mirror of
https://github.com/QuantumPackage/qp2.git
synced 2024-08-30 04:33:41 +02:00
fixed qmcpack basis info in converter
This commit is contained in:
parent
582652bed5
commit
620a9b7044
@ -377,16 +377,14 @@ def print_kpts_unblocked_upper(ints_k,outfilename,thresh):
|
||||
|
||||
|
||||
def get_kin_ao(mf):
|
||||
nao = mf.cell.nao_nr(cart=True)
|
||||
nao = mf.cell.nao_nr()
|
||||
Nk = len(mf.kpts)
|
||||
return np.reshape(mf.cell.pbc_intor('int1e_kin_cart',1,1,kpts=mf.kpts),(Nk,nao,nao))
|
||||
return np.reshape(mf.cell.pbc_intor('int1e_kin',1,1,kpts=mf.kpts),(Nk,nao,nao))
|
||||
|
||||
def get_ovlp_ao(mf):
|
||||
nao = mf.cell.nao_nr(cart=True)
|
||||
nao = mf.cell.nao_nr()
|
||||
Nk = len(mf.kpts)
|
||||
if mf.cell.cart:
|
||||
return np.reshape(mf.cell.pbc_intor('int1e_ovlp_cart',1,1,kpts=mf.kpts),(Nk,nao,nao))
|
||||
#return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
|
||||
return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
|
||||
|
||||
def get_pot_ao(mf):
|
||||
nao = mf.cell.nao_nr()
|
||||
@ -605,18 +603,18 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
||||
qph5.create_group('electrons')
|
||||
qph5.create_group('ao_basis')
|
||||
qph5.create_group('mo_basis')
|
||||
qph5.create_group('pseudo')
|
||||
qph5['pseudo'].attrs['do_pseudo']=False
|
||||
qph5.create_group('PBC_DATA')
|
||||
qph5.create_group('qmcpack')
|
||||
#qph5.create_group('pseudo')
|
||||
#qph5['pseudo'].attrs['do_pseudo']=False
|
||||
|
||||
if mf.cell.cart:
|
||||
mo_coeff = mf.mo_coeff.copy()
|
||||
else:
|
||||
# normalized can be one of ['all','sp',None]
|
||||
# we can either normalize here or after qp
|
||||
c2s = mf.cell.cart2sph_coeff(normalized='sp')
|
||||
mo_coeff = list(map(lambda x: np.dot(c2s,x),mf.mo_coeff))
|
||||
#mo_coeff = mf.mo_coeff
|
||||
#if mf.cell.cart:
|
||||
# mo_coeff = mf.mo_coeff.copy()
|
||||
#else:
|
||||
# # normalized can be one of ['all','sp',None]
|
||||
# # we can either normalize here or after qp
|
||||
# c2s = mf.cell.cart2sph_coeff(normalized='sp')
|
||||
# mo_coeff = list(map(lambda x: np.dot(c2s,x),mf.mo_coeff))
|
||||
mo_coeff = mf.mo_coeff
|
||||
# Mo_coeff actif
|
||||
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff)
|
||||
e_k = np.array([e[cas_idx] for e in mf.mo_energy] if cas_idx is not None else mf.mo_energy)
|
||||
@ -663,17 +661,19 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
||||
|
||||
|
||||
nprim_max = 0
|
||||
nfunc_tot = 0
|
||||
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
|
||||
for ib in range(sh0,sh1): # sets of contracted exponents
|
||||
nprim = cell.bas_nprim(ib)
|
||||
nfunc_tot += cell.bas_nctr(ib)
|
||||
if (nprim > nprim_max):
|
||||
nprim_max = nprim
|
||||
|
||||
qp_prim_num = np.zeros((nao),dtype=int)
|
||||
qp_coef = np.zeros((nao,nprim_max))
|
||||
qp_expo = np.zeros((nao,nprim_max))
|
||||
qp_nucl = np.zeros((nao),dtype=int)
|
||||
qp_pwr = np.zeros((nao,3),dtype=int)
|
||||
qp_prim_num = np.zeros((nfunc_tot),dtype=int)
|
||||
qp_coef = np.zeros((nfunc_tot,nprim_max))
|
||||
qp_expo = np.zeros((nfunc_tot,nprim_max))
|
||||
qp_nucl = np.zeros((nfunc_tot),dtype=int)
|
||||
qp_lbas = np.zeros((nfunc_tot),dtype=int)
|
||||
|
||||
clabels = cell.cart_labels(fmt=False)
|
||||
|
||||
