mirror of
https://github.com/QuantumPackage/qp2.git
synced 2025-04-27 18:54:42 +02:00
1049 lines
37 KiB
Python
1049 lines
37 KiB
Python
import numpy as np
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from functools import reduce
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def memoize(f):
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memo = {}
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def helper(x):
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if x not in memo:
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memo[x] = f(x)
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return memo[x]
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return helper
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@memoize
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def idx2_tri(iijj):
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'''
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iijj should be a 2-tuple
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return triangular compound index for (0-indexed counting)
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'''
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ij1=min(iijj)
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ij2=max(iijj)
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return ij1+(ij2*(ij2+1))//2
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# return ij1+(ij2*(ij2-1))//2
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def pad(arr_in,outshape):
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arr_out = np.zeros(outshape,dtype=np.complex128)
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dataslice = tuple(slice(0,arr_in.shape[dim]) for dim in range(len(outshape)))
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arr_out[dataslice] = arr_in
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return arr_out
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def idx40(i,j,k,l):
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return idx2_tri((idx2_tri((i,k)),idx2_tri((j,l))))
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def idx4(i,j,k,l):
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return idx2_tri((idx2_tri((i-1,k-1)),idx2_tri((j-1,l-1))))+1
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def stri4(i,j,k,l):
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return (4*'{:5d}').format(i,j,k,l)
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def stri4z(i,j,k,l,zr,zi):
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return (4*'{:5d}'+2*'{:25.16e}').format(i,j,k,l,zr,zi)
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def stri2z(i,j,zr,zi):
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return (2*'{:5d}'+2*'{:25.16e}').format(i,j,zr,zi)
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def strijklikjli4z(i,j,k,l,zr,zi):
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return ('{:10d}'+ 2*'{:8d}'+4*'{:5d}'+2*'{:25.16e}').format(idx4(i,j,k,l),idx2_tri((i-1,k-1))+1,idx2_tri((j-1,l-1))+1,i,j,k,l,zr,zi)
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def makesq(vlist,n1,n2):
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'''
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make hermitian matrices of size (n2 x n2) from from lower triangles
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vlist is n1 lower triangles in flattened form
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given: ([a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t],2,4)
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output a 2x4x4 array, where each 4x4 is the square constructed from the lower triangle
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[
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[
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[a b* d* g*]
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[b c e* h*]
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[d e f i*]
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[g h i j ]
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],
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[
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[k l* n* q*]
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[l m o* r*]
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[n o p s*]
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[q r s t ]
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]
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]
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'''
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out=np.zeros([n1,n2,n2],dtype=np.complex128)
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n0 = vlist.shape[0]
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lmask=np.tri(n2,dtype=bool)
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for i in range(n0):
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out[i][lmask] = vlist[i].conj()
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out2=out.transpose([0,2,1])
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for i in range(n0):
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out2[i][lmask] = vlist[i]
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return out2
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def makesq3(vlist,n2):
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'''
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make hermitian matrices of size (n2 x n2) from from lower triangles
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vlist is n1 lower triangles in flattened form
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given: ([a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r,s,t],2,4)
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output a 2x4x4 array, where each 4x4 is the square constructed from the lower triangle
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[
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[
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[a b* d* g*]
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[b c e* h*]
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[d e f i*]
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[g h i j ]
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],
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[
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[k l* n* q*]
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[l m o* r*]
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[n o p s*]
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[q r s t ]
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]
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]
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'''
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n0 = vlist.shape[0]
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out=np.zeros([n0,n2,n2],dtype=np.complex128)
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lmask=np.tri(n2,dtype=bool)
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for i in range(n0):
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out[i][lmask] = vlist[i].conj()
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out2=out.transpose([0,2,1])
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for i in range(n0):
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out2[i][lmask] = vlist[i]
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return out2
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def makesq2(vlist,n1,n2):
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out=np.zeros([n1,n2,n2],dtype=np.complex128)
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lmask=np.tri(n2,dtype=bool)
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tmp=np.zeros([n2,n2],dtype=np.complex128)
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tmp2=np.zeros([n2,n2],dtype=np.complex128)
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for i in range(n1):
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tmp[lmask] = vlist[i].conj()
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tmp2=tmp.T
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tmp2[lmask] = vlist[i]
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out[i] = tmp2.copy()
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return out
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def get_phase(cell, kpts, kmesh=None):
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'''
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The unitary transformation that transforms the supercell basis k-mesh
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adapted basis.
