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Python _ao2mo.nr_e2函数代码示例

原作者: [db:作者] 来自: [db:来源] 收藏 邀请

本文整理汇总了Python中pyscf.ao2mo._ao2mo.nr_e2函数的典型用法代码示例。如果您正苦于以下问题:Python nr_e2函数的具体用法?Python nr_e2怎么用?Python nr_e2使用的例子?那么恭喜您, 这里精选的函数代码示例或许可以为您提供帮助。



在下文中一共展示了nr_e2函数的20个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于我们的系统推荐出更棒的Python代码示例。

示例1: vind

    def vind(xys):
        nz = len(xys)
        if wfnsym is not None and mol.symmetry:
            # shape(nz,2,nocc,nvir): 2 ~ X,Y
            xys = numpy.copy(xys).reshape(nz,2,nocc,nvir)
            xys[:,:,sym_forbid] = 0
        dms = numpy.empty((nz,nao,nao))
        for i in range(nz):
            x, y = xys[i].reshape(2,nocc,nvir)
            # *2 for double occupancy
            dmx = reduce(numpy.dot, (orbo, x*2, orbv.T))
            dmy = reduce(numpy.dot, (orbv, y.T*2, orbo.T))
            dms[i] = dmx + dmy  # AX + BY

        v1ao = vresp(dms)
        v1ov = _ao2mo.nr_e2(v1ao, mo_coeff, (0,nocc,nocc,nmo)).reshape(-1,nocc,nvir)
        v1vo = _ao2mo.nr_e2(v1ao, mo_coeff, (nocc,nmo,0,nocc)).reshape(-1,nvir,nocc)
        hx = numpy.empty((nz,2,nocc,nvir), dtype=v1ov.dtype)
        for i in range(nz):
            x, y = xys[i].reshape(2,nocc,nvir)
            hx[i,0] = v1ov[i]
            hx[i,0]+= numpy.einsum('sp,qs->qp', fvv, x)  # AX
            hx[i,0]-= numpy.einsum('sp,pr->sr', foo, x)  # AX
            hx[i,1] =-v1vo[i].T
            hx[i,1]-= numpy.einsum('sp,qs->qp', fvv, y)  #-AY
            hx[i,1]+= numpy.einsum('sp,pr->sr', foo, y)  #-AY

        if wfnsym is not None and mol.symmetry:
            hx[:,:,sym_forbid] = 0
        return hx.reshape(nz,-1)
开发者ID:chrinide,项目名称:pyscf,代码行数:30,代码来源:rhf.py


示例2: vind

 def vind(mo1):
     mo1aa, mo1ab, mo1ba, mo1bb = _split_mo1(mo1)
     dm1aa = _dm1_mo2ao(mo1aa, orbva, orboa)
     dm1ab = _dm1_mo2ao(mo1ab, orbva, orbob)
     dm1ba = _dm1_mo2ao(mo1ba, orbvb, orboa)
     dm1bb = _dm1_mo2ao(mo1bb, orbvb, orbob)
     dm1 = lib.asarray([dm1aa+dm1aa.transpose(0,2,1),
                        dm1ab+dm1ba.transpose(0,2,1),
                        dm1ba+dm1ab.transpose(0,2,1),
                        dm1bb+dm1bb.transpose(0,2,1)])
     v1 = vresp(dm1)
     v1aa = _ao2mo.nr_e2(v1[0], mo_va_oa, (0,nvira,nvira,nvira+nocca))
     v1ab = _ao2mo.nr_e2(v1[1], mo_va_ob, (0,nvira,nvira,nvira+noccb))
     v1ba = _ao2mo.nr_e2(v1[2], mo_vb_oa, (0,nvirb,nvirb,nvirb+nocca))
     v1bb = _ao2mo.nr_e2(v1[3], mo_vb_ob, (0,nvirb,nvirb,nvirb+noccb))
     v1aa = v1aa.reshape(nset,nvira,nocca)
     v1ab = v1ab.reshape(nset,nvira,noccb)
     v1ba = v1ba.reshape(nset,nvirb,nocca)
     v1bb = v1bb.reshape(nset,nvirb,noccb)
     v1aa *= eai_aa
     v1ab *= eai_ab
     v1ba *= eai_ba
     v1bb *= eai_bb
     v1mo = numpy.hstack((v1aa.reshape(nset,-1),
                          v1ab.reshape(nset,-1),
                          v1ba.reshape(nset,-1),
                          v1bb.reshape(nset,-1)))
     return v1mo.ravel()
开发者ID:chrinide,项目名称:pyscf,代码行数:28,代码来源:uhf.py


示例3: _trans_aapp_

def _trans_aapp_(mo, ncore, ncas, fload, ao_loc=None):
    nmo = mo[0].shape[1]
    nocc = (ncore[0] + ncas, ncore[1] + ncas)
    c_nmo = ctypes.c_int(nmo)

    klshape = (0, nmo, 0, nmo)

