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updated converter

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This commit is contained in:
Kevin Gasperich 2020-03-12 16:06:31 -05:00
parent 01360efd84
commit 120e421239
4 changed files with 132 additions and 97 deletions
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1
src/utils_complex/Gen_Ezfio_from_integral_complex_3idx.sh
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@ -17,7 +17,6 @@ echo 'Create EZFIO'
qp_edit -c $ezfio &> /dev/null
#cp $ezfio/{ao,mo}_basis/ao_md5
qp_run import_kconserv $ezfio
#qp_run import_ao_2e_complex $ezfio
#qp_run dump_ao_2e_from_df $ezfio
#Read the integral

43
src/utils_complex/MolPyscfToQPkpts.py
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@ -681,6 +681,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
##########################################
with h5py.File(qph5path,'a') as qph5:
# k,mo,ao(,2)
mo_coef_f = np.array(mo_k.transpose((0,2,1)),order='c')
mo_coef_blocked=block_diag(*mo_k)
mo_coef_blocked_f = block_diag(*mo_coef_f)
@ -688,8 +689,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5.create_dataset('mo_basis/mo_coef_imag',data=mo_coef_blocked.imag)
qph5.create_dataset('mo_basis/mo_coef_kpts_real',data=mo_k.real)
qph5.create_dataset('mo_basis/mo_coef_kpts_imag',data=mo_k.imag)
qph5.create_dataset('mo_basis/mo_coef',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2)))
qph5.create_dataset('mo_basis/mo_coef_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2)))
qph5.create_dataset('mo_basis/mo_coef_complex',data=mo_coef_blocked_f.view(dtype=np.float64).reshape((Nk*nmo,Nk*nao,2)))
qph5.create_dataset('mo_basis/mo_coef_complex_kpts',data=mo_coef_f.view(dtype=np.float64).reshape((Nk,nmo,nao,2)))
print_kpts_unblocked(mo_k,'C.qp',mo_coef_threshold)
@ -704,11 +705,20 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
ovlp_ao = get_ovlp_ao(mf)
if print_ao_ints_mono:
kin_ao_blocked=block_diag(*kin_ao)
ovlp_ao_blocked=block_diag(*ovlp_ao)
ne_ao_blocked=block_diag(*ne_ao)
with h5py.File(qph5path,'a') as qph5:
kin_ao_blocked=block_diag(*kin_ao)
ovlp_ao_blocked=block_diag(*ovlp_ao)
ne_ao_blocked=block_diag(*ne_ao)
kin_ao_f = np.array(kin_ao.transpose((0,2,1)),order='c')
ovlp_ao_f = np.array(ovlp_ao.transpose((0,2,1)),order='c')
ne_ao_f = np.array(ne_ao.transpose((0,2,1)),order='c')
kin_ao_blocked_f = block_diag(*kin_ao_f)
ovlp_ao_blocked_f = block_diag(*ovlp_ao_f)
ne_ao_blocked_f = block_diag(*ne_ao_f)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_real',data=kin_ao_blocked.real)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic_imag',data=kin_ao_blocked.imag)
