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Fixing converter for qmcpack and qp2 with pbc and excited states

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anbenali 2020-10-19 13:26:16 -05:00 committed by Kevin Gasperich
parent 4f9c398ffc
commit 671dd70ba8
3 changed files with 41 additions and 145 deletions
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3
bin/qp_convert_h5_to_ezfio
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@ -287,9 +287,12 @@ def convert_kpts(filename,qph5path,qmcpack=True):
ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC']) ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
ezfio.set_qmcpack_qmc_cart(qph5['qmcpack'].attrs['cart']) ezfio.set_qmcpack_qmc_cart(qph5['qmcpack'].attrs['cart'])
ezfio.set_qmcpack_qmc_pseudo(qph5['qmcpack'].attrs['Pseudo'])
ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist()) ezfio.set_qmcpack_supertwist(qph5['qmcpack/Super_Twist'][()].tolist())
ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist()) ezfio.set_qmcpack_latticevectors(qph5['qmcpack/LatticeVectors'][()].tolist())
ezfio.set_qmcpack_qmc_phase(qph5['qmcpack/qmc_phase'][()].tolist())
ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist()) ezfio.set_qmcpack_qmc_mo_energy(qph5['qmcpack/eigenval'][()].tolist())
except AttributeError as err: except AttributeError as err:
print("################################################") print("################################################")
print("# ERROR: problem copying QMCPACK data to ezfio #") print("# ERROR: problem copying QMCPACK data to ezfio #")

2
scripts/ezfio_interface/ei_handler.py
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@ -398,7 +398,7 @@ def create_ezfio_stuff(dict_ezfio_cfg, config_or_default="config"):
try: try:
(begin, end) = list(map(str.strip, dim.split(":"))) (begin, end) = list(map(str.strip, dim.split(":")))
except ValueError: except ValueError:
a_size_raw.append(dim) a_size_raw.append(dim.strip())
else: else:
if begin[0] == '-': if begin[0] == '-':
a_size_raw.append("{0}+{1}+1".format(end, begin[1:])) a_size_raw.append("{0}+{1}+1".format(end, begin[1:]))

175
src/utils_complex/MolPyscfToQPkpts.py
View File

@ -124,8 +124,7 @@ def makesq2(vlist,n1,n2):
out[i] = tmp2.copy() out[i] = tmp2.copy()
return out return out
def get_supcellPhase(cell, kpts=[], kmesh=[]):
def get_phase(cell, kpts, kmesh=None):
''' '''
The unitary transformation that transforms the supercell basis k-mesh The unitary transformation that transforms the supercell basis k-mesh
adapted basis. adapted basis.
@ -134,7 +133,7 @@ def get_phase(cell, kpts, kmesh=None):
from pyscf import lib from pyscf import lib
latt_vec = cell.lattice_vectors() latt_vec = cell.lattice_vectors()
if kmesh is None: if len(kmesh)== 0:
# Guess kmesh # Guess kmesh
scaled_k = cell.get_scaled_kpts(kpts).round(8) scaled_k = cell.get_scaled_kpts(kpts).round(8)
kmesh = (len(np.unique(scaled_k[:,0])), kmesh = (len(np.unique(scaled_k[:,0])),
@ -153,58 +152,7 @@ def get_phase(cell, kpts, kmesh=None):
# R_rel_mesh has to be construct exactly same to the Ts in super_cell function # R_rel_mesh has to be construct exactly same to the Ts in super_cell function
scell = tools.super_cell(cell, kmesh) scell = tools.super_cell(cell, kmesh)
return scell, phase return scell,phase
def mo_k2gamma(cell, mo_energy, mo_coeff, kpts, kmesh=None):
'''
Transform MOs in Kpoints to the equivalents supercell
'''
from pyscf import lib
import scipy.linalg as la
scell, phase = get_phase(cell, kpts, kmesh)
E_g = np.hstack(mo_energy)
C_k = np.asarray(mo_coeff)
Nk, Nao, Nmo = C_k.shape
NR = phase.shape[0]
# Transform AO indices
C_gamma = np.einsum('Rk, kum -> Rukm', phase, C_k)
C_gamma = C_gamma.reshape(Nao*NR, Nk*Nmo)
E_sort_idx = np.argsort(E_g)
E_g = E_g[E_sort_idx]
C_gamma = C_gamma[:,E_sort_idx]
