Python time.clock() Examples

def make_ip(self):
        if not self._made_shared:
            self._make_shared()

        cput0 = (time.clock(), time.time())

        t1, t2, eris = self.t1, self.t2, self.eris

        # 0 or 1 virtuals
        self.Woooo, self.WooOO, _         , self.WOOOO = uintermediates.Woooo(t1, t2, eris)
        self.Wooov, self.WooOV, self.WOOov, self.WOOOV = uintermediates.Wooov(t1, t2, eris)
        self.Woovo, self.WooVO, self.WOOvo, self.WOOVO = uintermediates.Woovo(t1, t2, eris)

        self.made_ip_imds = True
        logger.timer_debug1(self, 'EOM-UCCSD IP intermediates', *cput0)
        return self 

def make_ee(self):
        if not self._made_shared:
            self._make_shared()

        cput0 = (time.clock(), time.time())

        kconserv = self.kconserv
        t1, t2, eris = self.t1, self.t2, self.eris

        if not self.made_ip_imds:
            # 0 or 1 virtuals
            self.Woooo = imd.Woooo(self._cc, t1, t2, eris, kconserv)
            self.Wooov = imd.Wooov(self._cc, t1, t2, eris, kconserv)
            self.Wovoo = imd.Wovoo(self._cc, t1, t2, eris, kconserv)
        if not self.made_ea_imds:
            # 3 or 4 virtuals
            self.Wvovv = imd.Wvovv(self._cc, t1, t2, eris, kconserv)
            self.Wvvvv = imd.Wvvvv(self._cc, t1, t2, eris, kconserv)
            self.Wvvvo = imd.Wvvvo(self._cc, t1, t2, eris, kconserv, self.Wvvvv)

        self.made_ee_imds = True
        logger.timer(self, 'EOM-CCSD EE intermediates', *cput0)
        return self 

def get_jk(self, mol=None, dm=None, hermi=1, with_j=True, with_k=True,
               omega=None):
        if mol is None: mol = self.mol
        if dm is None: dm = self.make_rdm1()
        cpu0 = (time.clock(), time.time())
        if self.direct_scf and self.opt is None:
            self.opt = self.init_direct_scf(mol)

        if with_j and with_k:
            vj, vk = get_jk(mol, dm, hermi, self.opt, with_j, with_k, omega)
        else:
            if with_j:
                prescreen = 'CVHFnrs8_vj_prescreen'
            else:
                prescreen = 'CVHFnrs8_vk_prescreen'
            with lib.temporary_env(self.opt, prescreen=prescreen):
                vj, vk = get_jk(mol, dm, hermi, self.opt, with_j, with_k, omega)

        logger.timer(self, 'vj and vk', *cpu0)
        return vj, vk 

def make_t3p2_ea(self, cc):
        cput0 = (time.clock(), time.time())

        t1, t2, eris = cc.t1, cc.t2, self.eris
        delta_E_tot, pt1, pt2, Wovoo, Wvvvo = \
            imd.get_t3p2_imds(cc, t1, t2, eris)
        self.t1 = pt1
        self.t2 = pt2

        self._made_shared_2e = False  # Force update
        self.make_ea()  # Make after t1/t2 updated
        self.Wvvvo = self.Wvvvo + Wvvvo

        self.made_ea_imds = True
        logger.timer_debug1(self, 'EOM-CCSD(T)a EA intermediates', *cput0)
        return self 

def _make_eris_incore(mycc, mo_coeff=None, ao2mofn=None):
    cput0 = (time.clock(), time.time())
    eris = _ChemistsERIs()
    eris._common_init_(mycc, mo_coeff)
    nocc = eris.nocc
    nmo = eris.fock.shape[0]

    if callable(ao2mofn):
        eri1 = ao2mofn(eris.mo_coeff).reshape([nmo]*4)
    else:
        eri1 = ao2mo.incore.full(mycc._scf._eri, eris.mo_coeff)
        eri1 = ao2mo.restore(1, eri1, nmo)
    eris.oooo = eri1[:nocc,:nocc,:nocc,:nocc].copy()
    eris.ovoo = eri1[:nocc,nocc:,:nocc,:nocc].copy()
    eris.ovov = eri1[:nocc,nocc:,:nocc,nocc:].copy()
    eris.oovv = eri1[:nocc,:nocc,nocc:,nocc:].copy()
    eris.ovvo = eri1[:nocc,nocc:,nocc:,:nocc].copy()
    eris.ovvv = eri1[:nocc,nocc:,nocc:,nocc:].copy()
    logger.timer(mycc, 'GW integral transformation', *cput0)
    return eris 