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'''
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from pyscf.pbc import tools
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from pyscf import lib
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latt_vec = cell.lattice_vectors()
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if kmesh is None:
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# Guess kmesh
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scaled_k = cell.get_scaled_kpts(kpts).round(8)
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kmesh = (len(np.unique(scaled_k[:,0])),
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len(np.unique(scaled_k[:,1])),
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len(np.unique(scaled_k[:,2])))
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R_rel_a = np.arange(kmesh[0])
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R_rel_b = np.arange(kmesh[1])
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R_rel_c = np.arange(kmesh[2])
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R_vec_rel = lib.cartesian_prod((R_rel_a, R_rel_b, R_rel_c))
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R_vec_abs = np.einsum('nu, uv -> nv', R_vec_rel, latt_vec)
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NR = len(R_vec_abs)
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phase = np.exp(1j*np.einsum('Ru, ku -> Rk', R_vec_abs, kpts))
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phase /= np.sqrt(NR) # normalization in supercell
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# R_rel_mesh has to be construct exactly same to the Ts in super_cell function
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scell = tools.super_cell(cell, kmesh)
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return scell, phase
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def mo_k2gamma(cell, mo_energy, mo_coeff, kpts, kmesh=None):
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'''
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Transform MOs in Kpoints to the equivalents supercell
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'''
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from pyscf import lib
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import scipy.linalg as la
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scell, phase = get_phase(cell, kpts, kmesh)
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E_g = np.hstack(mo_energy)
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C_k = np.asarray(mo_coeff)
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Nk, Nao, Nmo = C_k.shape
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NR = phase.shape[0]
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# Transform AO indices
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C_gamma = np.einsum('Rk, kum -> Rukm', phase, C_k)
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C_gamma = C_gamma.reshape(Nao*NR, Nk*Nmo)
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E_sort_idx = np.argsort(E_g)
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E_g = E_g[E_sort_idx]
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C_gamma = C_gamma[:,E_sort_idx]
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s = scell.pbc_intor('int1e_ovlp')
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assert(abs(reduce(np.dot, (C_gamma.conj().T, s, C_gamma))
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- np.eye(Nmo*Nk)).max() < 1e-7)
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# Transform MO indices
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E_k_degen = abs(E_g[1:] - E_g[:-1]).max() < 1e-5
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if np.any(E_k_degen):
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degen_mask = np.append(False, E_k_degen) | np.append(E_k_degen, False)
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shift = min(E_g[degen_mask]) - .1
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f = np.dot(C_gamma[:,degen_mask] * (E_g[degen_mask] - shift),
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C_gamma[:,degen_mask].conj().T)
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assert(abs(f.imag).max() < 1e-5)
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e, na_orb = la.eigh(f.real, s, type=2)
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C_gamma[:,degen_mask] = na_orb[:, e>0]
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if abs(C_gamma.imag).max() < 1e-7:
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print('!Warning Some complexe pollutions in MOs are present')
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C_gamma = C_gamma.real
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if abs(reduce(np.dot, (C_gamma.conj().T, s, C_gamma)) - np.eye(Nmo*Nk)).max() < 1e-7:
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print('!Warning Some complexe pollutions in MOs are present')
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s_k = cell.pbc_intor('int1e_ovlp', kpts=kpts)
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# overlap between k-point unitcell and gamma-point supercell
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s_k_g = np.einsum('kuv,Rk->kuRv', s_k, phase.conj()).reshape(Nk,Nao,NR*Nao)
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# The unitary transformation from k-adapted orbitals to gamma-point orbitals
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mo_phase = lib.einsum('kum,kuv,vi->kmi', C_k.conj(), s_k_g, C_gamma)
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return mo_phase
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def qp2rename():
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import shutil
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qp2names={}
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qp2names['mo_coef_complex'] = 'C.qp'
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qp2names['bielec_ao_complex'] = 'W.qp'
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qp2names['kinetic_ao_complex'] = 'T.qp'
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qp2names['ne_ao_complex'] = 'V.qp'
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qp2names['overlap_ao_complex'] = 'S.qp'
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for old,new in qp2names.items():
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shutil.move(old,new)
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shutil.copy('e_nuc','E.qp')
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def print_mo_bi(mf,kconserv=None,outfilename='W.mo.qp',cas_idx=None,bielec_int_threshold = 1E-8):
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cell = mf.cell
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kpts = mf.kpts
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#nao = mf.cell.nao
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#Nk = kpts.shape[0]
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mo_coeff = mf.mo_coeff
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# Mo_coeff actif
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mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
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Nk, nao, nmo = mo_k.shape
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if (kconserv is None):
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from pyscf.pbc import tools
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kconserv = tools.get_kconserv(cell, kpts)
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with open(outfilename,'w') as outfile:
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for d, kd in enumerate(kpts):
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for c, kc in enumerate(kpts):
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if c > d: break
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#idx2_cd = idx2_tri((c,d))
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for b, kb in enumerate(kpts):
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if b > d: break
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a = kconserv[b,c,d]
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if a > d: continue
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#if idx2_tri((a,b)) > idx2_cd: continue
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#if ((c==d) and (a>b)): continue
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ka = kpts[a]
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eri_4d_mo_kpt = mf.with_df.ao2mo([mo_k[a], mo_k[b], mo_k[c], mo_k[d]],
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[ka,kb,kc,kd],compact=False).reshape((nmo,)*4)
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eri_4d_mo_kpt *= 1./Nk
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for l in range(nmo):
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ll=l+d*nmo
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for j in range(nmo):
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jj=j+c*nmo
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if jj>ll: break
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idx2_jjll = idx2_tri((jj,ll))
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for k in range(nmo):
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kk=k+b*nmo
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if kk>ll: break
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for i in range(nmo):
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ii=i+a*nmo
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if idx2_tri((ii,kk)) > idx2_jjll: break
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if ((jj==ll) and (ii>kk)): break
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v=eri_4d_mo_kpt[i,k,j,l]
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if (abs(v) > bielec_int_threshold):
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outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,
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v.real,v.imag)+'\n')
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def print_ao_bi(mf,kconserv=None,outfilename='W.ao.qp',bielec_int_threshold = 1E-8):
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cell = mf.cell
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kpts = mf.kpts
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nao = mf.cell.nao
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Nk = kpts.shape[0]
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if (kconserv is None):
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from pyscf.pbc.tools import get_kconserv
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kconserv = get_kconserv(cell, kpts)