s = scell.pbc_intor('int1e_ovlp')
assert(abs(reduce(np.dot, (C_gamma.conj().T, s, C_gamma))
- np.eye(Nmo*Nk)).max() < 1e-7)
# Transform MO indices
E_k_degen = abs(E_g[1:] - E_g[:-1]).max() < 1e-5
if np.any(E_k_degen):
degen_mask = np.append(False, E_k_degen) | np.append(E_k_degen, False)
shift = min(E_g[degen_mask]) - .1
f = np.dot(C_gamma[:,degen_mask] * (E_g[degen_mask] - shift),
C_gamma[:,degen_mask].conj().T)
assert(abs(f.imag).max() < 1e-5)
e, na_orb = la.eigh(f.real, s, type=2)
C_gamma[:,degen_mask] = na_orb[:, e>0]
if abs(C_gamma.imag).max() < 1e-7:
print('!Warning Some complexe pollutions in MOs are present')
C_gamma = C_gamma.real
if abs(reduce(np.dot, (C_gamma.conj().T, s, C_gamma)) - np.eye(Nmo*Nk)).max() < 1e-7:
print('!Warning Some complexe pollutions in MOs are present')
s_k = cell.pbc_intor('int1e_ovlp', kpts=kpts)
# overlap between k-point unitcell and gamma-point supercell
s_k_g = np.einsum('kuv,Rk->kuRv', s_k, phase.conj()).reshape(Nk,Nao,NR*Nao)
# The unitary transformation from k-adapted orbitals to gamma-point orbitals
mo_phase = lib.einsum('kum,kuv,vi->kmi', C_k.conj(), s_k_g, C_gamma)
return mo_phase
def qp2rename(): def qp2rename():
import shutil import shutil
@ -594,6 +542,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
ne_threshold = int_threshold ne_threshold = int_threshold
bielec_int_threshold = int_threshold bielec_int_threshold = int_threshold
thresh_mono = int_threshold thresh_mono = int_threshold
loc_cell,phase=get_supcellPhase(cell=cell,kmesh=kmesh,kpts=kpts)
# qph5path = 'qpdat.h5' # qph5path = 'qpdat.h5'
@ -632,23 +581,39 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
########################################## ##########################################
natom = cell.natm natom = cell.natm
print('n_atom per kpt', natom) print('n_atom per kpt', natom)
atom_xyz = mf.cell.atom_coords() atom_xyz = mf.cell.atom_coords()
unit_bohr=1.0
if not(mf.cell.unit.startswith(('B','b','au','AU'))): if not(mf.cell.unit.startswith(('B','b','au','AU'))):
from pyscf.data.nist import BOHR from pyscf.data.nist import BOHR
atom_xyz /= BOHR # always convert to au atom_xyz /= BOHR # always convert to au
unit_bohr=BOHR
with h5py.File(qph5path,'a') as qph5: with h5py.File(qph5path,'a') as qph5:
qph5['nuclei'].attrs['kpt_num']=Nk qph5['nuclei'].attrs['kpt_num']=Nk
qph5['nuclei'].attrs['nucl_num']=natom
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
strtype=h5py.special_dtype(vlen=str) if len(kpts)!=0:
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype) nbatom=loc_cell.natm
for i in range(natom): qph5['nuclei'].attrs['nucl_num']=nbatom
atom_dset[i] = mf.cell.atom_pure_symbol(i) MyPos=qph5.create_dataset('nuclei/nucl_coord',(nbatom,3),dtype="f8")
for x in range(nbatom):
MyPos[x:]=loc_cell.atom_coord(x)/unit_bohr
qph5.create_dataset('nuclei/nucl_charge',data=loc_cell.atom_charges())
strtype=h5py.special_dtype(vlen=str)
atom_dset=qph5.create_dataset('nuclei/nucl_label',(nbatom,),dtype=strtype)
for i in range(nbatom):
atom_dset[i] = loc_cell.atom_pure_symbol(i)
else:
qph5['nuclei'].attrs['nucl_num']=natom
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
strtype=h5py.special_dtype(vlen=str)
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
for i in range(natom):
atom_dset[i] = mf.cell.atom_pure_symbol(i)
########################################## ##########################################
# # # #
@ -725,6 +690,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5.create_dataset('qmcpack/qmc_lbas',data=qp_lbas) qph5.create_dataset('qmcpack/qmc_lbas',data=qp_lbas)
# with h5py.File(qph5path,'a') as qph5: # with h5py.File(qph5path,'a') as qph5:
# qph5['mo_basis'].attrs['mo_num']=Nk*nmo # qph5['mo_basis'].attrs['mo_num']=Nk*nmo
# qph5['ao_basis'].attrs['ao_num']=Nk*nao # qph5['ao_basis'].attrs['ao_num']=Nk*nao
@ -890,90 +856,17 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
