mirror of
https://github.com/LCPQ/quantum_package
synced 2024-06-02 11:25:26 +02:00
b91c9ebad1
* 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
138 lines
4.2 KiB
Python
138 lines
4.2 KiB
Python
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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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