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working on complex converter

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This commit is contained in:
Kevin Gasperich 2020-02-11 16:39:08 -06:00
parent a28244e1d1
commit 8472e71df4
4 changed files with 92 additions and 33 deletions
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5
src/ao_two_e_ints/EZFIO.cfg
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@ -18,3 +18,8 @@ interface: ezfio,provider,ocaml
default: False default: False
ezfio_name: direct ezfio_name: direct
[df_num]
type: integer
doc: Size of df basis
interface: ezfio, provider

17
src/utils_periodic/Gen_Ezfio_from_integral_complex_3idx.sh
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@ -1,17 +1,18 @@
#!/bin/bash #!/bin/bash
ezfio=$1 ezfio=$1
h5file=$2
# Create the integral # Create the integral
echo 'Create Integral' echo 'Create Integral'
echo 'Create EZFIO' echo 'Create EZFIO'
read nel nmo natom <<< $(cat param) #read nel nmo natom <<< $(cat param)
read e_nucl <<< $(cat e_nuc) #read e_nucl <<< $(cat e_nuc)
read nao <<< $(cat num_ao) #read nao <<< $(cat num_ao)
read nkpts <<< $(cat num_kpts) #read nkpts <<< $(cat num_kpts)
read ndf <<< $(cat num_df) #read ndf <<< $(cat num_df)
#./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts ##./create_ezfio_complex_4idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts
./create_ezfio_complex_3idx.py $ezfio $nel $natom $nmo $e_nucl $nao $nkpts $ndf ./create_ezfio_complex_3idx.py $ezfio $h5file #$nel $natom $nmo $e_nucl $nao $nkpts $ndf
#Handle the orbital consitensy check #Handle the orbital consitensy check
qp_edit -c $ezfio &> /dev/null qp_edit -c $ezfio &> /dev/null
cp $ezfio/{ao,mo}_basis/ao_md5 cp $ezfio/{ao,mo}_basis/ao_md5
@ -23,7 +24,7 @@ echo 'Read Integral'
################################################ ################################################
## using AO mono, 4-idx from pyscf ## ## using AO mono, 4-idx from pyscf ##
################################################ ################################################
qp_run import_integrals_ao_periodic $ezfio #qp_run import_integrals_ao_periodic $ezfio
################################################ ################################################

25
src/utils_periodic/MolPyscfToQPkpts.py
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@ -489,6 +489,7 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
from pyscf.pbc import ao2mo from pyscf.pbc import ao2mo
from pyscf.pbc import tools from pyscf.pbc import tools
from pyscf.pbc.gto import ecp from pyscf.pbc.gto import ecp
from pyscf.data import nist
import h5py import h5py
import scipy import scipy
@ -507,9 +508,21 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
natom = cell.natm natom = cell.natm
nelec = cell.nelectron nelec = cell.nelectron
atom_xyz = mf.cell.atom_coords()
if not(mf.cell.unit.startswith(('B','b','au','AU'))):
atom_xyz /= nist.BOHR # always convert to au
strtype=h5py.special_dtype(vlen=str)
atom_dset=qph5.create_dataset('nuclei/nucl_label',(natom,),dtype=strtype)
for i in range(natom):
atom_dset[i] = mf.cell.atom_pure_symbol(i)
qph5.create_dataset('nuclei/nucl_coord',data=atom_xyz)
qph5.create_dataset('nuclei/nucl_charge',data=mf.cell.atom_charges())
print('n_atom per kpt', natom) print('n_atom per kpt', natom)
print('num_elec per kpt', nelec) print('num_elec per kpt', nelec)
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)
@ -523,14 +536,20 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
naux = mf.with_df.auxcell.nao naux = mf.with_df.auxcell.nao
print("n df fitting functions", naux) print("n df fitting functions", naux)
#in old version: param < nelec*Nk, nmo*Nk, natom*Nk #in old version: param << nelec*Nk, nmo*Nk, natom*Nk
qph5['electrons'].attrs['elec_alpha_num']=nelec*Nk qph5['electrons'].attrs['elec_alpha_num']=nelec*Nk
qph5['electrons'].attrs['elec_beta_num']=nelec*Nk qph5['electrons'].attrs['elec_beta_num']=nelec*Nk
qph5['mo_basis'].attrs['mo_num']=Nk*nmo qph5['mo_basis'].attrs['mo_num']=Nk*nmo
qph5['ao_basis'].attrs['ao_num']=Nk*nao qph5['ao_basis'].attrs['ao_num']=Nk*nao
qph5['nuclei'].attrs['nucl_num']=Nk*natom qph5['nuclei'].attrs['nucl_num']=Nk*natom
qph5['nuclei'].attrs['kpt_num']=Nk qph5['nuclei'].attrs['kpt_num']=Nk
qph5['ao_basis'].attrs['df_num']=naux qph5.create_group('ao_two_e_ints')
qph5['ao_two_e_ints'].attrs['df_num']=naux
qph5['ao_basis'].attrs['ao_basis']=mf.cell.basis
ao_nucl=[mf.cell.bas_atom(i)+1 for i in range(nao)]
qph5.create_dataset('ao_basis/ao_nucl',data=Nk*ao_nucl)
# _ # _
# |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._ # |\ | _ | _ _. ._ |_) _ ._ | _ o _ ._