if len(kpts)== 0: if len(kpts)== 0:
sp_twist=[0.0,0.0,0.0] sp_twist=[0.0,0.0,0.0]
with h5py.File(qph5path,'a') as qph5: with h5py.File(qph5path,'a') as qph5:
qph5['qmcpack'].attrs['PBC']=True qph5['qmcpack'].attrs['PBC']=True
qph5['qmcpack'].attrs['cart']=cell.cart qph5['qmcpack'].attrs['cart']=cell.cart
qph5['qmcpack'].attrs['Pseudo']=cell.has_ecp()
qph5.create_dataset('qmcpack/Super_Twist',(1,3),dtype="f8",data=sp_twist) qph5.create_dataset('qmcpack/Super_Twist',(1,3),dtype="f8",data=sp_twist)
qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors().T) if len(kpts)!= 0:
qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=loc_cell.lattice_vectors())
else:
qph5.create_dataset('qmcpack/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy) qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy)
qph5.create_dataset('qmcpack/qmc_phase',data=phase.view(dtype=float))
# ##########################################
# # #
# # ECP #
# # #
# ##########################################
#
# if (cell.has_ecp()):
# #atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
# #pyecp = mol._ecp
# ## nelec to remove for each atom
# #nuc_z_remov = [pyecp[i][0] for i in atsymb]
# #nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
# ## list of l-values for channels of each atom
# #ecp_l = [[pyecp[i][1][j][0] for j in range(len(pyecp[i][1]))] for i in atsymb]
# ## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
# #ecp_ac = [[pyecp[i][1][j][1] for j in range(len(pyecp[i][1]))] for i in atsymb]
# pyecp = [cell._ecp[cell.atom_pure_symbol(i)] for i in range(natom)]
# nzrmv=[0]*natom
# lmax=0
# klocmax=0
# knlmax=0
# for i,(nz,dat) in enumerate(pyecp):
# nzrmv[i]=nz
# for lval,ac in dat:
# if (lval==-1):
# klocmax=max(sum(len(j) for j in ac),klocmax)
# else:
# lmax=max(lval,lmax)
# knlmax=max(sum(len(j) for j in ac),knlmax)
# #psd_nk = np.zeros((natom,klocmax),dtype=int)
# #psd_vk = np.zeros((natom,klocmax),dtype=float)
# #psd_dzk = np.zeros((natom,klocmax),dtype=float)
# #psd_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
# #psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
# #psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
# klnlmax=max(klocmax,knlmax)
# psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
# psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
# psd_dz = np.zeros((lmax+2,klnlmax,natom),dtype=float)
# for i,(_,dat) in enumerate(pyecp):
# for lval,ac in dat:
# count=0
# for ri,aici in enumerate(ac):
# for ai,ci in aici:
# psd_n[lval+1,count,i] = ri-2
# psd_v[lval+1,count,i] = ci
# psd_dz[lval+1,count,i] = ai
# count += 1
# psd_nk = psd_n[0,:klocmax]
# psd_vk = psd_v[0,:klocmax]
# psd_dzk = psd_dz[0,:klocmax]
# psd_nkl = psd_n[1:,:knlmax]
# psd_vkl = psd_v[1:,:knlmax]
# psd_dzkl = psd_dz[1:,:knlmax]
# with h5py.File(qph5path,'a') as qph5:
# qph5['pseudo'].attrs['do_pseudo']=True
# qph5['pseudo'].attrs['pseudo_lmax']=lmax
# qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
# qph5['pseudo'].attrs['pseudo_kmax']=knlmax
# qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv)
# qph5.create_dataset('pseudo/pseudo_n_k',data=psd_nk)
# qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl)
# qph5.create_dataset('pseudo/pseudo_v_k',data=psd_vk)
# qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl)
# qph5.create_dataset('pseudo/pseudo_dz_k',data=psd_dzk)
# qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
#
# ## nelec to remove for each atom
# #nuc_z_remov = [i[0] for i in pyecp]
# #nl_per_atom = [len(i[1]) for i in pyecp]
# ## list of l-values for channels of each atom
# #ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
# #lmax = max(map(max,ecp_l))
# ## list of [exp,coef] for each channel (r**0,1,2,3,4,5,)
# #ecp_ac = [[ j[1] for j in i[1] ] for i in pyecp]
return return