    japcv = numpy.empty((ncas,nmo,ncore[0],nmo-ncore[0]))
    aapp = numpy.empty((ncas,ncas,nmo,nmo))
    aaPP = numpy.empty((ncas,ncas,nmo,nmo))
    appa = numpy.empty((ncas,nmo,nmo,ncas))
    apPA = numpy.empty((ncas,nmo,nmo,ncas))
    apCV = numpy.empty((ncas,nmo,ncore[1],nmo-ncore[1]))
    ppp = numpy.empty((nmo,nmo,nmo))
    for i in range(ncas):
        buf = _ao2mo.nr_e2(fload(ncore[0]+i), mo[0], klshape,
                            aosym='s4', mosym='s2', ao_loc=ao_loc)
        lib.unpack_tril(buf, out=ppp)
        aapp[i] = ppp[ncore[0]:nocc[0]]
        appa[i] = ppp[:,:,ncore[0]:nocc[0]]
        #japcp = avcp * 2 - acpv.transpose(0,2,1,3) - avcp.transpose(0,3,2,1)
        japcv[i] = ppp[:,:ncore[0],ncore[0]:] * 2 \
                 - ppp[:ncore[0],:,ncore[0]:].transpose(1,0,2) \
                 - ppp[ncore[0]:,:ncore[0],:].transpose(2,1,0)

        buf = _ao2mo.nr_e2(fload(ncore[0]+i), mo[1], klshape,
                            aosym='s4', mosym='s2', ao_loc=ao_loc)
        lib.unpack_tril(buf, out=ppp)
        aaPP[i] = ppp[ncore[0]:nocc[0]]
        apPA[i] = ppp[:,:,ncore[1]:nocc[1]]
        apCV[i] = ppp[:,:ncore[1],ncore[1]:]

    return aapp, aaPP, appa, apPA, japcv, apCV
开发者ID:eronca,项目名称:pyscf,代码行数:33,代码来源:mc_ao2mo_uhf.py


示例4: vind

 def vind(mo1):
     mo1a = mo1.reshape(-1,nova+novb)[:,:nova].reshape(-1,nvira,nocca)
     mo1b = mo1.reshape(-1,nova+novb)[:,nova:].reshape(-1,nvirb,noccb)
     nset = mo1a.shape[0]
     dm1a = _dm1_mo2ao(mo1a, orbva, orboa)
     dm1b = _dm1_mo2ao(mo1b, orbvb, orbob)
     dm1 = numpy.vstack([dm1a-dm1a.transpose(0,2,1),
                         dm1b-dm1b.transpose(0,2,1)])
     v1 = vresp(dm1)
     v1a = _ao2mo.nr_e2(v1[    :nset], mo_va_oa, (0,nvira,nvira,nvira+nocca))
     v1b = _ao2mo.nr_e2(v1[nset:    ], mo_vb_ob, (0,nvirb,nvirb,nvirb+noccb))
     v1mo = numpy.hstack((v1a.reshape(nset,-1), v1b.reshape(nset,-1)))
     return v1mo.ravel()
开发者ID:chrinide,项目名称:pyscf,代码行数:13,代码来源:test_uhf.py


示例5: trans_e1_incore

def trans_e1_incore(eri_ao, mo, ncore, ncas):
    nmo = mo.shape[1]
    nocc = ncore + ncas
    eri1 = pyscf.ao2mo.incore.half_e1(eri_ao, (mo,mo[:,:nocc]), compact=False)
    eri1 = eri1.reshape(nmo,nocc,-1)

    klppshape = (0, nmo, 0, nmo)
    klpashape = (0, nmo, ncore, nocc)
    aapp = numpy.empty((ncas,ncas,nmo,nmo))
    for i in range(ncas):
        _ao2mo.nr_e2(eri1[ncore+i,ncore:nocc], mo, klppshape,
                      aosym='s4', mosym='s1', out=aapp[i])
    ppaa = pyscf.lib.transpose(aapp.reshape(ncas*ncas,-1)).reshape(nmo,nmo,ncas,ncas)
    aapp = None

    papa = numpy.empty((nmo,ncas,nmo,ncas))
    for i in range(nmo):
        _ao2mo.nr_e2(eri1[i,ncore:nocc], mo, klpashape,
                      aosym='s4', mosym='s1', out=papa[i])

    pp = numpy.empty((nmo,nmo))
    j_cp = numpy.zeros((ncore,nmo))
    k_pc = numpy.zeros((nmo,ncore))
    for i in range(ncore):
        _ao2mo.nr_e2(eri1[i,i:i+1], mo, klppshape, aosym='s4', mosym='s1', out=pp)
        j_cp[i] = pp.diagonal()
    j_pc = j_cp.T.copy()

    pp = numpy.empty((ncore,ncore))
    for i in range(nmo):
        klshape = (i, i+1, 0, ncore)
        _ao2mo.nr_e2(eri1[i,:ncore], mo, klshape, aosym='s4', mosym='s1', out=pp)
        k_pc[i] = pp.diagonal()
    return j_pc, k_pc, ppaa, papa
开发者ID:berquist,项目名称:pyscf,代码行数:34,代码来源:mc_ao2mo.py


示例6: vind

 def vind(mo1):
     dm1 = _dm1_mo2ao(mo1.reshape(nset,nvir,nocc), orbv, orbo*2)  # *2 for double occupancy
     dm1 = dm1 + dm1.transpose(0,2,1)
     v1 = vresp(dm1)
     v1 = _ao2mo.nr_e2(v1, mo_v_o, (0,nvir,nvir,nmo)).reshape(nset,nvir,nocc)
     v1 *= eai
     return v1.ravel()
开发者ID:chrinide,项目名称:pyscf,代码行数:7,代码来源:rhf.py


