[rnl] = nl;
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}
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}
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else
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{
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//assign the index for radial orbital with (n,l) if repeated
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aos->NL[num] = (*rnl_it).second;
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}
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//increment number of basis functions
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num++;
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}
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return num;
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}
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