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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): def get_kin_ao(mf):
nao = mf.cell.nao_nr(cart=True) nao = mf.cell.nao_nr()
Nk = len(mf.kpts) 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): def get_ovlp_ao(mf):
nao = mf.cell.nao_nr(cart=True) nao = mf.cell.nao_nr()
Nk = len(mf.kpts) Nk = len(mf.kpts)
if mf.cell.cart: return np.reshape(mf.get_ovlp(cell=mf.cell,kpts=mf.kpts),(Nk,nao,nao))
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))
def get_pot_ao(mf): def get_pot_ao(mf):
nao = mf.cell.nao_nr() 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('electrons')
qph5.create_group('ao_basis') qph5.create_group('ao_basis')
qph5.create_group('mo_basis') qph5.create_group('mo_basis')
qph5.create_group('pseudo') qph5.create_group('qmcpack')
qph5['pseudo'].attrs['do_pseudo']=False #qph5.create_group('pseudo')
qph5.create_group('PBC_DATA') #qph5['pseudo'].attrs['do_pseudo']=False
if mf.cell.cart: #if mf.cell.cart:
mo_coeff = mf.mo_coeff.copy() # mo_coeff = mf.mo_coeff.copy()
else: #else:
# normalized can be one of ['all','sp',None] # # normalized can be one of ['all','sp',None]
# we can either normalize here or after qp # # we can either normalize here or after qp
c2s = mf.cell.cart2sph_coeff(normalized='sp') # c2s = mf.cell.cart2sph_coeff(normalized='sp')
mo_coeff = list(map(lambda x: np.dot(c2s,x),mf.mo_coeff)) # mo_coeff = list(map(lambda x: np.dot(c2s,x),mf.mo_coeff))
#mo_coeff = mf.mo_coeff mo_coeff = mf.mo_coeff
# Mo_coeff actif # Mo_coeff actif
mo_k = np.array([c[:,cas_idx] for c in mo_coeff] if cas_idx is not None else mo_coeff) 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) 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 nprim_max = 0
nfunc_tot = 0
for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()): for iatom, (sh0,sh1,ao0,ao1) in enumerate(cell.aoslice_by_atom()):
for ib in range(sh0,sh1): # sets of contracted exponents for ib in range(sh0,sh1): # sets of contracted exponents
nprim = cell.bas_nprim(ib) nprim = cell.bas_nprim(ib)
nfunc_tot += cell.bas_nctr(ib)
if (nprim > nprim_max): if (nprim > nprim_max):
nprim_max = nprim nprim_max = nprim
qp_prim_num = np.zeros((nao),dtype=int) qp_prim_num = np.zeros((nfunc_tot),dtype=int)
qp_coef = np.zeros((nao,nprim_max)) qp_coef = np.zeros((nfunc_tot,nprim_max))
qp_expo = np.zeros((nao,nprim_max)) qp_expo = np.zeros((nfunc_tot,nprim_max))
qp_nucl = np.zeros((nao),dtype=int) qp_nucl = np.zeros((nfunc_tot),dtype=int)
qp_pwr = np.zeros((nao,3),dtype=int) qp_lbas = np.zeros((nfunc_tot),dtype=int)
clabels = cell.cart_labels(fmt=False) 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: #else:
# nfuncmax = 2*l+1 # nfuncmax = 2*l+1
for ic in range(nctr): # sets of contraction coeffs 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(nfuncmax):
for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis? #for nfunc in range(((l+1)*(l+2))//2): # always use cart for qp ao basis?
qp_expo[tmp_idx,:nprim] = es[:] # qp_expo[tmp_idx,:nprim] = es[:]
qp_coef[tmp_idx,:nprim] = cs[:,ic] # qp_coef[tmp_idx,:nprim] = cs[:,ic]
qp_nucl[tmp_idx] = iatom + 1 # qp_nucl[tmp_idx] = iatom + 1
qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3]) # qp_pwr[tmp_idx,:] = xyzcount(clabels[tmp_idx][3])
qp_prim_num[tmp_idx] = nprim # qp_prim_num[tmp_idx] = nprim
tmp_idx += 1 # tmp_idx += 1
with h5py.File(qph5path,'a') as qph5: with h5py.File(qph5path,'a') as qph5:
qph5['mo_basis'].attrs['mo_num']=nmo qph5['mo_basis'].attrs['mo_num']=Nk*nmo
qph5['ao_basis'].attrs['ao_num']=nao qph5['ao_basis'].attrs['ao_num']=Nk*nao
#qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis #qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
qph5['ao_basis'].attrs['ao_basis']="dummy 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_nucl',data=Nk*ao_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['qmcpack'].attrs['qmc_nshell']=nfunc_tot
qph5.create_dataset('ao_basis/ao_coef',data=qp_coef.T) qph5['qmcpack'].attrs['qmc_prim_num_max']=nprim_max
qph5.create_dataset('ao_basis/ao_power',data=qp_pwr.T) 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: # 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: with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('PBC_DATA/PBE',(1,),dtype="b1",data=True) qph5.create_dataset('qmcpack/PBE',(1,),dtype="b1",data=True)
qph5.create_dataset('PBC_DATA/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('PBC_DATA/LatticeVectors',(3,3),dtype="f8",data=cell.lattice_vectors()) qph5.create_dataset('qmcpack/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/eigenval',(1,Nk*nmo),dtype="f8",data=mf.mo_energy)
########################################## # ##########################################