@ -692,27 +692,37 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
||||
#else:
|
||||
# nfuncmax = 2*l+1
|
||||
for ic in range(nctr): # sets of contraction coeffs
|
||||
qp_expo[tmp_idx,:nprim] = es[:]
|
||||
qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
||||
qp_nucl[tmp_idx] = iatom
|
||||
qp_lbas[tmp_idx] = l
|
||||
qp_prim_num[tmp_idx] = nprim
|
||||
tmp_idx += 1
|
||||
#for nfunc in range(nfuncmax):
|
||||
for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
|
||||
qp_expo[tmp_idx,:nprim] = es[:]
|
||||
qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
||||
qp_nucl[tmp_idx] = iatom + 1
|
||||
qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
|
||||
qp_prim_num[tmp_idx] = nprim
|
||||
tmp_idx += 1
|
||||
#for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
|
||||
# qp_expo[tmp_idx,:nprim] = es[:]
|
||||
# qp_coef[tmp_idx,:nprim] = cs[:,ic]
|
||||
# qp_nucl[tmp_idx] = iatom + 1
|
||||
# qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
|
||||
# qp_prim_num[tmp_idx] = nprim
|
||||
# tmp_idx += 1
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5['mo_basis'].attrs['mo_num']=nmo
|
||||
qph5['ao_basis'].attrs['ao_num']=nao
|
||||
qph5['mo_basis'].attrs['mo_num']=Nk*nmo
|
||||
qph5['ao_basis'].attrs['ao_num']=Nk*nao
|
||||
|
||||
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
|
||||
qph5['ao_basis'].attrs['ao_basis']="dummy basis"
|
||||
|
||||
qph5.create_dataset('ao_basis/ao_nucl',data=qp_nucl)
|
||||
qph5.create_dataset('ao_basis/ao_prim_num',data=qp_prim_num)
|
||||
qph5.create_dataset('ao_basis/ao_expo',data=qp_expo.T)
|
||||
qph5.create_dataset('ao_basis/ao_coef',data=qp_coef.T)
|
||||
qph5.create_dataset('ao_basis/ao_power',data=qp_pwr.T)
|
||||
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
|
||||
|
||||
qph5['qmcpack'].attrs['qmc_nshell']=nfunc_tot
|
||||
qph5['qmcpack'].attrs['qmc_prim_num_max']=nprim_max
|
||||
qph5.create_dataset('qmcpack/qmc_nucl',data=qp_nucl)
|
||||
qph5.create_dataset('qmcpack/qmc_prim_num',data=qp_prim_num)
|
||||
qph5.create_dataset('qmcpack/qmc_expo',data=qp_expo.T)
|
||||
qph5.create_dataset('qmcpack/qmc_coef',data=qp_coef.T)
|
||||
qph5.create_dataset('qmcpack/qmc_lbas',data=qp_lbas)
|
||||
|
||||
|
||||
# with h5py.File(qph5path,'a') as qph5:
|
||||
@ -882,87 +892,87 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
|
||||
|
||||
|
||||
with h5py.File(qph5path,'a') as qph5:
|
||||
qph5.create_dataset('PBC_DATA/PBE',(1,),dtype="b1",data=True)
|
||||
qph5.create_dataset('PBC_DATA/Super_Twist',(1,3),dtype="f8",data=sp_twist)
|
||||
qph5.create_dataset('PBC_DATA/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors())
|
||||
qph5.create_dataset('PBC_DATA/eigenval',(1,nmo),dtype="f8",data=mf.mo_energy)
|
||||
qph5.create_dataset('qmcpack/PBE',(1,),dtype="b1",data=True)
|
||||
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())
|
||||
qph5.create_dataset('qmcpack/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy)
|
||||
|
||||
|
||||
##########################################
|
||||
# #
|
||||
# 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]
|
||||
# ##########################################
|
||||
# # #
|
||||
# # 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
|
||||
|
||||
|
Loading…
Reference in New Issue
Block a user