mirror of
https://github.com/LCPQ/quantum_package
synced 2024-08-25 22:11:45 +02:00
Merge Anouar (#69)
* Converter for Pyscf * Scripts to read integrals and metadata and generates fake ezfio * update README * Trying to fix jbuilder bug in OCaml installation * Do AO->MO transformation from pyscf in QP * Optimization of reader due to format creux * Optimization of reader due to format creux 2
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@ -333,11 +333,14 @@ if do_pseudo:
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# |_/ (/_ |_
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#
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psi_coef = ezfio.get_determinants_psi_coef()
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psi_det = ezfio.get_determinants_psi_det()
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bit_kind = ezfio.get_determinants_bit_kind()
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nexcitedstate = ezfio.get_determinants_n_states()
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print ""
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print "BEGIN_DET"
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print ""
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@ -349,7 +352,11 @@ if "QP_STATE" in os.environ:
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state = int(os.environ["QP_STATE"])-1
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else:
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state = 0
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psi_coef = psi_coef[state]
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psi_coef_small = psi_coef[state]
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encode = 8*bit_kind
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@ -359,11 +366,35 @@ def bindigits(n, bits):
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decode = lambda det: ''.join(bindigits(i,encode)[::-1] for i in det)[:mo_num]
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for coef, (det_a, det_b) in zip(psi_coef, psi_det):
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MultiDetAlpha = []
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MultiDetBeta = []
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for coef, (det_a, det_b) in zip(psi_coef_small, psi_det):
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print coef
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print decode(det_a)
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print decode(det_b)
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MyDetA=decode(det_a)
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MyDetB=decode(det_b)
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print MyDetA
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print MyDetB
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print ''
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MultiDetAlpha.append( det_a )
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MultiDetBeta.append( det_b )
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print "END_DET"
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import h5py
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H5_qmcpack=h5py.File('MultiDet.h5','w')
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groupMultiDet=H5_qmcpack.create_group("MultiDet")
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groupMultiDet.create_dataset("NbDet",(1,),dtype="f8",data=len(psi_coef_small))
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groupMultiDet.create_dataset("Coeff",(len(psi_coef_small),),dtype="f8",data=psi_coef)
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groupMultiDet.create_dataset("nstate",(1,),dtype="i4",data=len(MyDetA))
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groupMultiDet.create_dataset("nexcitedstate",(1,),dtype="i4",data=nexcitedstate)
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groupMultiDet.create_dataset("Nbits",(1,),dtype="i4",data=len(det_a))
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print "temp=",MultiDetAlpha[0]
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mylen="S"+str(len(MyDetA))
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groupMultiDet.create_dataset("CI_Alpha",(len(psi_coef_small),len(det_a)),dtype='i8',data=MultiDetAlpha)
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mylen="S"+str(len(MyDetB))
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groupMultiDet.create_dataset("CI_Beta",(len(psi_coef_small),len(det_b)),dtype='i8',data=MultiDetBeta)
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H5_qmcpack.close()
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1
plugins/pyscf/NEEDED_CHILDREN_MODULES
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1
plugins/pyscf/NEEDED_CHILDREN_MODULES
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@ -0,0 +1 @@
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137
plugins/pyscf/PyscfToQp.py
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137
plugins/pyscf/PyscfToQp.py
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@ -0,0 +1,137 @@
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import numpy,re,sys
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def pyscf2QP(cell,mf, kpts=[], int_threshold = 1E-15):
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# The integral will be not printed in they are bellow that
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PBC=False
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ComputeMode= re.split('[. ]', str(mf))
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print 'ComputeMode=',ComputeMode
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for n in ComputeMode:
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if n in ("UHF","KUHF","UKS"):
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sys.exit('Unrestricted calculation unsupported in Quantum Package')
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if n == "pbc":
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PBC=True
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if PBC and len(kpts) == 0:
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sys.exit("ERROR (read!): You need to specify explicit the list of K-point (including gamma)")
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print 'Performing PBC?:',PBC
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if PBC:
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from pyscf.pbc import ao2mo
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from pyscf.pbc import tools
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else:
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from pyscf import ao2mo
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natom = len(cell.atom_coords())
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print 'n_atom', natom
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print 'num_elec', cell.nelectron
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print 'nucl_num', len(cell.atom_coords())
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print ''
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mo_coeff = mf.mo_coeff # List of mo_coeff for each k-point
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if not PBC:
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nmo = mo_coeff.shape[1]
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else:
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nmo = mo_coeff[0].shape[1]
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# Wrote all the parameter need to creat a dummy EZFIO folder who will containt the integral after.
