mirror of https://github.com/QMCPACK/qmcpack.git
Python2 and Python 3 converter
This commit is contained in:
anbenali
parent
ea23ca60d7
commit
b02b389d91
|
|
@ -23,7 +23,16 @@ def savetoqmcpack(cell,mf,title="Default",kpts=[]):
|
|||
Gamma=False
|
||||
UnRestricted=False
|
||||
Complex=False
|
||||
|
||||
Python3=False
|
||||
Python2=False
|
||||
|
||||
if sys.version_info >= (3, 0):
|
||||
sys.stdout.write("Using Python 3.x\n")
|
||||
Python3=True
|
||||
else:
|
||||
sys.stdout.write("Using Python 2.x\n")
|
||||
Python2=True
|
||||
|
||||
|
||||
val=str(mf)
|
||||
ComputeMode= re.split('[. ]',val)
|
||||
|
|
@ -44,11 +53,18 @@ def savetoqmcpack(cell,mf,title="Default",kpts=[]):
|
|||
IonName=dict([('H',1), ('He',2), ('Li',3),('Be',4), ('B', 5), ('C', 6), ('N', 7),('O', 8), ('F', 9), ('Ne',10), ('Na',11),('Mg',12), ('Al',13), ('Si',14), ('P', 15), ('S', 16),('Cl',17), ('Ar',18), ('K', 19), ('Ca',20), ('Sc',21), ('Ti',22), ('V', 23), ('Cr',24), ('Mn',25), ('Fe',26), ('Co',27), ('Ni',28), ('Cu',29), ('Zn',30), ('Ga',31), ('Ge',32), ('As',33), ('Se',34), ('Br',35), ('Kr',36), ('Rb',37), ('Sr',38), ('Y', 39), ('Zr',40), ('Nb',41), ('Mo',42), ('Tc',43), ('Ru',44), ('Rh',45), ('Pd',46), ('Ag',47), ('Cd',48), ('In',49), ('Sn',50), ('Sb',51), ('Te',52), ('I', 53), ('Xe',54), ('Cs',55), ('Ba',56), ('La',57), ('Ce',58), ('Pr',59), ('Nd',60), ('Pm',61), ('Sm',62), ('Eu',63), ('Gd',64), ('Tb',65), ('Dy',66), ('Ho',67), ('Er',68), ('Tm',69), ('Yb',70), ('Lu',71), ('Hf',72), ('Ta',73), ('W', 74), ('Re',75), ('Os',76), ('Ir',77), ('Pt',78), ('Au',79), ('Hg',80), ('Tl',81), ('Pb',82), ('Bi',83), ('Po',84), ('At',85), ('Rn',86), ('Fr',87), ('Ra',88), ('Ac',89), ('Th',90), ('Pa',91), ('U', 92), ('Np',93)])
|
||||
|
||||
|
||||
|
||||
H5_qmcpack=h5py.File(title+'.h5','w')
|
||||
groupApp=H5_qmcpack.create_group("application")
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
CodeData = groupApp.create_dataset("code",(1,),dtype=dt)
|
||||
CodeData[0:] = "PySCF"
|
||||
if Python3:
|
||||
strList=['PySCF']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
groupApp.create_dataset('code', (1,),'S5', asciiList)
|
||||
else:
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
CodeData = groupApp.create_dataset("code",(1,),dtype=dt)
|
||||
CodeData[0:] = "PySCF"
|
||||
|
||||
CodeVer = groupApp.create_dataset("version",(3,),dtype="i4")
|
||||
CodeVer[0:] = 1
|
||||
CodeVer[1:] = 4
|
||||
|
|
@ -100,10 +116,16 @@ def savetoqmcpack(cell,mf,title="Default",kpts=[]):
|
|||
atmname=str(uniq_atoms[x][0])
|
||||
groupSpecies=groupAtom.create_group("species_"+str(x))
|
||||
groupSpecies.create_dataset("atomic_number",(1,),dtype="i4",data=uniq_atoms[x][1])
|
||||
#mylen="S"+str(len(atmname))
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
AtmName=groupSpecies.create_dataset("name",(1,),dtype=dt)
|
||||
AtmName[0:]=atmname
|
||||
if Python3:
|
||||
mylen="S"+str(len(atmname))
|
||||
strList=[atmname]
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
groupSpecies.create_dataset('name', (1,),mylen, asciiList)
|
||||
else:
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
AtmName=groupSpecies.create_dataset("name",(1,),dtype=dt)
|
||||
AtmName[0:]=atmname
|
||||
|
||||
groupSpecies.create_dataset("charge",(1,),dtype="f8",data=uniq_atoms[x][2])
|
||||
groupSpecies.create_dataset("core",(1,),dtype="f8",data=uniq_atoms[x][3])
|
||||
SpeciesID=groupAtom.create_dataset("species_ids",(natom,),dtype="i4")
|
||||
|
|
@ -130,68 +152,124 @@ def savetoqmcpack(cell,mf,title="Default",kpts=[]):
|
|||