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap_real',data=ovlp_ao_blocked.real)
@ -716,6 +726,10 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_real', data=ne_ao_blocked.real)
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e_imag', data=ne_ao_blocked.imag)
qph5.create_dataset('ao_one_e_ints/ao_integrals_kinetic',data=kin_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_overlap',data=ovlp_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
qph5.create_dataset('ao_one_e_ints/ao_integrals_n_e', data=ne_ao_blocked_f.view(dtype=np.float64).reshape((Nk*nao,Nk*nao,2)))
for fname,ints in zip(('S.qp','V.qp','T.qp'),
(ovlp_ao, ne_ao, kin_ao)):
print_kpts_unblocked_upper(ints,fname,thresh_mono)
@ -750,15 +764,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
kconserv = tools.get_kconserv(cell, kpts)
with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('nuclei/kconserv',data=np.transpose(kconserv+1,(0,2,1)))
kcon_test = np.zeros((Nk,Nk,Nk),dtype=int)
for a in range(Nk):
for b in range(Nk):
for c in range(Nk):
kcon_test[a,c,b] = kconserv[a,b,c]+1
with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('nuclei/kconserv_test',data=kcon_test)
kcon_f_phys = np.array(kconserv.transpose((1,2,0)),order='c')
qph5.create_dataset('nuclei/kconserv',data=kcon_f_phys+1)
print_kcon_chem_to_phys(kconserv,'K.qp')
@ -783,8 +790,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
j3ao_new = get_j3ao_new(mf.with_df._cderi,nao,Nk)
with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_real',data=j3arr.transpose((2,3,1,0)).real)
qph5.create_dataset('ao_two_e_ints/df_ao_integrals_imag',data=j3arr.transpose((2,3,1,0)).imag)
#qph5.create_dataset('ao_two_e_ints/df_ao_integrals_real',data=j3arr.transpose((2,3,1,0)).real)
#qph5.create_dataset('ao_two_e_ints/df_ao_integrals_imag',data=j3arr.transpose((2,3,1,0)).imag)
qph5.create_dataset('ao_two_e_ints/df_ao_integrals',data=j3ao_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nao,nao,2)))
if print_mo_ints_df:
@ -795,8 +802,8 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
print_df(j3mo,'D.mo.qp',bielec_int_threshold)
with h5py.File(qph5path,'a') as qph5:
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_real',data=j3mo.transpose((2,3,1,0)).real)
qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=j3mo.transpose((2,3,1,0)).imag)
#qph5.create_dataset('mo_two_e_ints/df_mo_integrals_real',data=j3mo.transpose((2,3,1,0)).real)
#qph5.create_dataset('mo_two_e_ints/df_mo_integrals_imag',data=j3mo.transpose((2,3,1,0)).imag)
qph5.create_dataset('mo_two_e_ints/df_mo_integrals',data=j3mo_new.view(dtype=np.float64).reshape((nkpt_pairs,naux,nmo,nmo,2)))
if (print_ao_ints_bi):