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# More an implentation detail than a real thing
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with open('param','w') as f:
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f.write(' '.join(map(str,(cell.nelectron, nmo, natom))))
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# _
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# |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._
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# | \| |_| (_ | (/_ (_| | | \ (/_ |_) |_| | _> | (_) | |
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# |
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print 'mf, cell', mf.energy_nuc(), cell.energy_nuc()
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shift = tools.pbc.madelung(cell, numpy.zeros(3))*cell.nelectron * -.5 if PBC else 0
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e_nuc = cell.energy_nuc() + shift
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print 'nucl_repul', e_nuc
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with open('e_nuc','w') as f:
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f.write(str(e_nuc))
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from itertools import product
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# ___
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# | ._ _|_ _ _ ._ _. | _ |\/| _ ._ _
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# _|_ | | |_ (/_ (_| | (_| | _> | | (_) | | (_)
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# _|
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if PBC:
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h_ao = ('kinetic', mf.get_hcore(kpts=kpts) ) # Give only one k point ?
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dummy_ao = ('nuclear', numpy.zeros( (len(kpts),nmo,nmo), dtype=numpy.float ))
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else:
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h_ao = ('kinetic', mf.get_hcore() )
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dummy_ao = ('nuclear', numpy.zeros( (nmo,nmo), dtype=numpy.float ))
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def gen_mono_MO(mo_coeff,l_int,shift=0):
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# 2Id transfortion Transformation. For now we handle only one or zero K point.
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print 'l_int.shape=',l_int.shape
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l_int_mo = reduce(numpy.dot, (mo_coeff.T, l_int, mo_coeff)) #This formula is only right for one kpt.
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print 'l_int_mo=',l_int_mo
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for i,j in product(range(nmo), repeat=2):
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int_ = l_int_mo[i,j]
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yield (i+1+shift,j+1+shift, int_)
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# Print
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for name, ao in (h_ao,dummy_ao):
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with open('%s_mo' % name,'w') as f:
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print '%s_mo' % name
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if not PBC:
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for mono in gen_mono_MO(mo_coeff,ao):
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f.write('%s %s %s\n'% mono)
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else:
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for i,(m,a) in enumerate(zip(mo_coeff,ao)):
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for mono in gen_mono_MO(m,a,i):
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f.write('%s %s %s\n'% mono)
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# ___ _
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# | ._ _|_ _ _ ._ _. | _ |_) o
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# _|_ | | |_ (/_ (_| | (_| | _> |_) |
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# _|
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#
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def ao2mo_amazing(mo_coeff):
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if PBC:
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eri_4d= mf.with_df.ao2mo(mo_coeff,compact=False)
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else:
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eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False)
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return eri_4d.reshape((nmo,)*4)
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def write_amazing(eri_4d, shift=0):
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# HANDLE 8 FOLD by Scemama way. Maybe we can use compact=True
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for l in range(nmo):
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for k in range(nmo):
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for j in range(l,nmo):
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for i in range(max(j,k),nmo):
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v = eri_4d[i,k,j,l]
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if abs(v) > int_threshold:
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f.write('%s %s %s %s %s\n' % (i+1+shift,j+1+shift,k+1+shift,l+1+shift,v))
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if PBC:
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eri_4d= mf.with_df.ao2mo(mo_coeff[0],compact=False)
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else: #Molecular
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eri_4d= ao2mo.kernel(cell,mo_coeff,compact=False)
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eri_4d = eri_4d.reshape((nmo,)*4)
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f = open('bielec_mo','w')
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for i,mc in enumerate(mo_coeff):
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eri = ao2mo_amazing(mc)
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write_amazing(eri, nmo*i)
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21
plugins/pyscf/README.rst
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21
plugins/pyscf/README.rst
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@ -0,0 +1,21 @@
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=====
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pyscf
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=====
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Converter from Pyscf to Quatum Package for Molecules AND Solids
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Import this script in your Pyscf input.
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Use as follow:
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```
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from MolPyscfToQP import pyscf2QP
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pyscf2QP(cell,mf,kpts=kpts,int_threshold = 1E-15)
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```
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Needed Modules
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==============
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.. Do not edit this section It was auto-generated
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.. by the `update_README.py` script.
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Documentation
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=============
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.. Do not edit this section It was auto-generated
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.. by the `update_README.py` script.
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38
plugins/pyscf/pyscf.main.irp.f
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38
plugins/pyscf/pyscf.main.irp.f
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@ -0,0 +1,38 @@
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program pyscf
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implicit none
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BEGIN_DOC
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! TODO
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END_DOC
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print *, ' _/ '
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print *, ' -:\_?, _Jm####La '
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print *, 'J"(:" > _]#AZ#Z#UUZ##, '
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print *, '_,::./ %(|i%12XmX1*1XL _?, '
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print *, ' \..\ _\(vmWQwodY+ia%lnL _",/ ( '
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print *, ' .:< ]J=mQD?WXn<uQWmmvd, -.-:=!'