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with open(outfilename,'w') as outfile:
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for d, kd in enumerate(kpts):
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for c, kc in enumerate(kpts):
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if c > d: break
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#idx2_cd = idx2_tri((c,d))
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for b, kb in enumerate(kpts):
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if b > d: break
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a = kconserv[b,c,d]
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if a > d: continue
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#if idx2_tri((a,b)) > idx2_cd: continue
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#if ((c==d) and (a>b)): continue
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ka = kpts[a]
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],
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compact=False).reshape((nao,)*4)
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eri_4d_ao_kpt *= 1./Nk
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for l in range(nao):
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ll=l+d*nao
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for j in range(nao):
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jj=j+c*nao
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if jj>ll: break
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idx2_jjll = idx2_tri((jj,ll))
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for k in range(nao):
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kk=k+b*nao
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if kk>ll: break
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for i in range(nao):
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ii=i+a*nao
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if idx2_tri((ii,kk)) > idx2_jjll: break
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if ((jj==ll) and (ii>kk)): break
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v=eri_4d_ao_kpt[i,k,j,l]
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if (abs(v) > bielec_int_threshold):
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outfile.write(stri4z(ii+1,jj+1,kk+1,ll+1,
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v.real,v.imag)+'\n')
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def print_kcon_chem_to_phys(kcon,fname):
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'''
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input: kconserv in chem notation kcon_c[a,b,c] = d
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where (ab|cd) is allowed by symmetry
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output: kconserv in phys notation kcon_p[i,j,k] = l
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where <ij|kl> is allowed by symmetry
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(printed to file)
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'''
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Nk,n2,n3 = kcon.shape
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if (n2!=n3 or Nk!=n2):
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raise Exception('print_kcon_chem_to_phys called with non-cubic array')
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with open(fname,'w') as outfile:
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for a in range(Nk):
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for b in range(Nk):
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for c in range(Nk):
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d = kcon[a,b,c]
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outfile.write(stri4(a+1,c+1,b+1,d+1)+'\n')
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def print_kpts_unblocked(ints_k,outfilename,thresh):
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'''
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for ints_k of shape (Nk,n1,n2),
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print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n2) in file
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'''
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Nk,n1,n2 = ints_k.shape
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with open(outfilename,'w') as outfile:
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for ik in range(Nk):
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shift1 = ik*n1+1
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shift2 = ik*n2+1
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for i1 in range(n1):
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for i2 in range(n2):
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int_ij = ints_k[ik,i1,i2]
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if abs(int_ij) > thresh:
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outfile.write(stri2z(i1+shift1, i2+shift2, int_ij.real, int_ij.imag)+'\n')
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return
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def print_kpts_unblocked_upper(ints_k,outfilename,thresh):
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'''
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for hermitian ints_k of shape (Nk,n1,n1),
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print the elements of the corresponding block-diagonal matrix of shape (Nk*n1,Nk*n1) in file
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(only upper triangle is printed)
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'''
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Nk,n1,n2 = ints_k.shape
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if (n1!=n2):
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raise Exception('print_kpts_unblocked_upper called with non-square matrix')
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with open(outfilename,'w') as outfile:
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for ik in range(Nk):
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shift = ik*n1+1
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for i1 in range(n1):
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for i2 in range(i1,n1):
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int_ij = ints_k[ik,i1,i2]
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if abs(int_ij) > thresh:
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outfile.write(stri2z(i1+shift, i2+shift, int_ij.real, int_ij.imag)+'\n')
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return
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def get_kin_ao(mf):
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nao = mf.cell.nao_nr()
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Nk = len(mf.kpts)
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return np.reshape(mf.cell.pbc_intor('int1e_kin',1,1,kpts=mf.kpts),(Nk,nao,nao))
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def get_ovlp_ao(mf):
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nao = mf.cell.nao_nr()
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Nk = len(mf.kpts)
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return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
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def get_pot_ao(mf):
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nao = mf.cell.nao_nr()
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Nk = len(mf.kpts)
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if mf.cell.pseudo:
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v_kpts_ao = np.reshape(mf.with_df.get_pp(kpts=mf.kpts),(Nk,nao,nao))
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else:
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v_kpts_ao = np.reshape(mf.with_df.get_nuc(kpts=mf.kpts),(Nk,nao,nao))
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if len(mf.cell._ecpbas) > 0:
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from pyscf.pbc.gto import ecp
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v_kpts_ao += np.reshape(ecp.ecp_int(mf.cell, mf.kpts),(Nk,nao,nao))
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return v_kpts_ao
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def ao_to_mo_1e(ao_kpts,mo_coef):
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return np.einsum('kim,kij,kjn->kmn',mo_coef.conj(),ao_kpts,mo_coef)
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def get_j3ao_old(fname,nao,Nk):
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'''
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returns list of Nk_pair arrays of shape (naux,nao,nao)
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if naux is the same for each pair, returns numpy array
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if naux is not the same for each pair, returns array of arrays
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'''
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import h5py
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with h5py.File(fname,'r') as intfile:
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j3c = intfile.get('j3c')
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j3ckeys = list(j3c.keys())
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j3ckeys.sort(key=lambda strkey:int(strkey))
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# in new(?) version of PySCF, there is an extra layer of groups before the datasets
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# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
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# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
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j3clist = [j3c.get(i+'/0') for i in j3ckeys]
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#if j3clist==[None]*len(j3clist):
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if not(any(j3clist)):
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# if using older version, stop before last level
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j3clist = [j3c.get(i) for i in j3ckeys]
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|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
# dimensions are (kikj,iaux,jao,kao), where kikj is compound index of kpts i and j
|
|
# output dimensions should be reversed (nao, nao, naux, nkptpairs)
|
|
return np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
|
|
|
|
def get_j3ao(fname,nao,Nk):
|
|
'''
|
|
returns padded df AO array
|
|
fills in zeros when functions are dropped due to linear dependency
|
|
last AO index corresponds to smallest kpt index?
