mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-06-19 11:42:23 +02:00
Fixing converter for qmcpack and qp2 with pbc and excited states
This commit is contained in:
anbenali
Kevin Gasperich
parent
4f9c398ffc
commit
671dd70ba8
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@ -287,9 +287,12 @@ def convert_kpts(filename,qph5path,qmcpack=True):
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ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
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ezfio.set_qmcpack_qmc_cart(qph5['qmcpack'].attrs['cart'])
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ezfio.set_qmcpack_qmc_pseudo(qph5['qmcpack'].attrs['Pseudo'])
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ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist())
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ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist())
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ezfio.set_qmcpack_qmc_phase(qph5['qmcpack/qmc_phase'][()].tolist())
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ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist())
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except AttributeError as err:
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print("################################################")
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print("# ERROR: problem copying QMCPACK data to ezfio #")
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@ -398,7 +398,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
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try:
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(begin, end) = list(map(str.strip, dim.split(":")))
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except ValueError:
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a_size_raw.append(dim)
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a_size_raw.append(dim.strip())
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else:
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if begin[0] == '-':
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a_size_raw.append("{0}+{1}+1".format(end, begin[1:]))
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@ -124,8 +124,7 @@ def makesq2(vlist,n1,n2):
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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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def get_supcellPhase(cell, kpts=[], kmesh=[]):
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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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@ -134,7 +133,7 @@ def get_phase(cell, kpts, kmesh=None):
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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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if len(kmesh)== 0:
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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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@ -153,58 +152,7 @@ def get_phase(cell, kpts, kmesh=None):
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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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return scell,phase
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def qp2rename():
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import shutil
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@ -594,7 +542,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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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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loc_cell,phase=get_supcellPhase(cell=cell,kmesh=kmesh,kpts=kpts)
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# qph5path = 'qpdat.h5'
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# create hdf5 file, delete old data if exists
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@ -632,23 +581,39 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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##########################################
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natom = cell.natm
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print('n_atom per kpt', natom)
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print('n_atom per kpt', natom)
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atom_xyz = mf.cell.atom_coords()
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unit_bohr=1.0
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if not(mf.cell.unit.startswith(('B','b','au','AU'))):
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from pyscf.data.nist import BOHR
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atom_xyz /= BOHR # always convert to au
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unit_bohr=BOHR
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with h5py.File(qph5path,'a') as qph5:
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qph5['nuclei'].attrs['kpt_num']=Nk
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qph5['nuclei'].attrs['nucl_num']=natom
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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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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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if len(kpts)!=0:
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nbatom=loc_cell.natm
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qph5['nuclei'].attrs['nucl_num']=nbatom
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MyPos=qph5.create_dataset('nuclei/nucl_coord',(nbatom,3),dtype="f8")
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for x in range(nbatom):
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MyPos[x:]=loc_cell.atom_coord(x)/unit_bohr
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qph5.create_dataset('nuclei/nucl_charge',data=loc_cell.atom_charges())
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strtype=h5py.special_dtype(vlen=str)
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atom_dset=qph5.create_dataset('nuclei/nucl_label',(nbatom,),dtype=strtype)
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for i in range(nbatom):
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atom_dset[i] = loc_cell.atom_pure_symbol(i)
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else:
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qph5['nuclei'].attrs['nucl_num']=natom
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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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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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##########################################
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# #
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@ -725,6 +690,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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qph5.create_dataset('qmcpack/qmc_lbas',data=qp_lbas)
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# with h5py.File(qph5path,'a') as qph5:
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# qph5['mo_basis'].attrs['mo_num']=Nk*nmo
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# qph5['ao_basis'].attrs['ao_num']=Nk*nao
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@ -890,91 +856,18 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
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if len(kpts)== 0:
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sp_twist=[0.0,0.0,0.0]
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with h5py.File(qph5path,'a') as qph5:
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qph5['qmcpack'].attrs['PBC']=True
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qph5['qmcpack'].attrs['cart']=cell.cart
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qph5['qmcpack'].attrs['Pseudo']=cell.has_ecp()
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qph5.create_dataset('qmcpack/Super_Twist',(1,3),dtype="f8",data=sp_twist)
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qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors().T)
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if len(kpts)!= 0:
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qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=loc_cell.lattice_vectors())
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else:
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qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
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qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy)
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qph5.create_dataset('qmcpack/qmc_phase',data=phase.view(dtype=float))
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# ##########################################
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# # #
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# # ECP #
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# # #
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# ##########################################
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#
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# if (cell.has_ecp()):
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# #atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
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# #pyecp = mol._ecp
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# ## nelec to remove for each atom
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# #nuc_z_remov = [pyecp[i][0] for i in atsymb]
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# #nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
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# ## list of l-values for channels of each atom
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# #ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
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# ## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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# #ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
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# pyecp = [cell._ecp[cell.atom_pure_symbol(i)] for i in range(natom)]
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# nzrmv=[0]*natom
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# lmax=0
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# klocmax=0
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# knlmax=0
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# for i,(nz,dat) in enumerate(pyecp):
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# nzrmv[i]=nz
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# for lval,ac in dat:
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# if (lval==-1):
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# klocmax=max(sum(len(j) for j in ac),klocmax)
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# else:
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# lmax=max(lval,lmax)
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# knlmax=max(sum(len(j) for j in ac),knlmax)
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# #psd_nk = np.zeros((natom,klocmax),dtype=int)
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# #psd_vk = np.zeros((natom,klocmax),dtype=float)
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# #psd_dzk = np.zeros((natom,klocmax),dtype=float)
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# #psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
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# #psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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# #psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
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# klnlmax=max(klocmax,knlmax)
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# psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
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# psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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# psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
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# for i,(_,dat) in enumerate(pyecp):
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# for lval,ac in dat:
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# count=0
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# for ri,aici in enumerate(ac):
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# for ai,ci in aici:
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# psd_n[lval+1,count,i] = ri-2
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# psd_v[lval+1,count,i] = ci
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# psd_dz[lval+1,count,i] = ai
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# count += 1
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# psd_nk = psd_n[0,:klocmax]
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# psd_vk = psd_v[0,:klocmax]
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# psd_dzk = psd_dz[0,:klocmax]
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# psd_nkl = psd_n[1:,:knlmax]
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# psd_vkl = psd_v[1:,:knlmax]
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# psd_dzkl = psd_dz[1:,:knlmax]
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# with h5py.File(qph5path,'a') as qph5:
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# qph5['pseudo'].attrs['do_pseudo']=True
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# qph5['pseudo'].attrs['pseudo_lmax']=lmax
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# qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
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# qph5['pseudo'].attrs['pseudo_kmax']=knlmax
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# qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
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# qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
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# qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
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# qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
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# qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
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# qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
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# qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
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#
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# ## nelec to remove for each atom
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# #nuc_z_remov = [i[0] for i in pyecp]
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# #nl_per_atom = [len(i[1]) for i in pyecp]
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# ## list of l-values for channels of each atom
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# #ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
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# #lmax = max(map(max,ecp_l))
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# ## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
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# #ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
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return
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def pyscf2QP2_mol(mf, cas_idx=None, int_threshold = 1E-8,
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