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print *, ' "{Z jC]QW|=3Zv)Bi3BmXv3 = _7'
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print *, ' ]h[Z6)WQ;)jZs]C;|$BZv+, : ./ '
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print *, ' -#sJX%$Wmm#ev]hinW#Xi:` c ; '
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print *, ' #X#X23###1}vI$WWmX1>|,)nr" '
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print *, ' 4XZ#Xov1v}=)vnXAX1nnv;1n" '
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print *, ' ]XX#ZXoovvvivnnnlvvo2*i7 '
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print *, ' "23Z#1S2oo2XXSnnnoSo2>v" '
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print *, ' miX#L -~`""!!1}oSoe|i7 '
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print *, ' 4cn#m, v221=|v[ '
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print *, ' ]hI3Zma,;..__wXSe=+vo '
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print *, ' ]Zov*XSUXXZXZXSe||vo2 '
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print *, ' ]Z#><iiii|i||||==vn2( '
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print *, ' ]Z#i<ii||+|=||=:{no2[ '
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print *, ' ]ZUsiiiiivi|=||=vo22[ '
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print *, ' ]XZvlliiIi|i=|+|vooo '
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print *, ' =v1llli||||=|||||lii( '
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print *, ' ]iillii||||||||=>=|< '
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print *, ' -ziiiii||||||+||==+> '
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print *, ' -%|+++||=|=+|=|==/ '
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print *, ' -a>====+|====-:- '
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print *, ' "~,- -- /- '
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print *, ' -. )> '
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print *, ' .~ +- '
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print *, ' . .... : . '
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print *, ' -------~ '
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print *, ''
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end
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17
plugins/read_integral/Gen_Ezfio_from_integral.sh
Executable file
17
plugins/read_integral/Gen_Ezfio_from_integral.sh
Executable file
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#!/bin/bash
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ezfio=$1
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# Create the integral
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echo 'Create Integral'
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echo 'Create EZFIO'
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read nel nmo natom <<< $(cat param)
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read e_nucl <<< $(cat e_nuc)
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./create_ezfio.py $ezfio $nel $natom $nmo $e_nucl
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#Handle the orbital consitensy check
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qp_edit -c $ezfio &> /dev/null
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cp $ezfio/{ao,mo}_basis/ao_md5
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#Read the integral
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echo 'Read Integral'
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qp_run read_integrals_mo $ezfio
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@ -3,6 +3,7 @@ read_integral
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=============
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Warning: CAN NOT CHANGE THE NUMBER OF MO !
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Scripts to read integrals and metadata and generates fake ezfio
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Needed Modules
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==============
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48
plugins/read_integral/create_ezfio.py
Executable file
48
plugins/read_integral/create_ezfio.py
Executable file
@ -0,0 +1,48 @@
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#!/usr/bin/env python
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from ezfio import ezfio
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import sys
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filename = sys.argv[1]
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num_elec, nucl_num, mo_tot_num = map(int,sys.argv[2:5])
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nuclear_repulsion = float(sys.argv[5])
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ezfio.set_file(filename)
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#Important !