def make_t3p2_ip(self, cc):
        cput0 = (time.clock(), time.time())

        t1, t2, eris = cc.t1, cc.t2, self.eris
        delta_E_tot, pt1, pt2, Wovoo, Wvvvo = \
            imd.get_t3p2_imds(cc, t1, t2, eris)
        self.t1 = pt1
        self.t2 = pt2

        self._made_shared_2e = False  # Force update
        self.make_ip()  # Make after t1/t2 updated
        self.Wovoo = self.Wovoo + Wovoo

        self.made_ip_imds = True
        logger.timer_debug1(self, 'EOM-CCSD(T)a IP intermediates', *cput0)
        return self 

def _make_shared_2e(self):
        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.stdout, self.verbose)

        t1,t2,eris = self.t1, self.t2, self.eris
        kconserv = self.kconserv

        # TODO: check whether to hold Wovov Wovvo in memory
        if self._fimd is None:
            self._fimd = lib.H5TmpFile()
        nkpts, nocc, nvir = t1.shape
        self._fimd.create_dataset('ovov', (nkpts,nkpts,nkpts,nocc,nvir,nocc,nvir), t1.dtype.char)
        self._fimd.create_dataset('ovvo', (nkpts,nkpts,nkpts,nocc,nvir,nvir,nocc), t1.dtype.char)

        # 2 virtuals
        self.Wovov = imd.Wovov(t1,t2,eris,kconserv, self._fimd['ovov'])
        self.Wovvo = imd.Wovvo(t1,t2,eris,kconserv, self._fimd['ovvo'])
        self.Woovv = eris.oovv

        log.timer('EOM-CCSD shared two-electron intermediates', *cput0) 

def solve_nos1(fvind, mo_energy, mo_occ, h1,
               max_cycle=20, tol=1e-9, hermi=False, verbose=logger.WARN):
    '''For field independent basis. First order overlap matrix is zero'''
    log = logger.new_logger(verbose=verbose)
    t0 = (time.clock(), time.time())

    e_a = mo_energy[mo_occ==0]
    e_i = mo_energy[mo_occ>0]
    e_ai = 1 / lib.direct_sum('a-i->ai', e_a, e_i)
    mo1base = h1 * -e_ai

    def vind_vo(mo1):
        v = fvind(mo1.reshape(h1.shape)).reshape(h1.shape)
        v *= e_ai
        return v.ravel()
    mo1 = lib.krylov(vind_vo, mo1base.ravel(),
                     tol=tol, max_cycle=max_cycle, hermi=hermi, verbose=log)
    log.timer('krylov solver in CPHF', *t0)
    return mo1.reshape(h1.shape), None

# h1 shape is (:,nocc+nvir,nocc) 

def make_ip(self, ip_partition=None):
        self._make_shared_1e()
        if self._made_shared_2e is False and ip_partition != 'mp':
            self._make_shared_2e()
            self._made_shared_2e = True

        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.stdout, self.verbose)

        t1,t2,eris = self.t1, self.t2, self.eris
        kconserv = self.kconserv

        nkpts, nocc, nvir = t1.shape
        self._fimd.create_dataset('oooo', (nkpts,nkpts,nkpts,nocc,nocc,nocc,nocc), t1.dtype.char)
        self._fimd.create_dataset('ooov', (nkpts,nkpts,nkpts,nocc,nocc,nocc,nvir), t1.dtype.char)
        self._fimd.create_dataset('ovoo', (nkpts,nkpts,nkpts,nocc,nvir,nocc,nocc), t1.dtype.char)