GroupBasisSet=H5_qmcpack.create_group("basisset")
|
||||
#Dataset Number Of Atoms
|
||||
GroupBasisSet.create_dataset("NbElements",(1,),dtype="i4",data=NbSpecies)
|
||||
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
LCAOName=GroupBasisSet.create_dataset("name",(1,),dtype=dt)
|
||||
LCAOName[0:]="LCAOBSet"
|
||||
if Python3:
|
||||
strList=['LCAOBSet']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
GroupBasisSet.create_dataset('name', (1,),'S8', asciiList)
|
||||
else:
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
LCAOName=GroupBasisSet.create_dataset("name",(1,),dtype=dt)
|
||||
LCAOName[0:]="LCAOBSet"
|
||||
|
||||
#atomicBasisSets Group
|
||||
for x in range(NbSpecies):
|
||||
|
||||
MyIdx=idxAtomstoSpecies[x]
|
||||
atomicBasisSetGroup=GroupBasisSet.create_group("atomicBasisSet"+str(x))
|
||||
mylen="S"+str(len(uniq_atoms[x][0]))
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
elemtype=atomicBasisSetGroup.create_dataset("elementType",(1,),dtype=dt)
|
||||
elemtype[0:]=uniq_atoms[x][0]
|
||||
if cell.cart==True:
|
||||
Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype=dt)
|
||||
ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype=dt)
|
||||
Angular[0:]="cartesian"
|
||||
ExpandYLM[0:]="Gamess"
|
||||
|
||||
if Python3:
|
||||
mylen="S"+str(len(uniq_atoms[x][0]))
|
||||
strList=[uniq_atoms[x][0]]
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('elementType', (1,),mylen, asciiList)
|
||||
if cell.cart==True:
|
||||
strList=['cartesian']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('angular', (1,),'S9', asciiList)
|
||||
|
||||
strList=['Gamess']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('expandYlm', (1,),'S6', asciiList)
|
||||
|
||||
else:
|
||||
strList=['spherical']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('angular', (1,),'S9', asciiList)
|
||||
|
||||
strList=['pyscf']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('expandYlm', (1,),'S5', asciiList)
|
||||
else:
|
||||
Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype=dt)
|
||||
ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype=dt)
|
||||
Angular[0:]="spherical"
|
||||
ExpandYLM[0:]="pyscf"
|
||||
dt = h5py.special_dtype(vlen=str)
|
||||
elemtype=atomicBasisSetGroup.create_dataset("elementType",(1,),dtype=dt)
|
||||
elemtype[0:]=uniq_atoms[x][0]
|
||||
if cell.cart==True:
|
||||
Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype=dt)
|
||||
ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype=dt)
|
||||
Angular[0:]="cartesian"
|
||||
ExpandYLM[0:]="Gamess"
|
||||
else:
|
||||
Angular=atomicBasisSetGroup.create_dataset("angular",(1,),dtype=dt)
|
||||
Angular[0:]="spherical"
|
||||
ExpandYLM=atomicBasisSetGroup.create_dataset("expandYlm",(1,),dtype=dt)
|
||||
ExpandYLM[0:]="pyscf"
|
||||
|
||||
|
||||
|
||||
atomicBasisSetGroup.create_dataset("grid_npts",(1,),dtype="i4",data=1001)
|
||||
atomicBasisSetGroup.create_dataset("grid_rf",(1,),dtype="i4",data=100)
|
||||
atomicBasisSetGroup.create_dataset("grid_ri",(1,),dtype="f8",data=1e-06)
|
||||
gridType=atomicBasisSetGroup.create_dataset("grid_type",(1,),dtype=dt)
|
||||
gridType[0:]="log"
|
||||
|
||||
|
||||
if (len(cell.basis)<=2):
|
||||
nameBase=atomicBasisSetGroup.create_dataset("name",(1,),dtype=dt)
|
||||
nameBase[0:]="gaussian"
|
||||
|
||||
if Python3:
|
||||
strList=['log']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('grid_type', (1,),'S3', asciiList)
|
||||
if (len(cell.basis)<=2):
|
||||
strList=['gaussian']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('name', (1,),'S8', asciiList)