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import math
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ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
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ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
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#Important
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ezfio.set_nuclei_nucl_num(nucl_num)
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ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
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ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
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ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
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ezfio.set_nuclei_disk_access_nuclear_repulsion('Read')
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ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
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# Ao num
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ao_num = mo_tot_num
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ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
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ezfio.set_ao_basis_ao_num(ao_num)
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ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
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#Just need one
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ao_prim_num_max = 5
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d = [ [0] *ao_prim_num_max]*ao_num
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ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
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ezfio.set_ao_basis_ao_power(d)
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ezfio.set_ao_basis_ao_coef(d)
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ezfio.set_ao_basis_ao_expo(d)
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#Dummy one
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ao_md5 = '3b8b464dfc95f282129bde3efef3c502'
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ezfio.set_ao_basis_ao_md5(ao_md5)
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ezfio.set_mo_basis_ao_md5(ao_md5)
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ezfio.set_mo_basis_mo_tot_num(mo_tot_num)
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ezfio.set_mo_basis_mo_coef([ [0]*mo_tot_num] * ao_num)
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47
plugins/read_integral/read_integrals_achocol.irp.f
Normal file
47
plugins/read_integral/read_integrals_achocol.irp.f
Normal file
@ -0,0 +1,47 @@
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program read_integrals
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PROVIDE ezfio_filename
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call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("None")
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call run
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end
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subroutine run
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use map_module
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implicit none
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integer :: iunit
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integer :: getunitandopen
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integer ::i,j,k,l
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double precision :: integral
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double precision, allocatable :: A(:,:)
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integer :: n_integrals
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integer(key_kind), allocatable :: buffer_i(:)
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real(integral_kind), allocatable :: buffer_values(:)
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integer(key_kind) :: key
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call ezfio_set_integrals_monoelec_disk_access_ao_one_integrals("Read")
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allocate(buffer_i(ao_num**4/8), buffer_values(ao_num**4/8))
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iunit = getunitandopen('bielec_ao','r')
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n_integrals=0
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do
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read (iunit,*,end=13) i,j,k,l, integral
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n_integrals += 1
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call bielec_integrals_index(i, j, k, l, buffer_i(n_integrals) )
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buffer_values(n_integrals) = integral
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enddo
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13 continue
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close(iunit)
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call insert_into_ao_integrals_map(n_integrals,buffer_i,buffer_values)
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call map_sort(ao_integrals_map)
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call map_unique(ao_integrals_map)
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call map_save_to_disk(trim(ezfio_filename)//'/work/ao_ints',ao_integrals_map)
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call ezfio_set_integrals_bielec_disk_access_ao_integrals('Read')
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end
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86
plugins/read_integral/read_integrals_mo_chocol.irp.f
Normal file
86
plugins/read_integral/read_integrals_mo_chocol.irp.f
Normal file
@ -0,0 +1,86 @@
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program read_integrals
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BEGIN_DOC
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! Reads the integrals from the following files:
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! - kinetic_mo
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! - nuclear_mo
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! - bielec_mo
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END_DOC
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integer :: iunit
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integer :: getunitandopen
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integer :: i,j,n
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PROVIDE ezfio_filename
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call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("None")
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logical :: has
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call ezfio_has_mo_basis_mo_tot_num(has)
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if (.not.has) then
|
||||
|
||||
iunit = getunitandopen('nuclear_mo','r')
|
||||
n=0
|
||||
do
|
||||
read (iunit,*,end=12) i
|
||||
n = max(n,i)
|
||||
enddo
|
||||
12 continue
|
||||
close(iunit)
|
||||
call ezfio_set_mo_basis_mo_tot_num(n)
|
||||
|
||||
call ezfio_has_ao_basis_ao_num(has)
|
||||
mo_label = "None"
|
||||
if (has) then
|
||||
call huckel_guess
|
||||
else
|
||||
call ezfio_set_ao_basis_ao_num(n)
|
||||
endif
|
||||
endif
|
||||
call run
|
||||
end
|
||||
|
||||
subroutine run
|
||||
use map_module
|
||||
implicit none
|
||||
|
||||
integer :: iunit
|
||||
integer :: getunitandopen
|
||||
|
||||
integer ::i,j,k,l
|
||||
double precision :: integral
|
||||
double precision, allocatable :: A(:,:)
|
||||
|
||||
integer :: n_integrals
|
||||
integer(key_kind), allocatable :: buffer_i(:)
|
||||
real(integral_kind), allocatable :: buffer_values(:)
|
||||
integer(key_kind) :: key
|
||||
|
||||
call ezfio_get_mo_basis_mo_tot_num(mo_tot_num)
|
||||
|
||||
allocate (A(mo_tot_num,mo_tot_num))
|
||||
A = 0.d0
|
||||
|
||||
iunit = getunitandopen('kinetic_mo','r')
|
||||
do
|
||||
read (iunit,*,end=10) i,j, integral
|
||||
A(i,j) = integral
|
||||
enddo
|
||||
10 continue
|
||||
close(iunit)
|
||||
call write_one_e_integrals('mo_kinetic_integral', A, size(A,1), size(A,2))
|
||||
|
||||
|
||||
iunit = getunitandopen('nuclear_mo','r')
|
||||
do
|
||||
read (iunit,*,end=12) i,j, integral
|
||||
A(i,j) = integral
|
||||
enddo
|
||||
12 continue
|
||||
close(iunit)
|
||||
call write_one_e_integrals('mo_ne_integral', A, size(A,1), size(A,2))
|
||||
|
||||
call write_one_e_integrals('mo_pseudo_integral', mo_pseudo_integral,&
|
||||
size(mo_pseudo_integral,1), size(mo_pseudo_integral,2))
|
||||
|
||||
|
||||
call ezfio_set_integrals_monoelec_disk_access_mo_one_integrals("Read")
|
||||
end
|
Loading…
Reference in New Issue
Block a user