        # 0 or 1 virtuals
        if ip_partition != 'mp':
            self.Woooo = imd.Woooo(t1,t2,eris,kconserv, self._fimd['oooo'])
        self.Wooov = imd.Wooov(t1,t2,eris,kconserv, self._fimd['ooov'])
        self.Wovoo = imd.Wovoo(t1,t2,eris,kconserv, self._fimd['ovoo'])
        self.made_ip_imds = True
        log.timer('EOM-CCSD IP intermediates', *cput0) 

def _make_shared(self):
        cput0 = (time.clock(), time.time())

        t1, t2, eris = self.t1, self.t2, self.eris
        self.Foo, self.FOO = kintermediates_uhf.Foo(self._cc, t1, t2, eris)
        self.Fvv, self.FVV = kintermediates_uhf.Fvv(self._cc, t1, t2, eris)
        self.Fov, self.FOV = kintermediates_uhf.Fov(self._cc, t1, t2, eris)

        # 2 virtuals
        self.Wovvo, self.WovVO, self.WOVvo, self.WOVVO = kintermediates_uhf.Wovvo(self._cc, t1, t2, eris)
        self.Woovv, self.WooVV, self.WOOvv, self.WOOVV = kintermediates_uhf.Woovv(self._cc, t1, t2, eris)
        self.Wovov = eris.ovov - np.asarray(eris.ovov).transpose(2,1,0,5,4,3,6)
        self.WOVOV = eris.OVOV - np.asarray(eris.OVOV).transpose(2,1,0,5,4,3,6)
        self.WovOV = eris.ovOV
        self.WOVov = None

        self._made_shared = True
        logger.timer_debug1(self, 'EOM-KCCSD shared intermediates', *cput0)
        return self 

def make_ip(self):
        if not self._made_shared:
            self._make_shared()

        kconserv = self.kconserv
        cput0 = (time.clock(), time.time())

        t1, t2, eris = self.t1, self.t2, self.eris

        # 0 or 1 virtuals
        self.Woooo, self.WooOO, _         , self.WOOOO = kintermediates_uhf.Woooo(self._cc, t1, t2, eris)
        self.Wooov, self.WooOV, self.WOOov, self.WOOOV = kintermediates_uhf.Wooov(self._cc, t1, t2, eris, kconserv)  # TODO
        self.Woovo, self.WooVO, self.WOOvo, self.WOOVO = kintermediates_uhf.Woovo(self._cc, t1, t2, eris)  # TODO

        self.made_ip_imds = True
        logger.timer_debug1(self, 'EOM-KUCCSD IP intermediates', *cput0)
        return self 

def make_ea(self):
        if not self._made_shared:
            self._make_shared()

        cput0 = (time.clock(), time.time())

        t1, t2, eris = self.t1, self.t2, self.eris

        # 3 or 4 virtuals
        #self.Wvovv, self.WvoVV, self.WVOvv, self.WVOVV = kintermediates_uhf.Wvovv(self._cc, t1, t2, eris)
        self.Wvvov, self.WvvOV, self.WVVov, self.WVVOV = kintermediates_uhf.Wvvov(self._cc, t1, t2, eris)
        if eris.vvvv is not None:
            self.Wvvvv, self.WvvVV, self.WVVVV = Wvvvv = kintermediates_uhf.Wvvvv(self._cc, t1, t2, eris)
        else:
            self.Wvvvv = self.WvvVV = self.WVVVV = None
        self.Wvvvo, self.WvvVO, self.WVVvo, self.WVVVO = kintermediates_uhf.Wvvvo(self._cc, t1, t2, eris)

        self.made_ea_imds = True
        logger.timer_debug1(self, 'EOM-KUCCSD EA intermediates', *cput0)
        return self 

def kernel(self, mo_energy=None, mo_coeff=None, td_e=None, td_xy=None,
               eris=None, orbs=None):
        if mo_coeff is None:
            mo_coeff = self._scf.mo_coeff
        if mo_energy is None:
            mo_energy = self._scf.mo_energy
        if td_e is None:
            td_e = self._tdscf.e
        if td_xy is None:
            td_xy = self._tdscf.xy

        cput0 = (time.clock(), time.time())
        self.dump_flags()
        self.converged, self.mo_energy, self.mo_coeff = \
                kernel(self, mo_energy, mo_coeff, td_e, td_xy,
                       eris=eris, orbs=orbs, verbose=self.verbose)

        logger.timer(self, 'GW', *cput0)
        return self.mo_energy 

def make_ip(self):
        if self._made_shared is False:
            self._make_shared()
            self._made_shared = True