|
|
(k, mu, i, j) where i.kpt >= j.kpt
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
nkpairs = len(j3ckeys)
|
|
|
|
# get num order instead of lex order
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
|
|
|
|
naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
|
|
|
|
for i,kpair in enumerate(j3ckeys):
|
|
iaux,dim2 = j3c[kpair+keysub].shape
|
|
if (dim2==naosq):
|
|
j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
else:
|
|
j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()],nao) * nkinvsq
|
|
#j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
|
|
|
|
return j3arr
|
|
|
|
def get_j3ao_new(fname,nao,Nk):
|
|
'''
|
|
returns padded df AO array
|
|
fills in zeros when functions are dropped due to linear dependency
|
|
last AO index corresponds to largest kpt index?
|
|
(k, mu, j, i) where i.kpt >= j.kpt
|
|
'''
|
|
import h5py
|
|
with h5py.File(fname,'r') as intfile:
|
|
j3c = intfile.get('j3c')
|
|
j3ckeys = list(j3c.keys())
|
|
nkpairs = len(j3ckeys)
|
|
|
|
# get num order instead of lex order
|
|
j3ckeys.sort(key=lambda strkey:int(strkey))
|
|
|
|
# in new(?) version of PySCF, there is an extra layer of groups before the datasets
|
|
# datasets used to be [/j3c/0, /j3c/1, /j3c/2, ...]
|
|
# datasets now are [/j3c/0/0, /j3c/1/0, /j3c/2/0, ...]
|
|
keysub = '/0' if bool(j3c.get('0/0',getclass=True)) else ''
|
|
|
|
naux = max(map(lambda k: j3c[k+keysub].shape[0],j3c.keys()))
|
|
|
|
naosq = nao*nao
|
|
naotri = (nao*(nao+1))//2
|
|
nkinvsq = 1./np.sqrt(Nk)
|
|
|
|
j3arr = np.zeros((nkpairs,naux,nao,nao),dtype=np.complex128)
|
|
|
|
for i,kpair in enumerate(j3ckeys):
|
|
iaux,dim2 = j3c[kpair+keysub].shape
|
|
if (dim2==naosq):
|
|
j3arr[i,:iaux,:,:] = j3c[kpair+keysub][()].reshape([iaux,nao,nao]).transpose((0,2,1)) * nkinvsq
|
|
else:
|
|
j3arr[i,:iaux,:,:] = makesq3(j3c[kpair+keysub][()].conj(),nao) * nkinvsq
|
|
|
|
return j3arr
|
|
|
|
def print_df(j3arr,fname,thresh):
|
|
with open(fname,'w') as outfile:
|
|
for k,kpt_pair in enumerate(j3arr):
|
|
for iaux,dfbasfunc in enumerate(kpt_pair):
|
|
for i,i0 in enumerate(dfbasfunc):
|
|
for j,v in enumerate(i0):
|
|
if (abs(v) > thresh):
|
|
outfile.write(stri4z(i+1,j+1,iaux+1,k+1,v.real,v.imag)+'\n')
|
|
return
|
|
|
|
def df_pad_ref_test(j3arr,nao,naux,nkpt_pairs):
|
|
df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
|
|
for k,kpt_pair in enumerate(j3arr):
|
|
for iaux,dfbasfunc in enumerate(kpt_pair):
|
|
for i,i0 in enumerate(dfbasfunc):
|
|
for j,v in enumerate(i0):
|
|
df_ao_tmp[i,j,iaux,k]=v
|
|
return df_ao_tmp
|
|
|
|
|
|
def df_ao_to_mo(j3ao,mo_coef):
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
kpair_list = ((i,j,idx2_tri((i,j))) for (i,j) in product(range(Nk),repeat=2) if (i>=j))
|
|
return np.array([
|
|
np.einsum('mij,ik,jl->mkl',j3ao[kij],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj,kij in kpair_list])
|
|
|
|
|
|
def df_ao_to_mo_new(j3ao,mo_coef):
|
|
#TODO: fix this (C/F ordering, conj, transpose, view cmplx->float)
|
|
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
return np.array([
|
|
np.einsum('mji,ik,jl->mlk',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)],dtype=np.complex128)
|
|
|
|
def df_ao_to_mo_test(j3ao,mo_coef):
|
|
from itertools import product
|
|
Nk = mo_coef.shape[0]
|
|
return np.array([
|
|
np.einsum('mij,ik,jl->mkl',j3ao[idx2_tri((ki,kj))],mo_coef[ki].conj(),mo_coef[kj])
|
|
for ki,kj in product(range(Nk),repeat=2) if (ki>=kj)])
|
|
|
|
def pyscf2QP2_mo(cell,mf,kpts,kmesh=None,cas_idx=None, int_threshold = 1E-8,qph5path='qpdat.h5'):
|
|
pyscf2QP2(cell,mf,kpts,kmesh,cas_idx,int_threshold,qph5path,
|
|
print_ao_ints_df=False,
|
|
print_mo_ints_df=True,
|
|
print_ao_ints_mono=False,
|
|
print_mo_ints_mono=True)
|
|
return
|
|
|
|
|
|
|
|
def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
|
qph5path = 'qpdat.h5',
|
|
print_ao_ints_bi=False,
|
|
print_mo_ints_bi=False,
|
|
print_ao_ints_df=True,
|
|
print_mo_ints_df=False,
|
|
print_ao_ints_mono=True,
|
|
print_mo_ints_mono=False,
|
|
print_debug=False):
|
|
'''
|
|
kpts = List of kpoints coordinates. Cannot be null, for gamma is other script
|
|
kmesh = Mesh of kpoints (optional)
|
|
cas_idx = List of active MOs. If not specified all MOs are actives
|
|
int_threshold = The integral will be not printed in they are bellow that