示例7: get_vind

    def get_vind(self, zs):
        mol = self.mol
        mo_coeff = self._scf.mo_coeff
        mo_energy = self._scf.mo_energy
        nao, nmo = mo_coeff.shape
        nocc = (self._scf.mo_occ>0).sum()
        nvir = nmo - nocc
        orbv = mo_coeff[:,nocc:]
        orbo = mo_coeff[:,:nocc]
        eai = pyscf.lib.direct_sum('a-i->ai', mo_energy[nocc:], mo_energy[:nocc])
        dai = numpy.sqrt(eai).ravel()

        nz = len(zs)
        dmvo = numpy.empty((nz,nao,nao))
        for i, z in enumerate(zs):
            dm = reduce(numpy.dot, (orbv, (dai*z).reshape(nvir,nocc), orbo.T))
            dmvo[i] = dm + dm.T # +cc for A+B and K_{ai,jb} in A == K_{ai,bj} in B

        mem_now = pyscf.lib.current_memory()[0]
        max_memory = max(2000, self.max_memory*.9-mem_now)
        v1ao = _contract_xc_kernel(self, self._scf.xc, dmvo,
                                   singlet=self.singlet, max_memory=max_memory)

        if self.singlet:
            vj = self._scf.get_j(mol, dmvo, hermi=1)
            v1ao += vj * 2

        v1vo = _ao2mo.nr_e2(v1ao, mo_coeff, (nocc,nmo,0,nocc)).reshape(-1,nvir*nocc)
        edai = eai.ravel() * dai
        for i, z in enumerate(zs):
            # numpy.sqrt(eai) * (eai*dai*z + v1vo)
            v1vo[i] += edai*z
            v1vo[i] *= dai
        return v1vo.reshape(nz,-1)
开发者ID:berquist,项目名称:pyscf,代码行数:34,代码来源:rks.py


示例8: _trans

def _trans(mo, ncore, ncas, fload, cvcv=None, ao_loc=None):
    nao, nmo = mo.shape
    nocc = ncore + ncas
    nvir = nmo - nocc
    nav = nmo - ncore

    if cvcv is None:
        cvcv = numpy.zeros((ncore*nvir,ncore*nvir))
    pacv = numpy.empty((nmo,ncas,ncore*nvir))
    aapp = numpy.empty((ncas,ncas,nmo*nmo))
    papa = numpy.empty((nmo,ncas,nmo*ncas))
    vcv = numpy.empty((nav,ncore*nvir))
    apa = numpy.empty((ncas,nmo*ncas))
    vpa = numpy.empty((nav,nmo*ncas))
    app = numpy.empty((ncas,nmo*nmo))
    for i in range(ncore):
        buf = fload(i, i+1)
        klshape = (0, ncore, nocc, nmo)
        _ao2mo.nr_e2(buf, mo, klshape,
                      aosym='s4', mosym='s1', out=vcv, ao_loc=ao_loc)
        cvcv[i*nvir:(i+1)*nvir] = vcv[ncas:]
        pacv[i] = vcv[:ncas]

        klshape = (0, nmo, ncore, nocc)
        _ao2mo.nr_e2(buf[:ncas], mo, klshape,
                      aosym='s4', mosym='s1', out=apa, ao_loc=ao_loc)
        papa[i] = apa
    for i in range(ncas):
        buf = fload(ncore+i, ncore+i+1)
        klshape = (0, ncore, nocc, nmo)
        _ao2mo.nr_e2(buf, mo, klshape,
                      aosym='s4', mosym='s1', out=vcv, ao_loc=ao_loc)
        pacv[ncore:,i] = vcv

        klshape = (0, nmo, ncore, nocc)
        _ao2mo.nr_e2(buf, mo, klshape,
                      aosym='s4', mosym='s1', out=vpa, ao_loc=ao_loc)
        papa[ncore:,i] = vpa

        klshape = (0, nmo, 0, nmo)
        _ao2mo.nr_e2(buf[:ncas], mo, klshape,
                      aosym='s4', mosym='s1', out=app, ao_loc=ao_loc)
        aapp[i] = app
    #pyscf.lib.transpose(aapp.reshape(ncas**2, -1), inplace=True)
    ppaa = pyscf.lib.transpose(aapp.reshape(ncas**2,-1))
    return (ppaa.reshape(nmo,nmo,ncas,ncas), papa.reshape(nmo,ncas,nmo,ncas),
            pacv.reshape(nmo,ncas,ncore,nvir), cvcv)
开发者ID:ushnishray,项目名称:pyscf,代码行数:47,代码来源:icmpspt.py


示例9: loop_ao2mo

 def loop_ao2mo(self, mo_coeff, nocc):
     mo = numpy.asarray(mo_coeff, order='F')
     nmo = mo.shape[1]
     ijslice = (0, nocc, nocc, nmo)
     Lov = None
     for eri1 in self._scf.with_df.loop():
         Lov = _ao2mo.nr_e2(eri1, mo, ijslice, aosym='s2', out=Lov)
         yield Lov
开发者ID:eronca,项目名称:pyscf,代码行数:8,代码来源:dfmp2.py