        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.cc.stdout, self.cc.verbose)

        t1,t2,eris = self.cc.t1, self.cc.t2, self.cc.eris

        # 0 or 1 virtuals
        self.Woooo = imd.Woooo(t1,t2,eris)
        self.Wooov = imd.Wooov(t1,t2,eris)
        self.Wovoo = imd.Wovoo(t1,t2,eris)

        self.made_ip_imds = True
        log.timer('EOM-CCSD IP intermediates', *cput0) 

def make_ea(self):
        if self._made_shared is False:
            self._make_shared()
            self._made_shared = True

        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.cc.stdout, self.cc.verbose)

        t1,t2,eris = self.cc.t1, self.cc.t2, self.cc.eris

        # 3 or 4 virtuals
        self.Wvovv = imd.Wvovv(t1,t2,eris)
        self.Wvvvv = imd.Wvvvv(t1,t2,eris)
        self.Wvvvo = imd.Wvvvo(t1,t2,eris,self.Wvvvv)

        self.made_ea_imds = True
        log.timer('EOM-CCSD EA intermediates', *cput0) 

def make_t3p2_ea(self, cc):
        cput0 = (time.clock(), time.time())

        t1, t2, eris = cc.t1, cc.t2, self.eris
        delta_E_corr, pt1, pt2, Wovoo, Wvvvo = \
            imd.get_t3p2_imds_slow(cc, t1, t2, eris)
        self.t1 = pt1
        self.t2 = pt2

        self._made_shared = False  # Force update
        self.make_ea()  # Make after t1/t2 updated
        self.Wvvvo = self.Wvvvo + Wvvvo

        self.made_ea_imds = True
        logger.timer_debug1(self, 'EOM-CCSD(T)a EA intermediates', *cput0)
        return self 

def make_ea(self):
        if not self._made_shared:
            self._make_shared()

        cput0 = (time.clock(), time.time())

        kconserv = self.kconserv
        t1, t2, eris = self.t1, self.t2, self.eris

        # FIXME DELETE WOOOO
        # 0 or 1 virtuals
        self.Woooo = imd.Woooo(self._cc, t1, t2, eris, kconserv)
        # 3 or 4 virtuals
        self.Wvovv = imd.Wvovv(self._cc, t1, t2, eris, kconserv)
        self.Wvvvv = imd.Wvvvv(self._cc, t1, t2, eris, kconserv)
        self.Wvvvo = imd.Wvvvo(self._cc, t1, t2, eris, kconserv)

        self.made_ea_imds = True
        logger.timer_debug1(self, 'EOM-CCSD EA intermediates', *cput0)
        return self 

def make_ip(self):
        if not self._made_shared:
            self._make_shared()

        cput0 = (time.clock(), time.time())

        kconserv = self.kconserv
        t1, t2, eris = self.t1, self.t2, self.eris

        # 0 or 1 virtuals
        self.Woooo = imd.Woooo(self._cc, t1, t2, eris, kconserv)
        self.Wooov = imd.Wooov(self._cc, t1, t2, eris, kconserv)
        self.Wovoo = imd.Wovoo(self._cc, t1, t2, eris, kconserv)

        self.made_ip_imds = True
        logger.timer_debug1(self, 'EOM-CCSD IP intermediates', *cput0)
        return self 

def _make_shared(self):
        cput0 = (time.clock(), time.time())

        kconserv = self.kconserv
        t1, t2, eris = self.t1, self.t2, self.eris

        self.Foo = imd.Foo(self._cc, t1, t2, eris, kconserv)
        self.Fvv = imd.Fvv(self._cc, t1, t2, eris, kconserv)
        self.Fov = imd.Fov(self._cc, t1, t2, eris, kconserv)