|
|
'''
|
|
|
|
# from pyscf.pbc import ao2mo
|
|
from pyscf.pbc import tools
|
|
import h5py
|
|
# import scipy
|
|
from scipy.linalg import block_diag
|
|
|
|
mo_coef_threshold = int_threshold
|
|
ovlp_threshold = int_threshold
|
|
kin_threshold = int_threshold
|
|
ne_threshold = int_threshold
|
|
bielec_int_threshold = int_threshold
|
|
thresh_mono = int_threshold
|
|
|
|
|
|
# qph5path = 'qpdat.h5'
|
|
# create hdf5 file, delete old data if exists
|
|
with h5py.File(qph5path,'w') as qph5:
|
|
qph5.create_group('nuclei')
|
|
qph5.create_group('electrons')
|
|
qph5.create_group('ao_basis')
|
|
qph5.create_group('mo_basis')
|
|
|
|
mo_coeff = mf.mo_coeff
|
|
# Mo_coeff actif
|
|
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
|
e_k = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
|
|
|
Nk, nao, nmo = mo_k.shape
|
|
|
|
print("n Kpts", Nk)
|
|
print("n active Mos per kpt", nmo)
|
|
print("n AOs per kpt", nao)
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclei #
|
|
# #
|
|
##########################################
|
|
|
|
natom = cell.natm
|
|
print('n_atom per kpt', natom)
|
|
|
|
atom_xyz = mf.cell.atom_coords()
|
|
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
|
|
from pyscf.data.nist import BOHR
|
|
atom_xyz /= BOHR # always convert to au
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['kpt_num']=Nk
|
|
qph5['nuclei'].attrs['nucl_num']=natom
|
|
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
|
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
|
|
|
|
strtype=h5py.special_dtype(vlen=str)
|
|
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
|
for i in range(natom):
|
|
atom_dset[i] = mf.cell.atom_pure_symbol(i)
|
|
|
|
##########################################
|
|
# #
|
|
# Basis #
|
|
# #
|
|
##########################################
|
|
|
|
# nucleus on which each AO is centered
|
|
ao_nucl=[i[0] for i in mf.cell.ao_labels(fmt=False,base=1)]
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
|
qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
|
|
|
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
|
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
|
|
|
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
|
|
|
##########################################
|
|
# #
|
|
# Electrons #
|
|
# #
|
|
##########################################
|
|
|
|
nelec = cell.nelectron
|
|
neleca,nelecb = cell.nelec
|
|
|
|
print('num_elec per kpt', nelec)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
|
|
qph5['electrons'].attrs['elec_alpha_num']=neleca*Nk
|
|
qph5['electrons'].attrs['elec_beta_num']=nelecb*Nk
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclear Repulsion #
|
|
# #
|
|
##########################################
|
|
|
|
#Total energy shift due to Ewald probe charge = -1/2 * Nelec*madelung/cell.vol =
|
|
shift = tools.pbc.madelung(cell, kpts)*cell.nelectron * -.5
|
|
e_nuc = (cell.energy_nuc() + shift)*Nk
|
|
|
|
print('nucl_repul', e_nuc)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
|
|
|
##########################################
|
|
# #
|
|
# MO Coef #
|
|
# #
|
|
##########################################
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
# k,mo,ao(,2)
|
|
mo_coef_f = np.array(mo_k.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
#mo_coef_blocked=block_diag(*mo_k)
|
|
mo_coef_blocked_f = block_diag(*mo_coef_f)
|
|
qph5.create_dataset('mo_basis/mo_coef_complex',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2)))
|
|
qph5.create_dataset('mo_basis/mo_coef_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2)))
|
|
|
|
if print_debug:
|
|
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
|
|
|
|
##########################################
|
|
# #
|
|
# Integrals Mono #
|
|
# #
|
|
##########################################
|
|
|
|
ne_ao = get_pot_ao(mf)
|
|
kin_ao = get_kin_ao(mf)
|
|
ovlp_ao = get_ovlp_ao(mf)
|
|
|
|
if print_ao_ints_mono:
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kin_ao_f = np.array(kin_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ovlp_ao_f = np.array(ovlp_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ne_ao_f = np.array(ne_ao.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_kpts',data=kin_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_kpts',data=ovlp_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_kpts', data=ne_ao_f.view(dtype=np.float64).reshape((Nk,nao,nao,2)))