示例10: ao2mo

 def ao2mo(self, mo_coeffs, compact=True):
     if isinstance(mo_coeffs, numpy.ndarray) and mo_coeffs.ndim == 2:
         mo_coeffs = (mo_coeffs,) * 4
     ijmosym, nij_pair, moij, ijslice = _conc_mos(mo_coeffs[0], mo_coeffs[1], compact)
     klmosym, nkl_pair, mokl, klslice = _conc_mos(mo_coeffs[2], mo_coeffs[3], compact)
     mo_eri = numpy.zeros((nij_pair,nkl_pair))
     sym = (iden_coeffs(mo_coeffs[0], mo_coeffs[2]) and
            iden_coeffs(mo_coeffs[1], mo_coeffs[3]))
     Lij = Lkl = None
     for eri1 in self.loop():
         Lij = _ao2mo.nr_e2(eri1, moij, ijslice, aosym='s2', mosym=ijmosym, out=Lij)
         if sym:
             Lkl = Lij
         else:
             Lkl = _ao2mo.nr_e2(eri1, mokl, klslice, aosym='s2', mosym=klmosym, out=Lkl)
         lib.dot(Lij.T, Lkl, 1, mo_eri, 1)
     return mo_eri
开发者ID:eronca,项目名称:pyscf,代码行数:17,代码来源:df.py


示例11: _trans_aapp_

def _trans_aapp_(mo, ncore, ncas, fload, ao_loc=None):
    nmo = mo[0].shape[1]
    nocc = (ncore[0] + ncas, ncore[1] + ncas)
    c_nmo = ctypes.c_int(nmo)
    funpack = pyscf.lib.numpy_helper._np_helper.NPdunpack_tril

    klshape = (0, nmo, 0, nmo)

    japcv = numpy.empty((ncas,nmo,ncore[0],nmo-ncore[0]))
    aapp = numpy.empty((ncas,ncas,nmo,nmo))
    aaPP = numpy.empty((ncas,ncas,nmo,nmo))
    appa = numpy.empty((ncas,nmo,nmo,ncas))
    apPA = numpy.empty((ncas,nmo,nmo,ncas))
    apCV = numpy.empty((ncas,nmo,ncore[1],nmo-ncore[1]))
    ppp = numpy.empty((nmo,nmo,nmo))
    for i in range(ncas):
        buf = _ao2mo.nr_e2(fload(ncore[0]+i), mo[0], klshape,
                            aosym='s4', mosym='s2', ao_loc=ao_loc)
        for j in range(nmo):
            funpack(c_nmo, buf[j].ctypes.data_as(ctypes.c_void_p),
                    ppp[j].ctypes.data_as(ctypes.c_void_p), ctypes.c_int(1))
        aapp[i] = ppp[ncore[0]:nocc[0]]
        appa[i] = ppp[:,:,ncore[0]:nocc[0]]
        #japcp = avcp * 2 - acpv.transpose(0,2,1,3) - avcp.transpose(0,3,2,1)
        japcv[i] = ppp[:,:ncore[0],ncore[0]:] * 2 \
                 - ppp[:ncore[0],:,ncore[0]:].transpose(1,0,2) \
                 - ppp[ncore[0]:,:ncore[0],:].transpose(2,1,0)

        buf = _ao2mo.nr_e2(fload(ncore[0]+i), mo[1], klshape,
                            aosym='s4', mosym='s2', ao_loc=ao_loc)
        for j in range(nmo):
            funpack(c_nmo, buf[j].ctypes.data_as(ctypes.c_void_p),
                    ppp[j].ctypes.data_as(ctypes.c_void_p), ctypes.c_int(1))
        aaPP[i] = ppp[ncore[0]:nocc[0]]
        apPA[i] = ppp[:,:,ncore[1]:nocc[1]]
        apCV[i] = ppp[:,:ncore[1],ncore[1]:]

    return aapp, aaPP, appa, apPA, japcv, apCV
开发者ID:berquist,项目名称:pyscf,代码行数:38,代码来源:mc_ao2mo_uhf.py


示例12: vind

 def vind(zs):
     nz = len(zs)
     dmov = numpy.empty((nz,nao,nao))
     for i, z in enumerate(zs):
         # *2 for double occupancy
         dm = reduce(numpy.dot, (orbo, (d_ia*z).reshape(nocc,nvir)*2, orbv.T))
         dmov[i] = dm + dm.T # +cc for A+B and K_{ai,jb} in A == K_{ai,bj} in B
     v1ao = vresp(dmov)
     v1ov = _ao2mo.nr_e2(v1ao, mo_coeff, (0,nocc,nocc,nmo)).reshape(-1,nocc*nvir)
     for i, z in enumerate(zs):
         # numpy.sqrt(e_ia) * (e_ia*d_ia*z + v1ov)
         v1ov[i] += ed_ia*z
         v1ov[i] *= d_ia
     return v1ov.reshape(nz,-1)
开发者ID:chrinide,项目名称:pyscf,代码行数:14,代码来源:rks.py


示例13: vind

        def vind(zs):
            nz = len(zs)
            if wfnsym is not None and mol.symmetry:
                zs = numpy.copy(zs)
                zs[:,sym_forbid] = 0
            dmov = numpy.empty((2,nz,nao,nao))
            for i in range(nz):
                z = d_ia * zs[i]
                za = z[:nocca*nvira].reshape(nocca,nvira)
                zb = z[nocca*nvira:].reshape(noccb,nvirb)
                dm = reduce(numpy.dot, (orboa, za, orbva.T))
                dmov[0,i] = dm + dm.T
                dm = reduce(numpy.dot, (orbob, zb, orbvb.T))
                dmov[1,i] = dm + dm.T

            v1ao = vresp(dmov)
            v1a = _ao2mo.nr_e2(v1ao[0], mo_coeff[0], (0,nocca,nocca,nmo))
            v1b = _ao2mo.nr_e2(v1ao[1], mo_coeff[1], (0,noccb,noccb,nmo))
            hx = numpy.hstack((v1a.reshape(nz,-1), v1b.reshape(nz,-1)))
            for i, z in enumerate(zs):
                hx[i] += ed_ia * z
                hx[i] *= d_ia
            return hx
开发者ID:chrinide,项目名称:pyscf,代码行数:23,代码来源:uks.py