        # 2 virtuals
        self.Wovvo = imd.Wovvo(self._cc, t1, t2, eris, kconserv)
        self.Woovv = eris.oovv

        self._made_shared = True
        logger.timer_debug1(self, 'EOM-CCSD shared intermediates', *cput0)
        return self 

def kernel(self, mo_energy=None, mo_coeff=None, mo_occ=None, atmlst=None):
        cput0 = (time.clock(), time.time())
        if mo_energy is None: mo_energy = self.base.mo_energy
        if mo_coeff is None: mo_coeff = self.base.mo_coeff
        if mo_occ is None: mo_occ = self.base.mo_occ
        if atmlst is None:
            atmlst = self.atmlst
        else:
            self.atmlst = atmlst

        if self.verbose >= logger.INFO:
            self.dump_flags()

        de = self.grad_elec(mo_energy, mo_coeff, mo_occ, atmlst)
        self.de = de + self.grad_nuc(atmlst=atmlst)
        logger.timer(self, 'SCF gradients', *cput0)
        self._finalize()
        return self.de 

def make_ip(self, ip_partition=None):
        self._make_shared_1e()
        if self._made_shared_2e is False and ip_partition != 'mp':
            self._make_shared_2e()
            self._made_shared_2e = True

        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.stdout, self.verbose)

        t1,t2,eris = self.t1, self.t2, self.eris

        # 0 or 1 virtuals
        if ip_partition != 'mp':
            self.Woooo = imd.Woooo(t1,t2,eris)
        self.Wooov = imd.Wooov(t1,t2,eris)
        self.Wovoo = imd.Wovoo(t1,t2,eris)
        self.made_ip_imds = True
        log.timer('EOM-CCSD IP intermediates', *cput0) 

def test_write_conf(self):
        rdd = self.sc.parallelize([{'key':i, 'text':i, 'int':i} for i in range(10)])
        save = partial(rdd.saveToCassandra, self.keyspace, self.table)

        save(batch_size=100)
        save(batch_buffer_size=100)
        save(batch_grouping_key='replica_set')
        save(batch_grouping_key='partition')
        save(consistency_level='ALL')
        save(consistency_level=ConsistencyLevel.LOCAL_QUORUM)
        save(parallelism_level=10)
        save(throughput_mibps=10)
        save(ttl=5)
        save(ttl=timedelta(minutes=30))
        save(timestamp=time.clock() * 1000 * 1000)
        save(timestamp=datetime.now())
        save(metrics_enabled=True)
        save(write_conf=WriteConf(ttl=3, metrics_enabled=True)) 

def make_ea(self, ea_partition=None):
        self._make_shared_1e()
        if self._made_shared_2e is False and ea_partition != 'mp':
            self._make_shared_2e()
            self._made_shared_2e = True

        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.stdout, self.verbose)

        t1,t2,eris = self.t1, self.t2, self.eris

        # 3 or 4 virtuals
        self.Wvovv = imd.Wvovv(t1,t2,eris)
        if ea_partition == 'mp':
            self.Wvvvo = imd.Wvvvo(t1,t2,eris)
        else:
            self.Wvvvv = imd.Wvvvv(t1,t2,eris)
            self.Wvvvo = imd.Wvvvo(t1,t2,eris,self.Wvvvv)
        self.made_ea_imds = True
        log.timer('EOM-CCSD EA intermediates', *cput0) 

def _make_shared(self):
        cput0 = (time.clock(), time.time())

        t1, t2, eris = self.t1, self.t2, self.eris
        self.Foo, self.FOO = uintermediates.Foo(t1, t2, eris)
        self.Fvv, self.FVV = uintermediates.Fvv(t1, t2, eris)
        self.Fov, self.FOV = uintermediates.Fov(t1, t2, eris)

        # 2 virtuals
        self.Wovvo, self.WovVO, self.WOVvo, self.WOVVO, self.WoVVo, self.WOvvO = \
                uintermediates.Wovvo(t1, t2, eris)
        Wovov = np.asarray(eris.ovov)
        WOVOV = np.asarray(eris.OVOV)
        Wovov = Wovov - Wovov.transpose(0,3,2,1)
        WOVOV = WOVOV - WOVOV.transpose(0,3,2,1)
        self.Wovov = Wovov
        self.WovOV = eris.ovOV
        self.WOVov = None
        self.WOVOV = WOVOV

        self._made_shared = True
        logger.timer_debug1(self, 'EOM-CCSD shared intermediates', *cput0)
        return self 