|
|
|
|
if print_debug:
|
|
for fname,ints in zip(('S.qp','V.qp','T.qp'),
|
|
(ovlp_ao, ne_ao, kin_ao)):
|
|
print_kpts_unblocked_upper(ints,fname,thresh_mono)
|
|
|
|
if print_mo_ints_mono:
|
|
kin_mo = ao_to_mo_1e(kin_ao,mo_k)
|
|
ovlp_mo = ao_to_mo_1e(ovlp_ao,mo_k)
|
|
ne_mo = ao_to_mo_1e(ne_ao,mo_k)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kin_mo_f = np.array(kin_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ovlp_mo_f = np.array(ovlp_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
ne_mo_f = np.array(ne_mo.transpose((0,2,1)),order='c',dtype=np.complex128)
|
|
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_kinetic_kpts',data=kin_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_overlap_kpts',data=ovlp_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
qph5.create_dataset('mo_one_e_ints/mo_integrals_n_e_kpts', data=ne_mo_f.view(dtype=np.float64).reshape((Nk,nmo,nmo,2)))
|
|
if print_debug:
|
|
for fname,ints in zip(('S.mo.qp','V.mo.qp','T.mo.qp'),
|
|
(ovlp_mo, ne_mo, kin_mo)):
|
|
print_kpts_unblocked_upper(ints,fname,thresh_mono)
|
|
|
|
|
|
##########################################
|
|
# #
|
|
# k-points #
|
|
# #
|
|
##########################################
|
|
|
|
kconserv = tools.get_kconserv(cell, kpts)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c')
|
|
qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1)
|
|
|
|
if print_debug:
|
|
print_kcon_chem_to_phys(kconserv,'K.qp')
|
|
|
|
##########################################
|
|
# #
|
|
# Integrals Bi #
|
|
# #
|
|
##########################################
|
|
|
|
j3ao_new = get_j3ao_new(mf.with_df._cderi,nao,Nk)
|
|
|
|
# test? nkpt_pairs should be (Nk*(Nk+1))//2
|
|
nkpt_pairs, naux, _, _ = j3ao_new.shape
|
|
|
|
print("n df fitting functions", naux)
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_group('ao_two_e_ints')
|
|
qph5['ao_two_e_ints'].attrs['df_num']=naux
|
|
|
|
if print_ao_ints_df:
|
|
if print_debug:
|
|
print_df(j3ao_new,'D.qp',bielec_int_threshold)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('ao_two_e_ints/df_ao_integrals',data=j3ao_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nao,nao,2)))
|
|
|
|
if print_mo_ints_df:
|
|
|
|
j3mo_new = df_ao_to_mo_new(j3ao_new,mo_k)
|
|
|
|
if print_debug:
|
|
print_df(j3mo_new,'D.mo.qp',bielec_int_threshold)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('mo_two_e_ints/df_mo_integrals',data=j3mo_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nmo,nmo,2)))
|
|
|
|
if (print_ao_ints_bi):
|
|
print_ao_bi(mf,kconserv,'W.qp',bielec_int_threshold)
|
|
if (print_mo_ints_bi):
|
|
print_mo_bi(mf,kconserv,'W.mo.qp',cas_idx,bielec_int_threshold)
|
|
return
|
|
|
|
def xyzcount(s):
|
|
return list(map(s.count,['x','y','z']))
|
|
|
|
def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
|
|
qph5path = 'qpdat.h5',
|
|
print_debug=False):
|
|
'''
|
|
cas_idx = List of active MOs. If not specified all MOs are actives
|
|
int_threshold = The integral will be not printed in they are bellow that
|
|
norm should be one of 'sp', 'all', or None
|
|
'''
|
|
|
|
import h5py
|
|
|
|
norm='sp'
|
|
mol = mf.mol
|
|
nao_c = mol.nao_cart()
|
|
|
|
mo_coef_threshold = int_threshold
|
|
ovlp_threshold = int_threshold
|
|
kin_threshold = int_threshold
|
|
ne_threshold = int_threshold
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bielec_int_threshold = int_threshold
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thresh_mono = int_threshold
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# qph5path = 'qpdat.h5'
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# create hdf5 file, delete old data if exists
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with h5py.File(qph5path,'w') as qph5:
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qph5.create_group('nuclei')
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qph5.create_group('electrons')
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qph5.create_group('ao_basis')
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qph5.create_group('mo_basis')