示例14: loop_ao2mo

    def loop_ao2mo(self, mo_coeff, nocc):
        mo = numpy.asarray(mo_coeff, order='F')
        nmo = mo.shape[1]
        ijslice = (0, nocc, nocc, nmo)
        Lov = None
        with_df = self.with_df

        nvir = nmo - nocc
        naux = with_df.get_naoaux()
        mem_now = lib.current_memory()[0]
        max_memory = max(2000, self.max_memory*.9-mem_now)
        blksize = int(min(naux, max(with_df.blockdim,
                                    (max_memory*1e6/8-nocc*nvir**2*2)/(nocc*nvir))))
        for eri1 in with_df.loop(blksize=blksize):
            Lov = _ao2mo.nr_e2(eri1, mo, ijslice, aosym='s2', out=Lov)
            yield Lov
开发者ID:chrinide,项目名称:pyscf,代码行数:16,代码来源:dfmp2.py


示例15: _exact_paaa

        def _exact_paaa(self, mo, u, out=None):
            if self.with_df:
                nmo = mo.shape[1]
                ncore = self.ncore
                ncas = self.ncas
                nocc = ncore + ncas
                mo1 = numpy.dot(mo, u)
                mo1_cas = mo1[:,ncore:nocc]

                paaa = numpy.zeros((nmo*ncas,ncas*ncas))
                moij = numpy.asarray(numpy.hstack((mo1, mo1_cas)), order='F')
                ijshape = (0, nmo, nmo, nmo+ncas)
                for eri1 in self.with_df.loop():
                    bufpa = _ao2mo.nr_e2(eri1, moij, ijshape, 's2', 's1')
                    bufaa = numpy.asarray(buf1[ncore:nocc,:], order='C')
                    pyscf.lib.dot(bufpa.T, bufaa, 1, paaa, 1)
                return paaa.reshape(nmo,ncas,ncas,ncas)
            else:
                return casscf_class._exact_paaa(self, mol, u, out)
开发者ID:berquist,项目名称:pyscf,代码行数:19,代码来源:df.py


示例16: _trans_cvcv_

def _trans_cvcv_(mo, ncore, ncas, fload, ao_loc=None):
    nmo = mo[0].shape[1]
    c_nmo = ctypes.c_int(nmo)
    funpack = pyscf.lib.numpy_helper._np_helper.NPdunpack_tril

    jc_pp = numpy.empty((ncore[0],nmo,nmo))
    jc_PP = numpy.zeros((nmo,nmo))
    kc_pp = numpy.empty((ncore[0],nmo,nmo))
    jcvcv = numpy.zeros((ncore[0],nmo-ncore[0],ncore[0],nmo-ncore[0]))
    cvCV = numpy.empty((ncore[0],nmo-ncore[0],ncore[1],nmo-ncore[1]))
    vcp = numpy.empty((nmo-ncore[0],ncore[0],nmo))
    cpp = numpy.empty((ncore[0],nmo,nmo))
    for i in range(ncore[0]):
        buf = fload(i)
        klshape = (0, ncore[1], ncore[1], nmo)
        _ao2mo.nr_e2(buf[ncore[0]:nmo], mo[1], klshape,
                      aosym='s4', mosym='s1', out=cvCV[i], ao_loc=ao_loc)

        klshape = (0, nmo, 0, nmo)
        tmp = _ao2mo.nr_e2(buf[i:i+1], mo[1], klshape, aosym='s4',
                            mosym='s1', ao_loc=ao_loc)
        jc_PP += tmp.reshape(nmo,nmo)

        klshape = (0, ncore[0], 0, nmo)
        _ao2mo.nr_e2(buf[ncore[0]:nmo], mo[0], klshape,
                      aosym='s4', mosym='s1', out=vcp, ao_loc=ao_loc)
        kc_pp[i,ncore[0]:] = vcp[:,i]

        klshape = (0, nmo, 0, nmo)
        _ao2mo.nr_e2(buf[:ncore[0]], mo[0], klshape,
                      aosym='s4', mosym='s2', out=buf[:ncore[0]],
                      ao_loc=ao_loc)
        for j in range(ncore[0]):
            funpack(c_nmo, buf[j].ctypes.data_as(ctypes.c_void_p),
                    cpp[j].ctypes.data_as(ctypes.c_void_p), ctypes.c_int(1))
        jc_pp[i] = cpp[i]
        kc_pp[i,:ncore[0]] = cpp[:,i]

        #jcvcv = cvcv * 2 - cvcv.transpose(2,1,0,3) - ccvv.transpose(0,2,1,3)
        jcvcv[i] = vcp[:,:,ncore[0]:] * 2 \
                 - vcp[:,:,ncore[0]:].transpose(2,1,0) \
                 - cpp[:,ncore[0]:,ncore[0]:].transpose(1,0,2)

    return jc_pp, jc_PP, kc_pp, jcvcv, cvCV
开发者ID:berquist,项目名称:pyscf,代码行数:44,代码来源:mc_ao2mo_uhf.py