175
src/utils_complex/create_ezfio_complex_3idx.py
View File

@ -5,33 +5,37 @@ import h5py
import sys
import numpy as np
filename = sys.argv[1]
h5filename = sys.argv[2]
#num_elec, nucl_num, mo_num = map(int,sys.argv[2:5])
qph5path = sys.argv[2]
#nuclear_repulsion = float(sys.argv[5])
#ao_num = int(sys.argv[6])
#n_kpts = int(sys.argv[7])
#n_aux = int(sys.argv[8])
ezfio.set_file(filename)
qph5=h5py.File(h5filename,'r')
#qph5=h5py.File(qph5path,'r')
kpt_num = qph5['nuclei'].attrs['kpt_num']
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.electrons_elec_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
nucl_num = qph5['nuclei'].attrs['nucl_num']
nucl_num_per_kpt = nucl_num // kpt_num
ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_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
@ -57,30 +61,30 @@ ezfio.set_mo_basis_mo_num(mo_num)
#ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
#ezfio.set_nuclei_nucl_label( ['He'] * nucl_num )
ezfio.set_nuclei_nucl_num(nucl_num_per_kpt)
nucl_charge=qph5['nuclei/nucl_charge'][()].tolist()
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)
nucl_coord=qph5['nuclei/nucl_coord'][()].T.tolist()
ezfio.set_nuclei_nucl_coord(nucl_coord)
nucl_label=qph5['nuclei/nucl_label'][()].tolist()
ezfio.set_nuclei_nucl_label(nucl_label)
ezfio.set_nuclei_io_nuclear_repulsion('Read')
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
# Ao num
#ao_num = mo_num
#ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
ezfio.set_ao_basis_ao_num(ao_num)
#ezfio.set_ao_basis_ao_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
ezfio.set_ao_basis_ao_basis(qph5['ao_basis'].attrs['ao_basis'])
ezfio.set_ao_basis_ao_nucl(qph5['ao_basis/ao_nucl'][()].tolist())
##########################################
# #
# 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)
@ -94,67 +98,82 @@ ezfio.set_ao_basis_ao_expo(d)
ezfio.set_mo_basis_mo_num(mo_num)
#c_mo = [[1 if i==j else 0 for i in range(mo_num)] for j in range(ao_num)]
#ezfio.set_mo_basis_mo_coef([ [0]*mo_num] * ao_num)
##ezfio.set_mo_basis_mo_coef_real(c_mo)
mo_coef_re0 = qph5['mo_basis/mo_coef_real'][()].T
mo_coef_im0 = qph5['mo_basis/mo_coef_imag'][()].T
mo_coef_cmplx0 = np.stack((mo_coef_re0,mo_coef_im0),axis=-1).tolist()
#ezfio.set_mo_basis_mo_coef_real(qph5['mo_basis/mo_coef_real'][()].tolist())
#ezfio.set_mo_basis_mo_coef_imag(qph5['mo_basis/mo_coef_imag'][()].tolist())
ezfio.set_mo_basis_mo_coef_complex(mo_coef_cmplx0)
##########################################
# #
# 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])
ezfio.set_nuclei_is_complex(True)
# fortran-ordered re,im parts
kin_ao_re0=qph5['ao_one_e_ints/ao_integrals_kinetic_real'][()].T
kin_ao_im0=qph5['ao_one_e_ints/ao_integrals_kinetic_imag'][()].T
#test where to stack? (axis=0 or -1?)
kin_ao_cmplx0=np.stack((kin_ao_re0,kin_ao_im0),axis=-1).tolist()
##########################################
# #
# Integrals Mono #
# #
##########################################
with h5py.File(qph5path,'r') as qph5:
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()
ovlp_ao_re0=qph5['ao_one_e_ints/ao_integrals_overlap_real'][()].T
ovlp_ao_im0=qph5['ao_one_e_ints/ao_integrals_overlap_imag'][()].T
#test where to stack? (axis=0 or -1?)
ovlp_ao_cmplx0=np.stack((ovlp_ao_re0,ovlp_ao_im0),axis=-1).tolist()
ne_ao_re0=qph5['ao_one_e_ints/ao_integrals_n_e_real'][()].T
ne_ao_im0=qph5['ao_one_e_ints/ao_integrals_n_e_imag'][()].T
#test where to stack? (axis=0 or -1?)
ne_ao_cmplx0=np.stack((ne_ao_re0,ne_ao_im0),axis=-1).tolist()
ezfio.set_ao_one_e_ints_ao_integrals_kinetic_complex(kin_ao_cmplx0)
ezfio.set_ao_one_e_ints_ao_integrals_overlap_complex(ovlp_ao_cmplx0)
ezfio.set_ao_one_e_ints_ao_integrals_n_e_complex(ne_ao_cmplx0)
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')
##########################################
# #
# 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?
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_real' 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)
ezfio.set_ao_two_e_ints_io_df_ao_integrals('Read')
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)
ezfio.set_mo_two_e_ints_io_df_mo_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')
#TODO: add check and only do this if ints exist

10
src/utils_complex/dump_ao_1e_cplx.irp.f
View File

@ -13,6 +13,16 @@ subroutine run
do i=1,ao_num
write(*,'(200(E24.15))') ao_one_e_integrals_complex(i,:)
enddo
write(*,'(A)') 'ao_kinetic_integrals_complex'
write(*,'(A)') '---------------'
do i=1,ao_num
write(*,'(200(E24.15))') ao_kinetic_integrals_complex(i,:)
enddo
write(*,'(A)') 'ao_ne_integrals_complex'
write(*,'(A)') '---------------'
do i=1,ao_num
write(*,'(200(E24.15))') ao_integrals_n_e_complex(i,:)
enddo
write(*,'(A)') 'ao_overlap_complex'
write(*,'(A)') '---------------'
do i=1,ao_num