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if mf.mol.cart:
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mo_coeff = mf.mo_coeff.copy()
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else:
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#c2s = mol.cart2sph_coeff(normalized=norm)
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c2s = mol.cart2sph_coeff(normalized='sp')
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#c2s = mol.cart2sph_coeff(normalized='all')
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#c2s = mol.cart2sph_coeff(normalized=None)
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mo_coeff = np.dot(c2s,mf.mo_coeff)
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#TODO: clean this up; use mol.cart_labels(fmt=False)
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dnormlbl1=["dxx","dyy","dzz"]
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dnormfac1 = 2.0*np.sqrt(np.pi/5)
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dnormlbl2=["dxy","dxz","dyz"]
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dnormfac2 = 2.0*np.sqrt(np.pi/15)
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fnormlbl1=["fxxx","fyyy","fzzz"]
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fnormfac1 = 2.0*np.sqrt(np.pi/7)
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fnormlbl2=["fxxy","fxxz","fxyy","fxzz","fyyz","fyzz"]
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fnormfac2 = 2.0*np.sqrt(np.pi/35)
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|
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fnormlbl3=["fxyz"]
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fnormfac3 = 2.0*np.sqrt(np.pi/105)
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|
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gnormlbl1=["gxxxx","gyyyy","gzzzz"]
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gnormfac1 = 2.0*np.sqrt(np.pi/9)
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|
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gnormlbl2=["gxxxy","gxxxz","gxyyy","gxzzz","gyyyz","gyzzz"]
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gnormfac2 = 2.0*np.sqrt(np.pi/63)
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|
|
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gnormlbl3=["gxxyy","gxxzz","gyyzz"]
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gnormfac3 = 2.0*np.sqrt(np.pi/105)
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|
|
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gnormlbl4=["gxxyz","gxyyz","gxyzz"]
|
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gnormfac4 = 2.0*np.sqrt(np.pi/315)
|
|
|
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hnormlbl1=["hxxxxx","hyyyyy","hzzzzz"]
|
|
hnormfac1 = 2.0*np.sqrt(np.pi/11)
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|
|
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hnormlbl2=["hxxxxy","hxxxxz","hxyyyy","hxzzzz","hyyyyz","hyzzzz"]
|
|
hnormfac2 = 2.0*np.sqrt(np.pi/99)
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|
|
|
hnormlbl3=["hxxxyy","hxxxzz","hxxyyy","hxxzzz","hyyyzz","hyyzzz"]
|
|
hnormfac3 = 2.0*np.sqrt(np.pi/231)
|
|
|
|
hnormlbl4=["hxxxyz","hxyyyz","hxyzzz"]
|
|
hnormfac4 = 2.0*np.sqrt(np.pi/693)
|
|
|
|
hnormlbl5=["hxxyyz","hxxyzz","hxyyzz"]
|
|
hnormfac5 = 2.0*np.sqrt(np.pi/1155)
|
|
|
|
for i_lbl,mo_lbl in enumerate(mol.cart_labels()):
|
|
if any(i in mo_lbl for i in dnormlbl1):
|
|
mo_coeff[i_lbl,:] *= dnormfac1
|
|
elif any(i in mo_lbl for i in dnormlbl2):
|
|
mo_coeff[i_lbl,:] *= dnormfac2
|
|
elif any(i in mo_lbl for i in fnormlbl1):
|
|
mo_coeff[i_lbl,:] *= fnormfac1
|
|
elif any(i in mo_lbl for i in fnormlbl2):
|
|
mo_coeff[i_lbl,:] *= fnormfac2
|
|
elif any(i in mo_lbl for i in fnormlbl3):
|
|
mo_coeff[i_lbl,:] *= fnormfac3
|
|
elif any(i in mo_lbl for i in gnormlbl1):
|
|
mo_coeff[i_lbl,:] *= gnormfac1
|
|
elif any(i in mo_lbl for i in gnormlbl2):
|
|
mo_coeff[i_lbl,:] *= gnormfac2
|
|
elif any(i in mo_lbl for i in gnormlbl3):
|
|
mo_coeff[i_lbl,:] *= gnormfac3
|
|
elif any(i in mo_lbl for i in gnormlbl4):
|
|
mo_coeff[i_lbl,:] *= gnormfac4
|
|
elif any(i in mo_lbl for i in hnormlbl1):
|
|
mo_coeff[i_lbl,:] *= hnormfac1
|
|
elif any(i in mo_lbl for i in hnormlbl2):
|
|
mo_coeff[i_lbl,:] *= hnormfac2
|