|
||||
else:
|
||||
mylen="S"+str(len(cell.basis))
|
||||
strList=[cell.basis]
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('name', (1,),mylen, asciiList)
|
||||
strList=['no']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
atomicBasisSetGroup.create_dataset('normalized', (1,),'S2', asciiList)
|
||||
else:
|
||||
mylen="S"+str(len(cell.basis))
|
||||
nameBase=atomicBasisSetGroup.create_dataset("name",(1,),dtype=dt)
|
||||
nameBase[0:]=cell.basis
|
||||
gridType=atomicBasisSetGroup.create_dataset("grid_type",(1,),dtype=dt)
|
||||
gridType[0:]="log"
|
||||
if (len(cell.basis)<=2):
|
||||
nameBase=atomicBasisSetGroup.create_dataset("name",(1,),dtype=dt)
|
||||
nameBase[0:]="gaussian"
|
||||
else:
|
||||
nameBase=atomicBasisSetGroup.create_dataset("name",(1,),dtype=dt)
|
||||
nameBase[0:]=cell.basis
|
||||
|
||||
Normalized=atomicBasisSetGroup.create_dataset("normalized",(1,),dtype=dt)
|
||||
Normalized[0:]="no"
|
||||
|
||||
|
||||
|
||||
Normalized=atomicBasisSetGroup.create_dataset("normalized",(1,),dtype=dt)
|
||||
Normalized[0:]="no"
|
||||
|
||||
|
||||
|
||||
|
||||
nshell = cell.atom_shell_ids(MyIdx)
|
||||
n = 0
|
||||
n=0
|
||||
for i in nshell:
|
||||
l = cell.bas_angular(i)
|
||||
contracted_coeffs = cell.bas_ctr_coeff(i)
|
||||
contracted_exp =cell.bas_exp(i)
|
||||
for line in zip(*contracted_coeffs):
|
||||
BasisGroup=atomicBasisSetGroup.create_group("basisGroup"+str(n))
|
||||
basisType=BasisGroup.create_dataset("type",(1,),dtype=dt)
|
||||
basisType[0:]="Gaussian"
|
||||
|
||||
|
||||
mylen="S"+str(len((uniq_atoms[x][0]+str(n)+str(l))))
|
||||
RID=BasisGroup.create_dataset("rid",(1,),dtype=dt)
|
||||
RID[0:]=(uniq_atoms[x][0]+str(n)+str(l))
|
||||
|
||||
if Python3:
|
||||
strList=['Gaussian']
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
BasisGroup.create_dataset('type',(1,),'S8',asciiList)
|
||||
|
||||
mylen="S"+str(len((uniq_atoms[x][0]+str(n)+str(l))))
|
||||
strList=[uniq_atoms[x][0]+str(n)+str(l)]
|
||||
asciiList = [n.encode("ascii", "ignore") for n in strList]
|
||||
BasisGroup.create_dataset('rid', (1,),mylen, asciiList)
|
||||
else:
|
||||
basisType=BasisGroup.create_dataset("type",(1,),dtype=dt)
|
||||
basisType[0:]="Gaussian"
|
||||
RID=BasisGroup.create_dataset("rid",(1,),dtype=dt)
|
||||
RID[0:]=(uniq_atoms[x][0]+str(n)+str(l))
|
||||
|
||||
|
||||
BasisGroup.create_dataset("Shell_coord",(3,),dtype="f8",data=cell.bas_coord(i))
|
||||
|
|
@ -199,14 +277,14 @@ def savetoqmcpack(cell,mf,title="Default",kpts=[]):
|
|||
Val_l=BasisGroup.create_dataset("l",(1,),dtype="i4",data=l)
|
||||
Val_n=BasisGroup.create_dataset("n",(1,),dtype="i4",data=n)
|
||||
RadGroup=BasisGroup.create_group("radfunctions")
|
||||
# print "<basisGroup",n," rid=",uniq_atoms[x][0]+str(n)+str(l)," n=",n," l=",l ,"NbRadFunc=",cell.bas_nprim(i),"type=Gaussian>"
|
||||
#print "<basisGroup",n," rid=",uniq_atoms[x][0]+str(n)+str(l)," n=",n," l=",l ,"NbRadFunc=",cell.bas_nprim(i),"type=Gaussian>"
|
||||
IdRad=0
|
||||
|
||||
for e,c in zip(contracted_exp,line):
|
||||
DataRadGrp=RadGroup.create_group("DataRad"+str(IdRad))
|
||||
DataRadGrp.create_dataset("exponent",(1,),dtype="f8",data=e)
|
||||
DataRadGrp.create_dataset("contraction",(1,),dtype="f8",data=c)
|
||||
# print "<radfunc exponent=",e," contraction=",c, "DataRad=",n,"IdRad=",IdRad,"/>"
|
||||
#print "<radfunc exponent=",e," contraction=",c, "DataRad=",n,"IdRad=",IdRad,"/>"
|
||||
IdRad+=1
|
||||
n+=1
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue