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QuantumPackage/bin/qp_convert_h5_to_ezfio
Kevin Gasperich fe9ddc4d98 debugging cd ints
2022-09-21 15:47:51 -05:00

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#!/usr/bin/env python3
"""
convert hdf5 output (e.g. from PySCF) to ezfio
Usage:
qp_convert_h5_to_ezfio [--noqmc] [--rmg] [-o EZFIO_DIR] FILE
Options:
-o --output=EZFIO_DIR Produced directory
by default is FILE.ezfio
--noqmc don't include basis, cell, etc. for QMCPACK
--rmg h5 contains cholesky decomposition informatin, these h5 result from RMG and the pyscf AFQMC converter of QMCPACK.
"""
from ezfio import ezfio
import h5py
import sys
import numpy as np
import os
from docopt import docopt
import gzip
#fname = sys.argv[1]
#qph5name = sys.argv[2]
def idx2_tri(i,j):
"""
for 0-indexed counting
"""
p = max(i,j)
q = min(i,j)
return q + (p*(p+1))//2
def idx2_tri_1(i,j):
"""
for 1-indexed counting
"""
p = max(i,j)
q = min(i,j)
return q + (p*(p-1))//2
def idx4_cplx_1(i,j,k,l):
"""
original function from qp2 (fortran counting)
"""
p = idx2_tri_1(i,k)
q = idx2_tri_1(j,l)
i1 = idx2_tri_1(p,q)
return (i1,p,q)
def ao_idx_map_sign(i,j,k,l):
"""
qp2 indexing
"""
idx,ik,jl = idx4_cplx_1(i,j,k,l)
ij = idx2_tri_1(i,j)
kl = idx2_tri_1(k,l)
idx = 2*idx - 1
if (ij==kl):
sign = 0.0
use_map1 = False
else:
if ik==jl:
if i<k:
sign = 1.0
use_map1 = True
else:
sign = -1.0
use_map1 = True
elif i==k:
if j<l:
sign = 1.0
use_map1 = True
else:
sign = -1.0
use_map1 = True
elif j==l:
if i<k:
sign = 1.0
use_map1 = True
else:
sign = -1.0
use_map1 = True
elif ((i<k) == (j<l)):
if i<k:
sign = 1.0
use_map1 = True
else:
sign = -1.0
use_map1 = True
else:
if ((j<l) == (ik<jl)):
sign = 1.0
use_map1 = False
else:
sign = -1.0
use_map1 = False
return (idx, use_map1, sign)
def get_ao_int_cplx(i,j,k,l,map1,map2):
idx,use_m1,sgn = ao_idx_map_sign(i,j,k,l)
if use_m1:
tmp_re = map1[idx]
tmp_im = map1[idx+1]
tmp_im *= sgn
else:
tmp_re = map2[idx]
if sgn != 0.0:
tmp_im = map2[idx+1]
tmp_im *= sgn
else:
tmp_im = 0.0
return tmp_re + 1j*tmp_im
def kconserv_p_from_qkk2_mk(qkk2,mk):
nk, nk2 = qkk2.shape
assert(nk == nk2)
kcon_p = np.zeros((nk,nk,nk),dtype=int)
for i in range(nk):
for j in range(nk):
for k in range(nk):
kcon_p[i,j,k] = qkk2[mk[j],qkk2[k,i]]
assert(qkk2[mk[j],qkk2[k,i]] == qkk2[qkk2[j,k],i])
return kcon_p
def get_full_path(file_path):
file_path = os.path.expanduser(file_path)
file_path = os.path.expandvars(file_path)
# file_path = os.path.abspath(file_path)
return file_path
def make_reim_identity_kblocks(nk,nm,na=None):
if na is None:
na = nm
single_block = np.eye(nm, na, dtype=np.complex128).view(dtype=np.float64).reshape((nm, na, 2))
kblocks = np.tile(single_block,[nk, 1, 1, 1])
return kblocks
def make_reim_identity_block_diag(nk,nm,na=None):
from scipy.linalg import block_diag
kblocks = make_reim_identity_kblocks(nk,nm,na).view(dtype=np.complex128).squeeze()
kblockdiag = block_diag(*kblocks).view(dtype=np.float64).reshape((nk*nm,nk*na,2))
print(f'kblockdiag.shape = {kblockdiag.shape}')
return kblockdiag
def flatten(l):
res = []
for i in l:
if hasattr(i, "__iter__") and not isinstance(i, str):
res.extend(flatten(i))
else:
res.append(i)
return res
def save_array_do(ezfioname,subdir,data,chunksize=16384):
dims = list(reversed(data.shape))
rank = len(dims)
flatdata = data.reshape(-1)
dim_max = 1
for i in dims:
dim_max *= i
with gzip.open(os.path.join(ezfioname,subdir)+'.gz','wb') as f:
f.write(f'{rank:3d}\n'.encode())
for d in dims:
f.write(f'{d:20d} '.encode())
f.write("\n".encode())
fmtstring = chunksize*'{:24.15E}\n'
for i in range(dim_max//chunksize):
#f.write((chunksize*'{:24.15E}\n').format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
#f.write(fmtstring.format(*flatdata[i*chunksize:(i+1)*chunksize]).encode())
f.write((''.join("%24.15E\n" % xi for xi in flatdata[i*chunksize:(i+1)*chunksize])).encode())
print(f'{100.*i/(dim_max//chunksize):7.3f}% complete')
rem = dim_max%chunksize
if rem:
f.write((rem*'{:24.15E}\n').format(*flatdata[-rem:]).encode())
return
def convert_mol(filename,qph5path):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(False)
with h5py.File(qph5path,'r') as qph5:
nucl_num = qph5['nuclei'].attrs['nucl_num']
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num']
elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
ezfio.set_nuclei_nucl_num(nucl_num)
ezfio.set_ao_basis_ao_num(ao_num)
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.electrons_elec_alpha_num = elec_alpha_num
ezfio.electrons_elec_beta_num = elec_beta_num
##ao_num = mo_num
##Important !
#import math
#nelec_per_kpt = num_elec // n_kpts
#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
#
#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
#ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux)
#(old)Important
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nucl_charge(nucl_charge)
ezfio.set_nuclei_nucl_coord(nucl_coord)
if isinstance(nucl_label[0],bytes):
nucl_label = list(map(lambda x:x.decode(),nucl_label))
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
do_pseudo = qph5['pseudo'].attrs['do_pseudo']
ezfio.set_pseudo_do_pseudo(do_pseudo)
if (do_pseudo):
ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
#coeftmp = qph5['ao_basis/ao_coef'][()]
#expotmp = qph5['ao_basis/ao_expo'][()]
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
##########################################
# #
# MO Coef #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
mo_coef = qph5['mo_basis/mo_coef'][()].tolist()
ezfio.set_mo_basis_mo_coef(mo_coef)
#maybe fix qp so we don't need this?
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
return
def convert_kpts_cd(filename,qph5path,qmcpack=True,is_ao=True):
import json
from scipy.linalg import block_diag
dump_fci, dump_cd = (False, False)
#dump_fci, dump_cd = (True, False)
#dump_fci, dump_cd = (False, True)
#dump_fci2 = True
dump_fci2 = False
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(True)
# Dummy atom since AFQMC h5 has no atom information
#nucl_num = 1
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
kpt_num = qph5['Hamiltonian/KPoints'][()].shape[0]
ham_dims = qph5['Hamiltonian/dims'][()]
NMOPerKP = qph5['Hamiltonian/NMOPerKP'][()]
_, _, kpt_num, orb_num, elec_alpha_num_tot, elec_beta_num_tot, _, nchol_maybe = ham_dims
#for now, all kpts must have same number of MOs
for nmoi in NMOPerKP:
if nmoi != NMOPerKP[0]:
print("ERROR: all KPs must have same number of MOs")
raise ValueError
#TODO: fix na, nb in rmg
assert(elec_alpha_num_tot % kpt_num == 0)
assert(elec_beta_num_tot % kpt_num == 0)
elec_alpha_num_per_kpt = elec_alpha_num_tot // kpt_num
elec_beta_num_per_kpt = elec_beta_num_tot // kpt_num
#elec_alpha_num_per_kpt = qph5['Hamiltonian']['dims'][4]
#elec_beta_num_per_kpt = qph5['Hamiltonian']['dims'][5]
#orb_num = qph5['Hamiltonian']['dims'][3]
#try:
# is_ao = json.loads(qph5['metadata'][()].decode("utf-8").replace("'",'"'))['ortho_ao']
# if is_ao:
# ao_num = orb_num
# elif is_ao ==False:
# mo_num = orb_num
# else:
# raise ValueError('Problem with ortho_ao key in metadata')
#except:
# raise UnicodeDecodeError('metadata not correctly parsed from HDF5 file')
ezfio.set_nuclei_kpt_num(kpt_num)
kpt_pair_num = (kpt_num*kpt_num + kpt_num)//2
ezfio.set_nuclei_kpt_pair_num(kpt_pair_num)
# don't multiply nuclei by kpt_num
# work in k-space, not in equivalent supercell
#nucl_num_per_kpt = nucl_num
#ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
# these are totals (kpt_num * num_per_kpt)
# need to change if we want to truncate orbital space within pyscf
#if is_ao:
# ao_num = orb_num*kpt_num
#TODO: fix this?
ao_num_tot = orb_num
ao_num_per_kpt = NMOPerKP[0]
mo_num_tot = orb_num
mo_num_per_kpt = NMOPerKP[0]
#mo_num_per_kpt = ao_num_per_kpt
ezfio.set_ao_basis_ao_num(ao_num_per_kpt * kpt_num)
ezfio.set_mo_basis_mo_num(mo_num_per_kpt * kpt_num)
ezfio.set_ao_basis_ao_num_per_kpt(ao_num_per_kpt)
ezfio.set_mo_basis_mo_num_per_kpt(mo_num_per_kpt)
ezfio.electrons_elec_alpha_num = elec_alpha_num_per_kpt * kpt_num
ezfio.electrons_elec_beta_num = elec_beta_num_per_kpt * kpt_num
##########################################
# #
# Basis #
# #
##########################################
#TODO
nucl_num = 1
ezfio.set_nuclei_nucl_num(nucl_num)
ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
nucl_num_per_kpt = nucl_num
ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
ezfio.set_nuclei_io_kpt_symm('Read')
ezfio.set_ao_basis_ao_basis("dummy basis")
#nucleus on which each AO is centered
ao_nucl = [1 for i in range(ao_num_per_kpt)]*kpt_num
ezfio.set_ao_basis_ao_nucl(ao_nucl)
#Just need one (can clean this up later)
ao_prim_num_max = 5
d = [ [0] *ao_prim_num_max]*ao_num_tot
ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num_tot)
ezfio.set_ao_basis_ao_power(d)
ezfio.set_ao_basis_ao_coef(d)
ezfio.set_ao_basis_ao_expo(d)
##########################################
# #
# MOCoeff #
# #
##########################################
#TODO
#coef_per_kpt = np.eye(mo_num_per_kpt, ao_num_per_kpt, dtype=np.complex128).view(dtype=np.float64).reshape((mo_num_per_kpt, ao_num_per_kpt, 2))
#mo_coef_kpts = np.tile(coef_per_kpt,[kpt_num, 1, 1, 1])
#qph5.create_dataset('mo_basis/mo_coef_kpts',data=make_reim_identity_kblocks(kpt_num, mo_num_per_kpt, ao_num_per_kpt))
ezfio.set_mo_basis_mo_coef_kpts(make_reim_identity_kblocks(kpt_num, mo_num_per_kpt, ao_num_per_kpt))
ezfio.set_mo_basis_mo_coef_complex(make_reim_identity_block_diag(kpt_num, mo_num_per_kpt, ao_num_per_kpt))
##########################################
# #
# Integrals Mono #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
# we don't have separate kinetic, nuc-elec, pseudo 1e ints, so just combine in nuc-elec and set rest to zero
mono_ints_tot = np.zeros((kpt_num,ao_num_per_kpt,ao_num_per_kpt,2),dtype=np.float64)
for i in range(kpt_num):
mono_ints_tot[i] = qph5[f'Hamiltonian/H1_kp{i}'][()]
ovlp_ao_reim = make_reim_identity_kblocks(kpt_num,ao_num_per_kpt,ao_num_per_kpt)
kin_ao_reim = np.zeros((kpt_num,ao_num_per_kpt,ao_num_per_kpt,2),dtype=np.float64)
ne_ao_reim = mono_ints_tot
ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim)
ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read')
"""
with h5py.File(qph5path,'r') as qph5:
if is_ao:
kin_ao_reim=
ovlp_ao_reim=
ne_ao_reim=
ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim)
ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read')
else:
kin_mo_reim=
ovlp_mo_reim=
ne_mo_reim=
ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim)
ezfio.set_mo_one_e_ints_mo_integrals_overlap_kpts(ovlp_mo_reim)
ezfio.set_mo_one_e_ints_mo_integrals_n_e_kpts(ne_mo_reim)
ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
"""
##########################################
# #
# k-points #
# #
##########################################
#TODO
with h5py.File(qph5path,'r') as qph5:
#kconserv = qph5['nuclei/kconserv'][()].tolist()
minusk = qph5['Hamiltonian']['MinusK'][:]+1
QKTok2 = qph5['Hamiltonian']['QKTok2'][:]+1
#TODO: change this after rmg is fixed
#minusk = QKTok2[:,0]
kconserv = kconserv_p_from_qkk2_mk(QKTok2-1,minusk-1)+1
unique_kpt_num = len(qph5['Hamiltonian']['KPFactorized'])
unique_k_idx = []
for i in qph5['Hamiltonian']['KPFactorized'].keys():
unique_k_idx.append(int(i[1:])+1)
unique_k_idx.sort()
kpt_sparse_map = np.zeros(kpt_num,dtype=int)
isparse=0
#TODO: make robust: this assumes that for each pair, the one with data has a lower index
for i in range(kpt_num):
if i+1 in unique_k_idx:
kpt_sparse_map[i] = isparse+1
isparse += 1
else:
kpt_sparse_map[i] = -kpt_sparse_map[minusk[i]-1]
ezfio.set_nuclei_kconserv(kconserv.transpose(2,1,0))
ezfio.set_nuclei_io_kconserv('Read')
ezfio.set_nuclei_minusk(minusk)
ezfio.set_nuclei_qktok2(np.transpose(QKTok2)) #transposed for correct col-major ordering
ezfio.set_nuclei_kpt_sparse_map(kpt_sparse_map)
ezfio.set_nuclei_unique_kpt_num(unique_kpt_num)
# kpt_sparse_map
# unique_kpt_num
# io_kpt_symm
##########################################
# #
# Integrals Bi #
# #
##########################################
# should this be in ao_basis? ao_two_e_ints?
with h5py.File(qph5path,'r') as qph5:
nchol_per_kpt_all = qph5['Hamiltonian']['NCholPerKP'][:]
print(nchol_per_kpt_all)
#nchol_per_kpt = nchol_per_kpt_all[nchol_per_kpt_all != 0]
nchol_per_kpt = nchol_per_kpt_all[np.array(unique_k_idx,dtype=int)-1]
print(nchol_per_kpt)
print(unique_k_idx)
#for i in range(kpt_num):
# if i+1 in unique_k_idx:
# print('* ',i,nchol_per_kpt_all[i])
# else:
# print(' ',i,nchol_per_kpt_all[i])
nchol_per_kpt_max = max(nchol_per_kpt)
ezfio.set_ao_two_e_ints_chol_num(nchol_per_kpt)
ezfio.set_ao_two_e_ints_chol_num_max(nchol_per_kpt_max)
if is_ao:
#ao_num_per_kpt = ao_num//kpt_num
ezfio.set_ao_two_e_ints_io_chol_ao_integrals('Read')
#ao_chol_two_e_ints = np.zeros((2, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max, kpt_num, len(nchol_per_kpt)))
L_list = []
L_all = np.zeros((unique_kpt_num, kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max,2),dtype=np.float64)
print(kpt_sparse_map)
print(np.array(unique_k_idx)-1)
for i in range(unique_kpt_num):
ki = unique_k_idx[i]-1
print(i, ki)
L_i = qph5[f'Hamiltonian/KPFactorized/L{ki}'][()].reshape((kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt[kpt_sparse_map[ki]-1], 2))
#L.reshape(kpt_num, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt[i], 2)
#L = np.einsum("ijklm->ilkjm", A, B)
L_all[i,:,:,:,:nchol_per_kpt[kpt_sparse_map[ki]-1],:] = L_i
#(6, 5184, 2)
"""
for cmplx in range(2):
for ao_idx_i in range(ao_num_per_kpt):
for ao_idx_j in range(ao_num_per_kpt):
for chol_idx in range(nchol_per_kpt[i]):
for kpt_idx in range(kpt_num):
ao_chol_two_e_ints[cmplx][ao_idx_i][ao_idx_j][chol_idx][kpt_idx][i] = L[kpt_idx][ao_idx_i][ao_idx_j][chol_idx][cmplx]
"""
#ao_chol_two_e_ints = np.vstack(L_list)
#ao_chol_two_e_ints = ao_chol_two_e_ints.transpose()
#TODO: check dims/reshape/transpose
#ezfio.set_ao_two_e_ints_chol_ao_integrals_complex(L_all.transpose((5,2,3,4,1,0)))
ezfio.set_ao_two_e_ints_chol_ao_integrals_complex(L_all.transpose((0,1,4,3,2,5)))
def fortformat(x0):
x = f'{abs(x0):25.14E}'.strip()
xsign = '-' if (x0<0) else ''
e = x.find('E')
return xsign + f'0.{x[0]}{x[2:e]}{x[e:e+2]}{abs(int(x[e+1:])*1+1):02d}'
if dump_cd:
#for qi in range(unique_kpt_num):
# for ki in range(kpt_num):
# for i in range(ao_num_per_kpt):
# for j in range(ao_num_per_kpt):
# for ci in range(nchol_per_kpt_max):
# vr = L_all[qi,ki,i,j,ci,0]
# vi = L_all[qi,ki,i,j,ci,1]
# print(f'{qi:6d} {ki:6d} {i:6d} {j:6d} {ci:6d} {vr:25.15E} {vi:25.15E}')
Lnew = L_all.transpose((5,2,3,4,1,0))
#for qi in range(unique_kpt_num):
# for ki in range(kpt_num):
# for ci in range(nchol_per_kpt_max):
# for j in range(ao_num_per_kpt):
# for i in range(ao_num_per_kpt):
# vr = Lnew[0,i,j,ci,ki,qi]
# vi = Lnew[1,i,j,ci,ki,qi]
# print(f'{qi:6d} {ki:6d} {ci:6d} {j:6d} {i:6d} {vr:25.15E} {vi:25.15E}')
for qi in range(unique_kpt_num):
for ki in range(kpt_num):
for ci in range(nchol_per_kpt_max):
for i in range(ao_num_per_kpt):
for j in range(ao_num_per_kpt):
#vr = Lnew[0,i,j,ci,ki,qi]
#vi = Lnew[1,i,j,ci,ki,qi]
vr = L_all[qi,ki,i,j,ci,0]
vi = L_all[qi,ki,i,j,ci,1]
print(f'{qi+1:6d} {ki+1:6d} {ci+1:6d} {i+1:6d} {j+1:6d} {fortformat(vr):>25s} {fortformat(vi):>25s}')
if dump_fci:
Wfull = np.zeros((ao_num_tot, ao_num_tot, ao_num_tot, ao_num_tot), dtype=np.complex128)
for Qi in range(kpt_num):
Qloc = abs(kpt_sparse_map[Qi])-1
Qneg = (kpt_sparse_map[Qi] < 0)
LQ00 = L_all[Qloc]
#LQ0a = LQ00.view(dtype=np.complex128)
#print(f'LQ0a.shape {LQ0a.shape}')
#LQ0a1 = LQ0a.reshape((kpt_num,ao_num_per_kpt,ao_num_per_kpt,-1))
#print(f'LQ0a1.shape {LQ0a1.shape}')
LQ0 = LQ00[:,:,:,:,0] + 1j*LQ00[:,:,:,:,1]
#print(f'LQ0.shape {LQ0.shape}')
#print(f'abdiff {np.abs(LQ0a1 - LQ0).max()}')
for kp in range(kpt_num):
kr = QKTok2[Qi,kp]-1
for ks in range(kpt_num):
kq = QKTok2[Qi,ks]-1
if Qneg:
A = LQ0[kr].transpose((1,0,2)).conj()
B = LQ0[kq]
W = np.einsum('prn,sqn->pqrs',A,B)
else:
A = LQ0[kp]
B = LQ0[ks].transpose((1,0,2)).conj()
W = np.einsum('rpn,qsn->pqrs',A,B)
p0 = kp*ao_num_per_kpt
r0 = kr*ao_num_per_kpt
q0 = kq*ao_num_per_kpt
s0 = ks*ao_num_per_kpt
for ip in range(ao_num_per_kpt):
for iq in range(ao_num_per_kpt):
for ir in range(ao_num_per_kpt):
for i_s in range(ao_num_per_kpt):
v = W[ip,iq,ir,i_s]
print(f'{p0+ip:5d} {q0+iq:5d} {r0+ir:5d} {s0+i_s:5d} {v.real:25.15E} {v.imag:25.15E}')
Wfull[p0:p0+ao_num_per_kpt,q0:q0+ao_num_per_kpt,r0:r0+ao_num_per_kpt,s0:s0+ao_num_per_kpt] = W.copy()
H1 = np.zeros((ao_num_tot, ao_num_tot), dtype=np.complex128)
for Qi in range(kpt_num):
hi0 = qph5[f'Hamiltonian/H1_kp{Qi}'][()]
hi = hi0[:,:,0] + 1j*hi0[:,:,1]
H1[Qi*ao_num_per_kpt:(Qi+1)*ao_num_per_kpt,Qi*ao_num_per_kpt:(Qi+1)*ao_num_per_kpt] = hi.copy()
mo_occ = ([1,]* elec_alpha_num_per_kpt + [0,] * (ao_num_per_kpt - elec_alpha_num_per_kpt)) * kpt_num
E1=0
E2j=0
E2k=0
for imo, iocc in enumerate(mo_occ):
if iocc:
E1 += 2*H1[imo,imo]
for jmo, jocc in enumerate(mo_occ):
if jocc:
E2j += 2* Wfull[imo,jmo,imo,jmo]
E2k -= Wfull[imo,jmo,jmo,imo]
print(f'E1 = {E1:25.15E}')
print(f'E2j = {E2j:25.15E}')
print(f'E2k = {E2k:25.15E}')
print(f'E2 = {E2j+E2k:25.15E}')
if dump_fci2:
ao_map1 = {}
ao_map2 = {}
ao_map1_idx = {}
ao_map2_idx = {}
Wdict = {}
for kQ in range(kpt_num):
for kl in range(kpt_num):
kj = QKTok2[kQ,kl]-1
if (kj>kl):
continue
kjkl2 = idx2_tri(kj,kl)
Qneg = (kpt_sparse_map[kQ] < 0)
Qloc = abs(kpt_sparse_map[kQ]) - 1
if not Qneg:
ints_jl0 = L_all[Qloc,kl,:,:,:,:]
ints_jl = ints_jl0[:,:,:,0]+1j*ints_jl0[:,:,:,1]
else:
ints_jl0 = L_all[Qloc,kj,:,:,:,:]
ints_jl1 = ints_jl0[:,:,:,0]+1j*ints_jl0[:,:,:,1]
ints_jl = ints_jl1.transpose((1,0,2)).conj()
for kk in range(kl+1):
ki = QKTok2[minusk[kk]-1,kQ]-1 #TODO: check
if ki != kconserv[kl,kk,kj]-1:
print(ki,kconserv[kl,kk,kj],kl,kk,kj)
assert( ki == kconserv[kl,kk,kj]-1) #TODO: check
if (ki > kl):
continue
kikk2 = idx2_tri(ki,kk)
if not Qneg:
ints_ik0 = L_all[Qloc,ki,:,:,:]
ints_ik = ints_ik0[:,:,:,0] + 1j*ints_ik0[:,:,:,1]
else:
ints_ik0 = L_all[Qloc,kk,:,:,:]
ints_ik1 = ints_ik0[:,:,:,0]+1j*ints_ik0[:,:,:,1]
ints_ik = ints_ik1.transpose((1,0,2)).conj()
ints_jl_flat = ints_jl.reshape((ao_num_per_kpt**2, -1))
ints_ik_flat = ints_ik.reshape((ao_num_per_kpt**2, -1))
ints_ikjl = np.einsum('an,bn->ab',ints_ik_flat,ints_jl_flat).reshape((ao_num_per_kpt,)*4)
for il in range(ao_num_per_kpt):
l = il + kl*ao_num_per_kpt
for ij in range(ao_num_per_kpt):
j = ij + kj*ao_num_per_kpt
if (j>l):
break
jl2 = idx2_tri(j,l)
for ik in range(ao_num_per_kpt):
k = ik + kk*ao_num_per_kpt
if (k>l):
break
for ii in range(ao_num_per_kpt):
i = ii + ki*ao_num_per_kpt
if ((j==l) and (i>k)):
break
ik2 = idx2_tri(i,k)
if (ik2 > jl2):
break
integral = ints_ikjl[ii,ik,ij,il]
if abs(integral) < 1E-15:
continue
idx_tmp,use_map1,sign = ao_idx_map_sign(i+1,j+1,k+1,l+1)
tmp_re = integral.real
tmp_im = integral.imag
Wdict[i,j,k,l] = tmp_re + 1j*tmp_im
if use_map1:
if idx_tmp in ao_map1:
print(idx_tmp,1)
raise
ao_map1[idx_tmp] = tmp_re
ao_map1_idx[idx_tmp] = (i,j,k,l,'re')
if sign != 0.0:
ao_map1[idx_tmp+1] = tmp_im*sign
ao_map1_idx[idx_tmp+1] = (i,j,k,l,'im')
else:
if idx_tmp in ao_map2:
print(idx_tmp,2)
raise
ao_map2[idx_tmp] = tmp_re
ao_map2_idx[idx_tmp] = (i,j,k,l,'re')
if sign != 0.0:
ao_map2[idx_tmp+1] = tmp_im*sign
ao_map2_idx[idx_tmp+1] = (i,j,k,l,'im')
# for idx in ao_map1:
# i,j,k,l,ax = ao_map1_idx[idx]
# print(f'1,{idx},{i},{j},{k},{l},{ax},{ao_map1[idx]}')
# for idx in ao_map2:
# i,j,k,l,ax = ao_map2_idx[idx]
# print(f'2,{idx},{i},{j},{k},{l},{ax},{ao_map2[idx]}')
for idx in Wdict:
i,j,k,l = idx
v = Wdict[idx]
print(f'{i+1:6d} {j+1:6d} {k+1:6d} {l+1:6d} {fortformat(v.real):>25s} {fortformat(v.imag):>25s}')
#for Qi in range(kpt_num):
# Qloc = abs(kpt_sparse_map[Qi])-1
# Qneg = (kpt_sparse_map[Qi] < 0)
# LQ00 = L_all[Qloc]
# #LQ0a = LQ00.view(dtype=np.complex128)
# #print(f'LQ0a.shape {LQ0a.shape}')
# #LQ0a1 = LQ0a.reshape((kpt_num,ao_num_per_kpt,ao_num_per_kpt,-1))
# #print(f'LQ0a1.shape {LQ0a1.shape}')
# LQ0 = LQ00[:,:,:,:,0] + 1j*LQ00[:,:,:,:,1]
# #print(f'LQ0.shape {LQ0.shape}')
# #print(f'abdiff {np.abs(LQ0a1 - LQ0).max()}')
#
# for kp in range(kpt_num):
# kr = QKTok2[Qi,kp]-1
# for ks in range(kpt_num):
# kq = QKTok2[Qi,ks]-1
# if Qneg:
# A = LQ0[kr].transpose((1,0,2)).conj()
# B = LQ0[kq]
# W = np.einsum('prn,sqn->pqrs',A,B)
# else:
# A = LQ0[kp]
# B = LQ0[ks].transpose((1,0,2)).conj()
# W = np.einsum('rpn,qsn->pqrs',A,B)
# p0 = kp*ao_num_per_kpt
# r0 = kr*ao_num_per_kpt
# q0 = kq*ao_num_per_kpt
# s0 = ks*ao_num_per_kpt
# for ip in range(ao_num_per_kpt):
# for iq in range(ao_num_per_kpt):
# for ir in range(ao_num_per_kpt):
# for i_s in range(ao_num_per_kpt):
# v = W[ip,iq,ir,i_s]
# print(f'{p0+ip:5d} {q0+iq:5d} {r0+ir:5d} {s0+i_s:5d} {v.real:25.15E} {v.imag:25.15E}')
# Wfull[p0:p0+ao_num_per_kpt,q0:q0+ao_num_per_kpt,r0:r0+ao_num_per_kpt,s0:s0+ao_num_per_kpt] = W.copy()
#H1 = np.zeros((ao_num_tot, ao_num_tot), dtype=np.complex128)
#for Qi in range(kpt_num):
# hi0 = qph5[f'Hamiltonian/H1_kp{Qi}'][()]
# hi = hi0[:,:,0] + 1j*hi0[:,:,1]
# H1[Qi*ao_num_per_kpt:(Qi+1)*ao_num_per_kpt,Qi*ao_num_per_kpt:(Qi+1)*ao_num_per_kpt] = hi.copy()
#mo_occ = ([1,]* elec_alpha_num_per_kpt + [0,] * (ao_num_per_kpt - elec_alpha_num_per_kpt)) * kpt_num
#E1=0
#E2j=0
#E2k=0
#for imo, iocc in enumerate(mo_occ):
# if iocc:
# E1 += 2*H1[imo,imo]
# for jmo, jocc in enumerate(mo_occ):
# if jocc:
# E2j += 2* Wfull[imo,jmo,imo,jmo]
# E2k -= Wfull[imo,jmo,jmo,imo]
#print(f'E1 = {E1:25.15E}')
#print(f'E2j = {E2j:25.15E}')
#print(f'E2k = {E2k:25.15E}')
#print(f'E2 = {E2j+E2k:25.15E}')
#(2,ao_basis.ao_num_per_kpt,ao_basis.ao_num_per_kpt,ao_two_e_ints.chol_num_max,nuclei.kpt_num,nuclei.unique_kpt_num#)
"""
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
"""
else:
"""
ezfio.set_io_chol_mo_integrals('Read')
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
"""
#mo_num_per_kpt = ao_num//kpt_num
ezfio.set_io_chol_mo_integrals('Read')
#ao_chol_two_e_ints = np.zeros((2, ao_num_per_kpt, ao_num_per_kpt, nchol_per_kpt_max, kpt_num, len(nchol_per_kpt)))
L_list = []
for i in len(nchol_per_kpt):
L = qph5['Hamiltonian']['KPFactorized'][f'L{i}'][:]
L.reshape(kpt_num, mo_num_per_kpt, mo_num_per_kpt, nchol_per_kpt[i], 2)
L = np.einsum("ijklm->ilkjm", A, B)
L_list.append(L)
#(6, 5184, 2)
"""
for cmplx in range(2):
for ao_idx_i in range(ao_num_per_kpt):
for ao_idx_j in range(ao_num_per_kpt):
for chol_idx in range(nchol_per_kpt[i]):
for kpt_idx in range(kpt_num):
ao_chol_two_e_ints[cmplx][ao_idx_i][ao_idx_j][chol_idx][kpt_idx][i] = L[kpt_idx][ao_idx_i][ao_idx_j][chol_idx][cmplx]
"""
mo_chol_two_e_ints = np.vstack(L_list)
mo_chol_two_e_ints = mo_chol_two_e_ints.transpose()
ezfio.set_chol_mo_integrals_complex(mo_chol_two_e_ints)
return
def convert_kpts(filename,qph5path,qmcpack=True):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(True)
with h5py.File(qph5path,'r') as qph5:
kpt_num = qph5['nuclei'].attrs['kpt_num']
nucl_num = qph5['nuclei'].attrs['nucl_num']
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num']
elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
ezfio.set_nuclei_kpt_num(kpt_num)
kpt_pair_num = (kpt_num*kpt_num + kpt_num)//2
ezfio.set_nuclei_kpt_pair_num(kpt_pair_num)
# don't multiply nuclei by kpt_num
# work in k-space, not in equivalent supercell
nucl_num_per_kpt = nucl_num
ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
# these are totals (kpt_num * num_per_kpt)
# need to change if we want to truncate orbital space within pyscf
ezfio.set_ao_basis_ao_num(ao_num)
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.set_ao_basis_ao_num_per_kpt(ao_num//kpt_num)
ezfio.set_mo_basis_mo_num_per_kpt(mo_num//kpt_num)
ezfio.electrons_elec_alpha_num = elec_alpha_num
ezfio.electrons_elec_beta_num = elec_beta_num
##ao_num = mo_num
##Important !
#import math
#nelec_per_kpt = num_elec // n_kpts
#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
#
#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
#ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux)
#(old)Important
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nucl_charge(nucl_charge)
ezfio.set_nuclei_nucl_coord(nucl_coord)
if isinstance(nucl_label[0],bytes):
nucl_label = list(map(lambda x:x.decode(),nucl_label))
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
##########################################
# #
# Basis(Dummy) #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
#Just need one (can clean this up later)
ao_prim_num_max = 5
d = [ [0] *ao_prim_num_max]*ao_num
ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
ezfio.set_ao_basis_ao_power(d)
ezfio.set_ao_basis_ao_coef(d)
ezfio.set_ao_basis_ao_expo(d)
###########################################
## #
## Pseudo #
## #
###########################################
#with h5py.File(qph5path,'r') as qph5:
# do_pseudo = qph5['pseudo'].attrs['do_pseudo']
# ezfio.set_pseudo_do_pseudo(do_pseudo)
# if (do_pseudo):
# ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
# ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
# ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
# ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
# ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
# ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
# ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
# ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
# ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
# ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
##########################################
# #
# Basis(Dummy) #
# #
##########################################
#with h5py.File(qph5path,'r') as qph5:
# coeftmp = qph5['ao_basis/ao_coef'][()]
# expotmp = qph5['ao_basis/ao_expo'][()]
# ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
# ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
# ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
# ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
# ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
# ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
##########################################
# #
# Basis(QMC) #
# #
##########################################
if qmcpack:
try:
with h5py.File(qph5path,'r') as qph5:
ezfio.set_qmcpack_qmc_nshell(qph5['qmcpack'].attrs['qmc_nshell'])
ezfio.set_qmcpack_qmc_prim_num_max(qph5['qmcpack'].attrs['qmc_prim_num_max'])
ezfio.set_qmcpack_qmc_nucl(qph5['qmcpack/qmc_nucl'][()].tolist())
ezfio.set_qmcpack_qmc_prim_num(qph5['qmcpack/qmc_prim_num'][()].tolist())
ezfio.set_qmcpack_qmc_lbas(qph5['qmcpack/qmc_lbas'][()].tolist())
ezfio.set_qmcpack_qmc_coef(qph5['qmcpack/qmc_coef'][()].tolist())
ezfio.set_qmcpack_qmc_expo(qph5['qmcpack/qmc_expo'][()].tolist())
ezfio.set_qmcpack_qmc_pbc(qph5['qmcpack'].attrs['PBC'])
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_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())
except AttributeError as err:
print("################################################")
print("# ERROR: problem copying QMCPACK data to ezfio #")
print("# make sure qmcpack plugin is built #")
print("################################################")
#print(f"AttributeError: {err}")
print("to create ezfio without qmcpack data, use 'qp_convert_h5_to_ezfio --noqmc'")
raise
##########################################
# #
# MO Coef #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
mo_coef_kpts = qph5['mo_basis/mo_coef_kpts'][()].tolist()
mo_coef_cplx = qph5['mo_basis/mo_coef_complex'][()].tolist()
ezfio.set_mo_basis_mo_coef_kpts(mo_coef_kpts)
ezfio.set_mo_basis_mo_coef_complex(mo_coef_cplx)
#maybe fix qp so we don't need this?
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
##########################################
# #
# Integrals Mono #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
if 'ao_one_e_ints' in qph5.keys():
kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic_kpts'][()].tolist()
ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap_kpts'][()].tolist()
ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e_kpts'][()].tolist()
ezfio.set_ao_one_e_ints_ao_integrals_kinetic_kpts(kin_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_overlap_kpts(ovlp_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_n_e_kpts(ne_ao_reim)
ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read')
with h5py.File(qph5path,'r') as qph5:
if 'mo_one_e_ints' in qph5.keys():
kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic_kpts'][()].tolist()
ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap_kpts'][()].tolist()
ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e_kpts'][()].tolist()
ezfio.set_mo_one_e_ints_mo_integrals_kinetic_kpts(kin_mo_reim)
ezfio.set_mo_one_e_ints_mo_integrals_overlap_kpts(ovlp_mo_reim)
#ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
ezfio.set_mo_one_e_ints_mo_integrals_n_e_kpts(ne_mo_reim)
ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
#ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
##########################################
# #
# k-points #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
kconserv = qph5['nuclei/kconserv'][()].tolist()
ezfio.set_nuclei_kconserv(kconserv)
ezfio.set_nuclei_io_kconserv('Read')
##########################################
# #
# Integrals Bi #
# #
##########################################
# should this be in ao_basis? ao_two_e_ints?
with h5py.File(qph5path,'r') as qph5:
if 'ao_two_e_ints' in qph5.keys():
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
# dfao_re0=qph5['ao_two_e_ints/df_ao_integrals_real'][()].transpose((3,2,1,0))
# dfao_im0=qph5['ao_two_e_ints/df_ao_integrals_imag'][()].transpose((3,2,1,0))
# dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist()
# ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0)
#dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()]
save_array_do(filename,'ao_two_e_ints/df_ao_integrals_complex',dfao_reim)
#ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
#dfao_dims = list(reversed(dfao_reim.shape))
#test_write_df_ao(,5,dfao_dims,dfao_reim.size,dfao_reim.ravel())
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
if 'mo_two_e_ints' in qph5.keys():
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
# dfmo_re0=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0))
# dfmo_im0=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0))
# dfmo_cmplx0 = np.stack((dfmo_re0,dfmo_im0),axis=-1).tolist()
# ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_cmplx0)
dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
return
def convert_cplx(filename,qph5path):
ezfio.set_file(filename)
ezfio.set_nuclei_is_complex(True)
with h5py.File(qph5path,'r') as qph5:
kpt_num = qph5['nuclei'].attrs['kpt_num']
nucl_num = qph5['nuclei'].attrs['nucl_num']
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num']
elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
ezfio.set_nuclei_kpt_num(kpt_num)
kpt_pair_num = (kpt_num*kpt_num + kpt_num)//2
ezfio.set_nuclei_kpt_pair_num(kpt_pair_num)
# don't multiply nuclei by kpt_num
# work in k-space, not in equivalent supercell
nucl_num_per_kpt = nucl_num
ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
# these are totals (kpt_num * num_per_kpt)
# need to change if we want to truncate orbital space within pyscf
ezfio.set_ao_basis_ao_num(ao_num)
ezfio.set_mo_basis_mo_num(mo_num)
ezfio.electrons_elec_alpha_num = elec_alpha_num
ezfio.electrons_elec_beta_num = elec_beta_num
##ao_num = mo_num
##Important !
#import math
#nelec_per_kpt = num_elec // n_kpts
#nelec_alpha_per_kpt = int(math.ceil(nelec_per_kpt / 2.))
#nelec_beta_per_kpt = int(math.floor(nelec_per_kpt / 2.))
#
#ezfio.electrons_elec_alpha_num = int(nelec_alpha_per_kpt * n_kpts)
#ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.electrons_elec_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
#ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux)
#(old)Important
#ezfio.set_nuclei_nucl_num(nucl_num)
#ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
with h5py.File(qph5path,'r') as qph5:
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nucl_charge(nucl_charge)
ezfio.set_nuclei_nucl_coord(nucl_coord)
if isinstance(nucl_label[0],bytes):
nucl_label = list(map(lambda x:x.decode(),nucl_label))
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
##########################################
# #
# Basis #
# #
##########################################
# with h5py.File(qph5path,'r') as qph5:
# ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
# ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
#
#
# #Just need one (can clean this up later)
# ao_prim_num_max = 5
#
# d = [ [0] *ao_prim_num_max]*ao_num
# ezfio.set_ao_basis_ao_prim_num([ao_prim_num_max]*ao_num)
# ezfio.set_ao_basis_ao_power(d)
# ezfio.set_ao_basis_ao_coef(d)
# ezfio.set_ao_basis_ao_expo(d)
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
do_pseudo = qph5['pseudo'].attrs['do_pseudo']
ezfio.set_pseudo_do_pseudo(do_pseudo)
if (do_pseudo):
ezfio.set_pseudo_pseudo_lmax(qph5['pseudo'].attrs['pseudo_lmax'])
ezfio.set_pseudo_pseudo_klocmax(qph5['pseudo'].attrs['pseudo_klocmax'])
ezfio.set_pseudo_pseudo_kmax(qph5['pseudo'].attrs['pseudo_kmax'])
ezfio.set_pseudo_nucl_charge_remove(qph5['pseudo/nucl_charge_remove'][()].tolist())
ezfio.set_pseudo_pseudo_n_k(qph5['pseudo/pseudo_n_k'][()].tolist())
ezfio.set_pseudo_pseudo_n_kl(qph5['pseudo/pseudo_n_kl'][()].tolist())
ezfio.set_pseudo_pseudo_v_k(qph5['pseudo/pseudo_v_k'][()].tolist())
ezfio.set_pseudo_pseudo_v_kl(qph5['pseudo/pseudo_v_kl'][()].tolist())
ezfio.set_pseudo_pseudo_dz_k(qph5['pseudo/pseudo_dz_k'][()].tolist())
ezfio.set_pseudo_pseudo_dz_kl(qph5['pseudo/pseudo_dz_kl'][()].tolist())
##########################################
# #
# Basis #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
coeftmp = qph5['ao_basis/ao_coef'][()]
expotmp = qph5['ao_basis/ao_expo'][()]
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
ezfio.set_ao_basis_ao_prim_num(qph5['ao_basis/ao_prim_num'][()].tolist())
ezfio.set_ao_basis_ao_power(qph5['ao_basis/ao_power'][()].tolist())
ezfio.set_ao_basis_ao_coef(qph5['ao_basis/ao_coef'][()].tolist())
ezfio.set_ao_basis_ao_expo(qph5['ao_basis/ao_expo'][()].tolist())
##########################################
# #
# MO Coef #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
mo_coef_reim = qph5['mo_basis/mo_coef_complex'][()].tolist()
ezfio.set_mo_basis_mo_coef_complex(mo_coef_reim)
#maybe fix qp so we don't need this?
#ezfio.set_mo_basis_mo_coef([[i for i in range(mo_num)] * ao_num])
##########################################
# #
# Integrals Mono #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
if 'ao_one_e_ints' in qph5.keys():
kin_ao_reim=qph5['ao_one_e_ints/ao_integrals_kinetic'][()].tolist()
ovlp_ao_reim=qph5['ao_one_e_ints/ao_integrals_overlap'][()].tolist()
ne_ao_reim=qph5['ao_one_e_ints/ao_integrals_n_e'][()].tolist()
ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_reim)
ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(ne_ao_reim)
ezfio.set_ao_one_e_ints_io_ao_integrals_kinetic('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_overlap('Read')
ezfio.set_ao_one_e_ints_io_ao_integrals_n_e('Read')
with h5py.File(qph5path,'r') as qph5:
if 'mo_one_e_ints' in qph5.keys():
kin_mo_reim=qph5['mo_one_e_ints/mo_integrals_kinetic'][()].tolist()
#ovlp_mo_reim=qph5['mo_one_e_ints/mo_integrals_overlap'][()].tolist()
ne_mo_reim=qph5['mo_one_e_ints/mo_integrals_n_e'][()].tolist()
ezfio.set_mo_one_e_ints_mo_integrals_kinetic_complex(kin_mo_reim)
#ezfio.set_mo_one_e_ints_mo_integrals_overlap_complex(ovlp_mo_reim)
#ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
ezfio.set_mo_one_e_ints_mo_integrals_n_e_complex(ne_mo_reim)
ezfio.set_mo_one_e_ints_io_mo_integrals_kinetic('Read')
#ezfio.set_mo_one_e_ints_io_mo_integrals_overlap('Read')
#ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
ezfio.set_mo_one_e_ints_io_mo_integrals_n_e('Read')
##########################################
# #
# k-points #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
kconserv = qph5['nuclei/kconserv'][()].tolist()
ezfio.set_nuclei_kconserv(kconserv)
ezfio.set_nuclei_io_kconserv('Read')
##########################################
# #
# Integrals Bi #
# #
##########################################
# should this be in ao_basis? ao_two_e_ints?
with h5py.File(qph5path,'r') as qph5:
if 'ao_two_e_ints' in qph5.keys():
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
if 'df_ao_integrals' in qph5['ao_two_e_ints'].keys():
# dfao_re0=qph5['ao_two_e_ints/df_ao_integrals_real'][()].transpose((3,2,1,0))
# dfao_im0=qph5['ao_two_e_ints/df_ao_integrals_imag'][()].transpose((3,2,1,0))
# dfao_cmplx0 = np.stack((dfao_re0,dfao_im0),axis=-1).tolist()
# ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_cmplx0)
dfao_reim=qph5['ao_two_e_ints/df_ao_integrals'][()].tolist()
ezfio.set_ao_two_e_ints_df_ao_integrals_complex(dfao_reim)
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
if 'mo_two_e_ints' in qph5.keys():
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
# dfmo_re0=qph5['mo_two_e_ints/df_mo_integrals_real'][()].transpose((3,2,1,0))
# dfmo_im0=qph5['mo_two_e_ints/df_mo_integrals_imag'][()].transpose((3,2,1,0))
# dfmo_cmplx0 = np.stack((dfmo_re0,dfmo_im0),axis=-1).tolist()
# ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_cmplx0)
dfmo_reim=qph5['mo_two_e_ints/df_mo_integrals'][()].tolist()
ezfio.set_mo_two_e_ints_df_mo_integrals_complex(dfmo_reim)
ezfio.set_mo_two_e_ints_io_df_mo_integrals('Read')
return
if __name__ == '__main__':
ARGUMENTS = docopt(__doc__)
#for i in range(1,6):
# for j in range(1,6):
# for k in range(1,6):
# for l in range(1,6):
# idx,usem1,sgn = ao_idx_map_sign(i,j,k,l)
# print(f'{i:4d} {j:4d} {k:4d} {l:4d} {str(usem1)[0]:s} {idx:6d} {sgn:5.1f}')
FILE = get_full_path(ARGUMENTS['FILE'])
qmcpack = True
rmg = False
if ARGUMENTS["--output"]:
EZFIO_FILE = get_full_path(ARGUMENTS["--output"])
else:
EZFIO_FILE = "{0}.ezfio".format(FILE)
if ARGUMENTS["--noqmc"]:
qmcpack = False
if ARGUMENTS["--rmg"]:
rmg = True
with h5py.File(FILE,'r') as qph5:
try:
do_kpts = ('kconserv' in qph5['nuclei'].keys())
except:
do_kpts = False
if (do_kpts or rmg):
print("converting HDF5 to EZFIO for periodic system")
if rmg:
print("Using RMG and AFQMC h5")
convert_kpts_cd(EZFIO_FILE,FILE,qmcpack)
else:
convert_kpts(EZFIO_FILE,FILE,qmcpack)
else:
print("converting HDF5 to EZFIO for molecular system")
convert_mol(EZFIO_FILE,FILE)
# sys.stdout.flush()
# if os.system("qp_run save_ortho_mos "+EZFIO_FILE) != 0:
# print("""Warning: You need to run
#
# qp run save_ortho_mos
#
#to be sure your MOs will be orthogonal, which is not the case when
#the MOs are read from output files (not enough precision in output).""")
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