mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-11-13 17:43:50 +01:00
converter cleanup
This commit is contained in:
Kevin Gasperich
parent
b3390f2fa3
commit
1c09b7dcbc
@ -27,6 +27,19 @@ def pad(arr_in,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 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 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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@ -409,260 +422,110 @@ def pyscf2QP(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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#
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# eri_4d_ao = eri_4d_ao.reshape([Nk*nao]*4)
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if (print_ao_ints_bi or print_mo_ints_bi):
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if print_ao_ints_bi:
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with open('bielec_ao_complex','w') as outfile:
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pass
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if print_mo_ints_bi:
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with open('bielec_mo_complex','w') as outfile:
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pass
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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 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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if print_ao_ints_bi:
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with open('bielec_ao_complex','a') as outfile:
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],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('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
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if print_mo_ints_bi:
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with open('bielec_mo_complex','a') as outfile:
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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('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
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if (print_ao_ints_bi):
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print_ao_bi(mf,kconserv,'bielec_ao_complex',bielec_int_threshold)
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if (print_mo_ints_bi):
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print_mo_bi(mf,kconserv,'bielec_mo_complex',cas_idx,bielec_int_threshold)
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def testprintbi(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8):
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'''
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kpts = List of kpoints coordinates. Cannot be null, for gamma is other script
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kmesh = Mesh of kpoints (optional)
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cas_idx = List of active MOs. If not specified all MOs are actives
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int_threshold = The integral will be not printed in they are bellow that
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'''
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from pyscf.pbc import ao2mo
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from pyscf.pbc import tools
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from pyscf.pbc.gto import ecp
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from pyscf.data import nist
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import h5py
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import scipy
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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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bielec_int_threshold = int_threshold
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natom = cell.natm
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nelec = cell.nelectron
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neleca,nelecb = cell.nelec
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atom_xyz = mf.cell.atom_coords()
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if not(mf.cell.unit.startswith(('B','b','au','AU'))):
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atom_xyz /= nist.BOHR # always convert to au
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strtype=h5py.special_dtype(vlen=str)
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atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
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for i in range(natom):
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atom_dset[i] = mf.cell.atom_pure_symbol(i)
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qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
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qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
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print('n_atom per kpt', natom)
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print('num_elec per kpt', nelec)
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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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e_k = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
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Nk, nao, nmo = mo_k.shape
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print("n Kpts", Nk)
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print("n active Mos per kpt", nmo)
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print("n AOs per kpt", nao)
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naux = mf.with_df.auxcell.nao
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print("n df fitting functions", naux)
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#in old version: param << nelec*Nk, nmo*Nk, natom*Nk
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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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# ___ _
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# | ._ _|_ _ _ ._ _. | _ |_) o
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# _|_ | | |_ (/_ (_| | (_| | _> |_) |
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# _|
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#
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kconserv = tools.get_kconserv(cell, kpts)
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qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1)))
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kcon_test = np.zeros((Nk,Nk,Nk),dtype=int)
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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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kcon_test[a,c,b] = kconserv[a,b,c]+1
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qph5.create_dataset('nuclei/kconserv_test',data=kcon_test)
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with open('K.qp','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 = kconserv[a,b,c]
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outfile.write('%s %s %s %s\n' % (a+1,c+1,b+1,d+1))
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intfile=h5py.File(mf.with_df._cderi,'r')
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j3c = intfile.get('j3c')
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naosq = nao*nao
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naotri = (nao*(nao+1))//2
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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 using older version, stop before last level
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j3clist = [j3c.get(i) for i in j3ckeys]
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nkinvsq = 1./np.sqrt(Nk)
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# dimensions are (kikj,iaux,jao,kao), where kikj is compound index of kpts i and j
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# output dimensions should be reversed (nao, nao, naux, nkptpairs)
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j3arr=np.array([(i.value.reshape([-1,nao,nao]) if (i.shape[1] == naosq) else makesq3(i.value,nao)) * nkinvsq for i in j3clist])
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nkpt_pairs = j3arr.shape[0]
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df_ao_tmp = np.zeros((nao,nao,naux,nkpt_pairs),dtype=np.complex128)
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if print_ao_ints_df:
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with open('D.qp','w') as outfile:
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pass
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with open('D.qp','a') as outfile:
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for k,kpt_pair in enumerate(j3arr):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for i,i0 in enumerate(dfbasfunc):
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for j,v in enumerate(i0):
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if (abs(v) > bielec_int_threshold):
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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df_ao_tmp[i,j,iaux,k]=v
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qph5.create_dataset('ao_two_e_ints/df_ao_integrals_real',data=df_ao_tmp.real)
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qph5.create_dataset('ao_two_e_ints/df_ao_integrals_imag',data=df_ao_tmp.imag)
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if print_mo_ints_df:
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kpair_list=[]
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for i in range(Nk):
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for j in range(Nk):
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if(i>=j):
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kpair_list.append((i,j,idx2_tri((i,j))))
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j3mo = np.array([np.einsum('mij,ik,jl->mkl',j3arr[kij],mo_k[ki].conj(),mo_k[kj]) for ki,kj,kij in kpair_list])
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df_mo_tmp = np.zeros((nmo,nmo,naux,nkpt_pairs),dtype=np.complex128)
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with open('D_mo.qp','w') as outfile:
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pass
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with open('D_mo.qp','a') as outfile:
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for k,kpt_pair in enumerate(j3mo):
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for iaux,dfbasfunc in enumerate(kpt_pair):
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for i,i0 in enumerate(dfbasfunc):
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for j,v in enumerate(i0):
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if (abs(v) > bielec_int_threshold):
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outfile.write('%s %s %s %s %s %s\n' % (i+1,j+1,iaux+1,k+1,v.real,v.imag))
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df_mo_tmp[i,j,iaux,k]=v
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qph5.create_dataset('mo_two_e_ints/df_mo_integrals_real',data=df_mo_tmp.real)
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qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=df_mo_tmp.imag)
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with open(outfilename,'w') as outfile:
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pass
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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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with open(outfilename,'a') as outfile:
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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,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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# eri_4d_ao = np.zeros((Nk,nao,Nk,nao,Nk,nao,Nk,nao), dtype=np.complex)
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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 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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# v = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],compact=False).reshape((nao,)*4)
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# v *= 1./Nk
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# eri_4d_ao[a,:,b,:,c,:,d] = v
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#
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# eri_4d_ao = eri_4d_ao.reshape([Nk*nao]*4)
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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 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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pass
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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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with open(outfilename,'a') as outfile:
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],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,v.real,v.imag)+'\n')
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with open('W.qp','w') as outfile:
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pass
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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 idx2_tri((a,b)) > idx2_cd: continue
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if a>d: continue
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#if ((c==d) and (a>b)): continue
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ka = kpts[a]
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with open('W.qp','a') as outfile:
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eri_4d_ao_kpt = mf.with_df.get_ao_eri(kpts=[ka,kb,kc,kd],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('%s %s %s %s %s %s\n' % (ii+1,jj+1,kk+1,ll+1,v.real,v.imag))
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def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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