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fixed qmcpack basis info in converter

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This commit is contained in:
Kevin Gasperich 2020-08-31 17:51:55 -05:00 committed by Kevin Gasperich
parent 582652bed5
commit 620a9b7044
1 changed files with 125 additions and 115 deletions
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240
src/utils_complex/MolPyscfToQPkpts.py
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@ -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