示例17: _add_vvVV

def _add_vvVV(mycc, t1, t2ab, eris, out=None):
    '''Ht2 = np.einsum('iJcD,acBD->iJaB', t2ab, vvVV)
    without using symmetry in t2ab or Ht2
    '''
    time0 = time.clock(), time.time()
    if t2ab.size == 0:
        return np.zeros_like(t2ab)
    if t1 is not None:
        t2ab = make_tau_ab(t2ab, t1, t1)

    log = logger.Logger(mycc.stdout, mycc.verbose)
    nocca, noccb, nvira, nvirb = t2ab.shape

    if mycc.direct:  # AO direct CCSD
        if getattr(eris, 'mo_coeff', None) is not None:
            mo_a, mo_b = eris.mo_coeff
        else:
            moidxa, moidxb = mycc.get_frozen_mask()
            mo_a = mycc.mo_coeff[0][:,moidxa]
            mo_b = mycc.mo_coeff[1][:,moidxb]
        # Note tensor t2ab may be t2bbab from eom_uccsd code.  In that
        # particular case, nocca, noccb do not equal to the actual number of
        # alpha/beta occupied orbitals. orbva and orbvb cannot be indexed as
        # mo_a[:,nocca:] and mo_b[:,noccb:]
        orbva = mo_a[:,-nvira:]
        orbvb = mo_b[:,-nvirb:]
        tau = lib.einsum('ijab,pa->ijpb', t2ab, orbva)
        tau = lib.einsum('ijab,pb->ijap', tau, orbvb)
        time0 = logger.timer_debug1(mycc, 'vvvv-tau mo2ao', *time0)
        buf = eris._contract_vvVV_t2(mycc, tau, mycc.direct, out, log)
        mo = np.asarray(np.hstack((orbva, orbvb)), order='F')
        Ht2 = _ao2mo.nr_e2(buf.reshape(nocca*noccb,-1), mo.conj(),
                           (0,nvira,nvira,nvira+nvirb), 's1', 's1')
        return Ht2.reshape(t2ab.shape)
    else:
        return eris._contract_vvVV_t2(mycc, t2ab, mycc.direct, out, log)
开发者ID:wmizukami,项目名称:pyscf,代码行数:36,代码来源:uccsd.py


示例18: kernel

def kernel(mp, t2, atmlst=None, mf_grad=None, verbose=logger.INFO):
    if mf_grad is None: mf_grad = mp._scf.nuc_grad_method()

    log = logger.new_logger(mp, verbose)
    time0 = time.clock(), time.time()

    log.debug('Build mp2 rdm1 intermediates')
    d1 = mp2._gamma1_intermediates(mp, t2)
    doo, dvv = d1
    time1 = log.timer_debug1('rdm1 intermediates', *time0)

# Set nocc, nvir for half-transformation of 2pdm.  Frozen orbitals are exculded.
# nocc, nvir should be updated to include the frozen orbitals when proceeding
# the 1-particle quantities later.
    mol = mp.mol
    with_frozen = not (mp.frozen is None or mp.frozen is 0)
    OA, VA, OF, VF = _index_frozen_active(mp.get_frozen_mask(), mp.mo_occ)
    orbo = mp.mo_coeff[:,OA]
    orbv = mp.mo_coeff[:,VA]
    nao, nocc = orbo.shape
    nvir = orbv.shape[1]

# Partially transform MP2 density matrix and hold it in memory
# The rest transformation are applied during the contraction to ERI integrals
    part_dm2 = _ao2mo.nr_e2(t2.reshape(nocc**2,nvir**2),
                            numpy.asarray(orbv.T, order='F'), (0,nao,0,nao),
                            's1', 's1').reshape(nocc,nocc,nao,nao)
    part_dm2 = (part_dm2.transpose(0,2,3,1) * 4 -
                part_dm2.transpose(0,3,2,1) * 2)

    hf_dm1 = mp._scf.make_rdm1(mp.mo_coeff, mp.mo_occ)

    if atmlst is None:
        atmlst = range(mol.natm)
    offsetdic = mol.offset_nr_by_atom()
    diagidx = numpy.arange(nao)
    diagidx = diagidx*(diagidx+1)//2 + diagidx
    de = numpy.zeros((len(atmlst),3))
    Imat = numpy.zeros((nao,nao))
    fdm2 = lib.H5TmpFile()
    vhf1 = fdm2.create_dataset('vhf1', (len(atmlst),3,nao,nao), 'f8')

# 2e AO integrals dot 2pdm
    max_memory = max(0, mp.max_memory - lib.current_memory()[0])
    blksize = max(1, int(max_memory*.9e6/8/(nao**3*2.5)))
    Imat1 = 0
    Imat2 = 0

    for k, ia in enumerate(atmlst):
        shl0, shl1, p0, p1 = offsetdic[ia]
        ip1 = p0
        vhf = numpy.zeros((3,nao,nao))
        for b0, b1, nf in _shell_prange(mol, shl0, shl1, blksize):
            ip0, ip1 = ip1, ip1 + nf
            dm2buf = lib.einsum('pi,iqrj->pqrj', orbo[ip0:ip1], part_dm2)
            dm2buf+= lib.einsum('qi,iprj->pqrj', orbo, part_dm2[:,ip0:ip1])
            dm2buf = lib.einsum('pqrj,sj->pqrs', dm2buf, orbo)
            dm2buf = dm2buf + dm2buf.transpose(0,1,3,2)
            dm2buf = lib.pack_tril(dm2buf.reshape(-1,nao,nao)).reshape(nf,nao,-1)
            dm2buf[:,:,diagidx] *= .5