|
elif any(i in mo_lbl for i in hnormlbl3):
|
|
mo_coeff[i_lbl,:] *= hnormfac3
|
|
elif any(i in mo_lbl for i in hnormlbl4):
|
|
mo_coeff[i_lbl,:] *= hnormfac4
|
|
elif any(i in mo_lbl for i in hnormlbl5):
|
|
mo_coeff[i_lbl,:] *= hnormfac5
|
|
|
|
# Mo_coeff actif
|
|
mo_c = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
|
e_c = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
|
|
|
nao, nmo = mo_c.shape
|
|
|
|
print("n active MOs", nmo)
|
|
print("n AOs", nao)
|
|
assert nao==nao_c, "wrong number of AOs"
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclei #
|
|
# #
|
|
##########################################
|
|
|
|
natom = mol.natm
|
|
print('n_atom', natom)
|
|
|
|
atom_xyz = mol.atom_coords(unit='Bohr')
|
|
#if not(mol.unit.startswith(('B','b','au','AU'))):
|
|
# from pyscf.data.nist import BOHR
|
|
# atom_xyz /= BOHR # always convert to au
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nucl_num']=natom
|
|
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
|
|
qph5.create_dataset('nuclei/nucl_charge',data=mol.atom_charges())
|
|
|
|
strtype=h5py.special_dtype(vlen=str)
|
|
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
|
|
for i in range(natom):
|
|
atom_dset[i] = mol.atom_pure_symbol(i)
|
|
|
|
##########################################
|
|
# #
|
|
# Basis #
|
|
# #
|
|
##########################################
|
|
|
|
# nucleus on which each AO is centered
|
|
ao_nucl=[i[0] for i in mf.mol.ao_labels(fmt=False,base=1)]
|
|
|
|
|
|
nprim_max = 0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(mol.aoslice_by_atom()):
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
nprim = mol.bas_nprim(ib)
|
|
if (nprim > nprim_max):
|
|
nprim_max = nprim
|
|
|
|
qp_prim_num = np.zeros((nao),dtype=int)
|
|
qp_coef = np.zeros((nao,nprim_max))
|
|
qp_expo = np.zeros((nao,nprim_max))
|
|
qp_nucl = np.zeros((nao),dtype=int)
|
|
qp_pwr = np.zeros((nao,3),dtype=int)
|
|
|
|
clabels = mol.cart_labels(fmt=False)
|
|
|
|
tmp_idx=0
|
|
for iatom, (sh0,sh1,ao0,ao1) in enumerate(mol.aoslice_by_atom()):
|
|
# shell start,end; AO start,end (sph or cart) for each atom
|
|
for ib in range(sh0,sh1): # sets of contracted exponents
|
|
l = mol.bas_angular(ib) # angular momentum
|
|
nprim = mol.bas_nprim(ib) # numer of primitives
|
|
es = mol.bas_exp(ib) # exponents
|
|
cs = mol.bas_ctr_coeff(ib) # coeffs
|
|
nctr = mol.bas_nctr(ib) # number of contractions
|
|
print(iatom,ib,l,nprim,nctr,tmp_idx)
|
|
for ic in range(nctr): # sets of contraction coeffs
|
|
for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
|
|
qp_expo[tmp_idx,:nprim] = es[:]
|
|
qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
|
qp_nucl[tmp_idx] = iatom + 1
|
|
qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
|
|
qp_prim_num[tmp_idx] = nprim
|
|
tmp_idx += 1
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['mo_basis'].attrs['mo_num']=nmo
|
|
qph5['ao_basis'].attrs['ao_num']=nao
|
|
|
|
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
|
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
|
|
|
qph5.create_dataset('ao_basis/ao_nucl',data=qp_nucl)
|
|
qph5.create_dataset('ao_basis/ao_prim_num',data=qp_prim_num)
|
|
qph5.create_dataset('ao_basis/ao_expo',data=qp_expo.T)
|
|
qph5.create_dataset('ao_basis/ao_coef',data=qp_coef.T)
|
|
qph5.create_dataset('ao_basis/ao_power',data=qp_pwr.T)
|
|
|
|
##########################################
|
|
# #
|
|
# Electrons #
|
|
# #
|
|
##########################################
|
|
|
|
nelec = mol.nelectron
|
|
neleca,nelecb = mol.nelec
|
|
|
|
print('num_elec', nelec)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['electrons'].attrs['elec_alpha_num']=neleca
|
|
qph5['electrons'].attrs['elec_beta_num']=nelecb
|
|
|
|
##########################################
|
|
# #
|
|
# Nuclear Repulsion #
|
|
# #
|
|
##########################################
|
|
|
|
e_nuc = mol.energy_nuc()
|
|
|
|
print('nucl_repul', e_nuc)
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5['nuclei'].attrs['nuclear_repulsion']=e_nuc
|
|
|
|
##########################################
|
|
# #
|
|
# MO Coef #
|
|
# #
|
|
##########################################
|
|
|
|
with h5py.File(qph5path,'a') as qph5:
|
|
qph5.create_dataset('mo_basis/mo_coef',data=mo_c.T)
|
|
|
|
return
|