# # # # #
# ECP # # # ECP #
# # # # #
########################################## # ##########################################
#
if (cell.has_ecp()): # if (cell.has_ecp()):
#atsymb = [mol.atom_pure_symbol(i) for i in range(natom)] # #atsymb = [mol.atom_pure_symbol(i) for i in range(natom)]
#pyecp = mol._ecp # #pyecp = mol._ecp
## nelec to remove for each atom # ## nelec to remove for each atom
#nuc_z_remov = [pyecp[i][0] for i in atsymb] # #nuc_z_remov = [pyecp[i][0] for i in atsymb]
#nl_per_atom = [len(pyecp[i][1]) for i in atsymb] # #nl_per_atom = [len(pyecp[i][1]) for i in atsymb]
## list of l-values for channels of each atom # ## 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] # #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,) # ## 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] # #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)] # pyecp = [cell._ecp[cell.atom_pure_symbol(i)] for i in range(natom)]
nzrmv=[0]*natom # nzrmv=[0]*natom
lmax=0 # lmax=0
klocmax=0 # klocmax=0
knlmax=0 # knlmax=0
for i,(nz,dat) in enumerate(pyecp): # for i,(nz,dat) in enumerate(pyecp):
nzrmv[i]=nz # nzrmv[i]=nz
for lval,ac in dat: # for lval,ac in dat:
if (lval==-1): # if (lval==-1):
klocmax=max(sum(len(j) for j in ac),klocmax) # klocmax=max(sum(len(j) for j in ac),klocmax)
else: # else:
lmax=max(lval,lmax) # lmax=max(lval,lmax)
knlmax=max(sum(len(j) for j in ac),knlmax) # knlmax=max(sum(len(j) for j in ac),knlmax)
#psd_nk = np.zeros((natom,klocmax),dtype=int) # #psd_nk = np.zeros((natom,klocmax),dtype=int)
#psd_vk = np.zeros((natom,klocmax),dtype=float) # #psd_vk = np.zeros((natom,klocmax),dtype=float)
#psd_dzk = 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_nkl = np.zeros((natom,knlmax,lmax+1),dtype=int)
#psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float) # #psd_vkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
#psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float) # #psd_dzkl = np.zeros((natom,knlmax,lmax+1),dtype=float)
klnlmax=max(klocmax,knlmax) # klnlmax=max(klocmax,knlmax)
psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int) # psd_n = np.zeros((lmax+2,klnlmax,natom),dtype=int)
psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float) # psd_v = np.zeros((lmax+2,klnlmax,natom),dtype=float)
psd_dz = 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 i,(_,dat) in enumerate(pyecp):
for lval,ac in dat: # for lval,ac in dat:
count=0 # count=0
for ri,aici in enumerate(ac): # for ri,aici in enumerate(ac):
for ai,ci in aici: # for ai,ci in aici:
psd_n[lval+1,count,i] = ri-2 # psd_n[lval+1,count,i] = ri-2
psd_v[lval+1,count,i] = ci # psd_v[lval+1,count,i] = ci
psd_dz[lval+1,count,i] = ai # psd_dz[lval+1,count,i] = ai
count += 1 # count += 1
psd_nk = psd_n[0,:klocmax] # psd_nk = psd_n[0,:klocmax]
psd_vk = psd_v[0,:klocmax] # psd_vk = psd_v[0,:klocmax]
psd_dzk = psd_dz[0,:klocmax] # psd_dzk = psd_dz[0,:klocmax]
psd_nkl = psd_n[1:,:knlmax] # psd_nkl = psd_n[1:,:knlmax]
psd_vkl = psd_v[1:,:knlmax] # psd_vkl = psd_v[1:,:knlmax]
psd_dzkl = psd_dz[1:,:knlmax] # psd_dzkl = psd_dz[1:,:knlmax]
with h5py.File(qph5path,'a') as qph5: # with h5py.File(qph5path,'a') as qph5:
qph5['pseudo'].attrs['do_pseudo']=True # qph5['pseudo'].attrs['do_pseudo']=True
qph5['pseudo'].attrs['pseudo_lmax']=lmax # qph5['pseudo'].attrs['pseudo_lmax']=lmax
qph5['pseudo'].attrs['pseudo_klocmax']=klocmax # qph5['pseudo'].attrs['pseudo_klocmax']=klocmax
qph5['pseudo'].attrs['pseudo_kmax']=knlmax # qph5['pseudo'].attrs['pseudo_kmax']=knlmax
qph5.create_dataset('pseudo/nucl_charge_remove',data=nzrmv) # 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_k',data=psd_nk)
qph5.create_dataset('pseudo/pseudo_n_kl',data=psd_nkl) # 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_k',data=psd_vk)
qph5.create_dataset('pseudo/pseudo_v_kl',data=psd_vkl) # 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_k',data=psd_dzk)
qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl) # qph5.create_dataset('pseudo/pseudo_dz_kl',data=psd_dzkl)
#
## nelec to remove for each atom # ## nelec to remove for each atom
#nuc_z_remov = [i[0] for i in pyecp] # #nuc_z_remov = [i[0] for i in pyecp]
#nl_per_atom = [len(i[1]) for i in pyecp] # #nl_per_atom = [len(i[1]) for i in pyecp]
## list of l-values for channels of each atom # ## list of l-values for channels of each atom
#ecp_l = [[ j[0] for j in i[1] ] for i in pyecp] # #ecp_l = [[ j[0] for j in i[1] ] for i in pyecp]
#lmax = max(map(max,ecp_l)) # #lmax = max(map(max,ecp_l))
## list of [exp,coef] for each channel (r**0,1,2,3,4,5,) # ## 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_ac = [[ j[1] for j in i[1] ] for i in pyecp]
return return