            shls_slice = (b0,b1,0,mol.nbas,0,mol.nbas,0,mol.nbas)
            eri0 = mol.intor('int2e', aosym='s2kl', shls_slice=shls_slice)
            Imat += lib.einsum('ipx,iqx->pq', eri0.reshape(nf,nao,-1), dm2buf)
            eri0 = None

            eri1 = mol.intor('int2e_ip1', comp=3, aosym='s2kl',
                             shls_slice=shls_slice).reshape(3,nf,nao,-1)
            de[k] -= numpy.einsum('xijk,ijk->x', eri1, dm2buf) * 2
            dm2buf = None
# HF part
            for i in range(3):
                eri1tmp = lib.unpack_tril(eri1[i]).reshape(nf*nao,-1)
                eri1tmp = eri1tmp.reshape(nf,nao,nao,nao)
                vhf[i] += numpy.einsum('ijkl,ij->kl', eri1tmp, hf_dm1[ip0:ip1])
                vhf[i] -= numpy.einsum('ijkl,il->kj', eri1tmp, hf_dm1[ip0:ip1]) * .5
                vhf[i,ip0:ip1] += numpy.einsum('ijkl,kl->ij', eri1tmp, hf_dm1)
                vhf[i,ip0:ip1] -= numpy.einsum('ijkl,jk->il', eri1tmp, hf_dm1) * .5
            eri1 = eri1tmp = None
        vhf1[k] = vhf
        log.debug('2e-part grad of atom %d %s = %s', ia, mol.atom_symbol(ia), de[k])
        time1 = log.timer_debug1('2e-part grad of atom %d'%ia, *time1)

# Recompute nocc, nvir to include the frozen orbitals and make contraction for
# the 1-particle quantities, see also the kernel function in ccsd_grad module.
    mo_coeff = mp.mo_coeff
    mo_energy = mp._scf.mo_energy
    nao, nmo = mo_coeff.shape
    nocc = numpy.count_nonzero(mp.mo_occ > 0)
    Imat = reduce(numpy.dot, (mo_coeff.T, Imat, mp._scf.get_ovlp(), mo_coeff)) * -1

    dm1mo = numpy.zeros((nmo,nmo))
    if with_frozen:
        dco = Imat[OF[:,None],OA] / (mo_energy[OF,None] - mo_energy[OA])
        dfv = Imat[VF[:,None],VA] / (mo_energy[VF,None] - mo_energy[VA])
        dm1mo[OA[:,None],OA] = doo + doo.T
        dm1mo[OF[:,None],OA] = dco
        dm1mo[OA[:,None],OF] = dco.T
        dm1mo[VA[:,None],VA] = dvv + dvv.T
        dm1mo[VF[:,None],VA] = dfv
#.........这里部分代码省略.........
开发者ID:chrinide,项目名称:pyscf,代码行数:101,代码来源:mp2.py


示例19: general

def general(mol, mo_coeffs, erifile, auxbasis='weigend+etb', dataname='eri_mo', tmpdir=None,
            int3c='cint3c2e_sph', aosym='s2ij', int2c='cint2c2e_sph', comp=1,
            max_memory=2000, ioblk_size=256, verbose=0, compact=True):
    ''' Transform ij of (ij|L) to MOs.
    '''
    assert(aosym in ('s1', 's2ij'))
    time0 = (time.clock(), time.time())
    if isinstance(verbose, logger.Logger):
        log = verbose
    else:
        log = logger.Logger(mol.stdout, verbose)

    swapfile = tempfile.NamedTemporaryFile(dir=tmpdir)
    cholesky_eri_b(mol, swapfile.name, auxbasis, dataname,
                   int3c, aosym, int2c, comp, ioblk_size, verbose=log)
    fswap = h5py.File(swapfile.name, 'r')
    time1 = log.timer('AO->MO eri transformation 1 pass', *time0)

    nmoi = mo_coeffs[0].shape[1]
    nmoj = mo_coeffs[1].shape[1]
    nao = mo_coeffs[0].shape[0]
    auxmol = incore.format_aux_basis(mol, auxbasis)
    naoaux = auxmol.nao_nr()
    aosym = _stand_sym_code(aosym)
    if aosym == 's1':
        nao_pair = nao * nao
        aosym_as_nr_e2 = 's1'
    else:
        nao_pair = nao * (nao+1) // 2
        aosym_as_nr_e2 = 's2kl'

    ijmosym, nij_pair, moij, ijshape = \
            ao2mo.incore._conc_mos(mo_coeffs[0], mo_coeffs[1],
                                   compact and aosym != 's1')

    if h5py.is_hdf5(erifile):
        feri = h5py.File(erifile)
        if dataname in feri:
            del(feri[dataname])
    else:
        feri = h5py.File(erifile, 'w')
    if comp == 1:
        chunks = (min(int(64e3/nmoj),naoaux), nmoj) # 512K
        h5d_eri = feri.create_dataset(dataname, (naoaux,nij_pair), 'f8',
                                      chunks=chunks)
    else:
        chunks = (1, min(int(64e3/nmoj),naoaux), nmoj) # 512K
        h5d_eri = feri.create_dataset(dataname, (comp,naoaux,nij_pair), 'f8',
                                      chunks=chunks)
    aopairblks = len(fswap[dataname+'/0'])