def grad_elec(mf_grad, mo_energy=None, mo_coeff=None, mo_occ=None, atmlst=None):
    '''
    Electronic part of KRHF/KRKS gradients
    Args:
        mf_grad : pbc.grad.krhf.Gradients or pbc.grad.krks.Gradients object
    '''
    mf = mf_grad.base
    cell = mf_grad.cell
    kpts = mf.kpts
    nkpts = len(kpts)
    if mo_energy is None: mo_energy = mf.mo_energy
    if mo_occ is None:    mo_occ = mf.mo_occ
    if mo_coeff is None:  mo_coeff = mf.mo_coeff
    if atmlst is None: atmlst = range(cell.natm)

    log = logger.Logger(mf_grad.stdout, mf_grad.verbose)
    hcore_deriv = mf_grad.hcore_generator(cell, kpts)
    s1 = mf_grad.get_ovlp(cell, kpts)
    dm0 = mf.make_rdm1(mo_coeff, mo_occ)
    t0 = (time.clock(), time.time())
    log.debug('Computing Gradients of NR-HF Coulomb repulsion')
    vhf = mf_grad.get_veff(dm0, kpts)
    log.timer('gradients of 2e part', *t0)
    dme0 = mf_grad.make_rdm1e(mo_energy, mo_coeff, mo_occ)
    aoslices = cell.aoslice_by_atom()
    de = np.zeros([len(atmlst),3])
    for x, ia in enumerate(atmlst):
        p0, p1 = aoslices[ia,2:]
        h1ao = hcore_deriv(ia)
        de[x] += np.einsum('xkij,kji->x', h1ao, dm0).real
        # nabla was applied on bra in vhf, *2 for the contributions of nabla|ket>
        de[x] += np.einsum('xkij,kji->x', vhf[:,:,p0:p1], dm0[:,:,p0:p1]).real * 2
        de[x] -= np.einsum('kxij,kji->x', s1[:,:,p0:p1], dme0[:,:,p0:p1]).real * 2
        de[x] /= nkpts
        de[x] += mf_grad.extra_force(ia, locals())

    if log.verbose > logger.DEBUG:
        log.debug('gradients of electronic part')
        mf_grad._write(log, cell, de, atmlst)
    return de 

def get_k(self, dm=None, kpts=None, kpts_band=None):
        if kpts is None: kpts = self.kpts
        if dm is None: dm = self.base.make_rdm1()
        exxdiv = self.base.exxdiv
        cpu0 = (time.clock(), time.time())
        vk = self.base.with_df.get_k_e1(dm, kpts, kpts_band, exxdiv)
        logger.timer(self, 'vk', *cpu0)
        return vk 

def get_j(self, dm=None, kpts=None):
        if kpts is None: kpts = self.kpts
        if dm is None: dm = self.base.make_rdm1()
        cpu0 = (time.clock(), time.time())
        vj = self.base.with_df.get_j_e1(dm, kpts)
        logger.timer(self, 'vj', *cpu0)
        return vj 

def get_jk(self, dm=None, kpts=None):
        if kpts is None: kpts = self.kpts
        if dm is None: dm = self.base.make_rdm1()
        exxdiv = self.base.exxdiv
        cpu0 = (time.clock(), time.time())
        vj, vk = self.base.with_df.get_jk_e1(dm, kpts, exxdiv=exxdiv)
        logger.timer(self, 'vj and vk', *cpu0)
        return vj, vk 

def _log_data(self, net_info_type='active_only'):
        log_list = [self.num_gen, self.num_eval, time.clock(), self.pop[0].eval, self.pop[0].count_active_node()]
        if net_info_type == 'active_only':
            log_list.append(self.pop[0].active_net_list())
        elif net_info_type == 'full':
            log_list += self.pop[0].gene.flatten().tolist()
        else:
            pass
        return log_list 

def _make_shared_1e(self):
        cput0 = (time.clock(), time.time())
        log = logger.Logger(self.stdout, self.verbose)

        t1,t2,eris = self.t1, self.t2, self.eris
        self.Loo = imd.Loo(t1,t2,eris)
        self.Lvv = imd.Lvv(t1,t2,eris)
        self.Fov = imd.cc_Fov(t1,t2,eris)

        log.timer('EOM-CCSD shared one-electron intermediates', *cput0)