    iolen = min(int(ioblk_size*1e6/8/(nao_pair+nij_pair)), naoaux)
    totstep = (naoaux+iolen-1)//iolen * comp
    buf = numpy.empty((iolen, nao_pair))
    ti0 = time1
    for icomp in range(comp):
        istep = 0
        for row0, row1 in prange(0, naoaux, iolen):
            nrow = row1 - row0
            istep += 1

            log.debug('step 2 [%d/%d], [%d,%d:%d], row = %d',
                      istep, totstep, icomp, row0, row1, nrow)
            col0 = 0
            for ic in range(aopairblks):
                dat = fswap['%s/%d/%d'%(dataname,icomp,ic)]
                col1 = col0 + dat.shape[1]
                buf[:nrow,col0:col1] = dat[row0:row1]
                col0 = col1

            buf1 = _ao2mo.nr_e2(buf[:nrow], moij, ijshape, aosym_as_nr_e2, ijmosym)
            if comp == 1:
                h5d_eri[row0:row1] = buf1
            else:
                h5d_eri[icomp,row0:row1] = buf1

            ti0 = log.timer('step 2 [%d/%d], [%d,%d:%d], row = %d'%
                            (istep, totstep, icomp, row0, row1, nrow), *ti0)

    fswap.close()
    feri.close()
    log.timer('AO->MO CD eri transformation 2 pass', *time1)
    log.timer('AO->MO CD eri transformation', *time0)
    return erifile
开发者ID:berquist,项目名称:pyscf,代码行数:84,代码来源:outcore.py


示例20: general

def general(eri_ao, mo_coeffs, verbose=0, compact=True):
    r'''For the given four sets of orbitals, transfer the 8-fold or 4-fold 2e
    AO integrals to MO integrals.

    Args:
        eri_ao : ndarray
            AO integrals, can be either 8-fold or 4-fold symmetry.
        mo_coeffs : 4-item list of ndarray
            Four sets of orbital coefficients, corresponding to the four
            indices of (ij|kl)

    Kwargs:
        verbose : int
            Print level
        compact : bool
            When compact is True, depending on the four oribital sets, the
            returned MO integrals has (up to 4-fold) permutation symmetry.
            If it's False, the function will abandon any permutation symmetry,
            and return the "plain" MO integrals

    Returns:
        2D array of transformed MO integrals.  The MO integrals may or may not
        have the permutation symmetry, depending on the given orbitals, and
        the kwargs compact.  If the four sets of orbitals are identical, the
        MO integrals will at most have 4-fold symmetry.


    Examples:

    >>> from pyscf import gto
    >>> from pyscf.scf import _vhf
    >>> from pyscf import ao2mo
    >>> mol = gto.M(atom='O 0 0 0; H 0 1 0; H 0 0 1', basis='sto3g')
    >>> eri = _vhf.int2e_sph(mol._atm, mol._bas, mol._env)
    >>> mo1 = numpy.random.random((mol.nao_nr(), 10))
    >>> mo2 = numpy.random.random((mol.nao_nr(), 8))
    >>> mo3 = numpy.random.random((mol.nao_nr(), 6))
    >>> mo4 = numpy.random.random((mol.nao_nr(), 4))
    >>> eri1 = ao2mo.incore.general(eri, (mo1,mo2,mo3,mo4))
    >>> print(eri1.shape)
    (80, 24)
    >>> eri1 = ao2mo.incore.general(eri, (mo1,mo2,mo3,mo3))
    >>> print(eri1.shape)
    (80, 21)
    >>> eri1 = ao2mo.incore.general(eri, (mo1,mo2,mo3,mo3), compact=False)
    >>> print(eri1.shape)
    (80, 36)
    >>> eri1 = ao2mo.incore.general(eri, (mo1,mo1,mo2,mo2))
    >>> print(eri1.shape)
    (55, 36)
    >>> eri1 = ao2mo.incore.general(eri, (mo1,mo2,mo1,mo2))
    >>> print(eri1.shape)
    (80, 80)

    '''
    if isinstance(verbose, logger.Logger):
        log = verbose
    else:
        log = logger.Logger(sys.stdout, verbose)

    nao = mo_coeffs[0].shape[0]
    nao_pair = nao*(nao+1)//2
    assert(eri_ao.size in (nao_pair**2, nao_pair*(nao_pair+1)//2))

# transform e1
    eri1 = half_e1(eri_ao, mo_coeffs, compact)
    klmosym, nkl_pair, mokl, klshape = _conc_mos(mo_coeffs[2], mo_coeffs[3], compact)

    if eri1.shape[0] == 0 or nkl_pair == 0:
        # 0 dimension sometimes causes blas problem
        return numpy.zeros((nij_pair,nkl_pair))

#    if nij_pair > nkl_pair:
#        log.warn('low efficiency for AO to MO trans!')

# transform e2
    eri1 = _ao2mo.nr_e2(eri1, mokl, klshape, aosym='s4', mosym=klmosym)
    return eri1
开发者ID:berquist,项目名称:pyscf,代码行数:78,代码来源:incore.py



注:本文中的pyscf.ao2mo._ao2mo.nr_e2函数示例由纯净天空整理自Github/MSDocs等源码及文档管理平台,相关代码片段筛选自各路编程大神贡献的开源项目,源码版权归原作者所有,传播和使用请参考对应项目的License;未经允许,请勿转载。


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