78
src/utils_periodic/create_ezfio_complex_3idx.py
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@ -12,28 +12,38 @@ h5filename = sys.argv[2]
#n_kpts = int(sys.argv[7]) #n_kpts = int(sys.argv[7])
#n_aux = int(sys.argv[8]) #n_aux = int(sys.argv[8])
ezfio.set_file(filename) ezfio.set_file(filename)
qph5=h5py.File(h5filename.'r') qph5=h5py.File(h5filename,'r')
kpt_num = qph5['nuclei'].attrs['kpt_num']
ezfio.set_nuclei_kpt_num(kpt_num)
# should this be in ao_basis? ao_two_e_ints?
df_num = qph5['ao_two_e_ints'].attrs['df_num']
ezfio.set_ao_two_e_ints_df_num(df_num)
# 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_alpha_num = qph5['electrons'].attrs['elec_alpha_num']
ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num'] ezfio.electrons_elec_beta_num = qph5['electrons'].attrs['elec_beta_num']
nucl_num = qph5['nuclei'].attrs['nucl_num'] nucl_num = qph5['nuclei'].attrs['nucl_num']
kpt_num = qph5['nuclei'].attrs['kpt_num'] nucl_num_per_kpt = nucl_num // kpt_num
df_num = qph5['ao_basis'].attrs['df_num']
ao_num = qph5['ao_basis'].attrs['ao_num'] ao_num = qph5['ao_basis'].attrs['ao_num']
mo_num = qph5['mo_basis'].attrs['mo_num'] mo_num = qph5['mo_basis'].attrs['mo_num']
ezfio.set_mo_basis_mo_num(mo_num) ezfio.set_mo_basis_mo_num(mo_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) ##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_alpha_num = int(math.ceil(num_elec / 2.))
#ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.)) #ezfio.electrons_elec_beta_num = int(math.floor(num_elec / 2.))
@ -41,13 +51,26 @@ ezfio.electrons_elec_beta_num = int(nelec_beta_per_kpt * n_kpts)
#ezfio.set_utils_num_kpts(n_kpts) #ezfio.set_utils_num_kpts(n_kpts)
#ezfio.set_integrals_bielec_df_num(n_aux) #ezfio.set_integrals_bielec_df_num(n_aux)
#Important #(old)Important
ezfio.set_nuclei_nucl_num(nucl_num) #ezfio.set_nuclei_nucl_num(nucl_num)
ezfio.set_nuclei_nucl_charge([0.]*nucl_num) #ezfio.set_nuclei_nucl_charge([0.]*nucl_num)
ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num ) #ezfio.set_nuclei_nucl_coord( [ [0.], [0.], [0.] ]*nucl_num )
ezfio.set_nuclei_nucl_label( ['He'] * 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()
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') ezfio.set_nuclei_io_nuclear_repulsion('Read')
nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion) ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
# Ao num # Ao num
@ -56,7 +79,11 @@ ezfio.set_ao_basis_ao_basis("Dummy one. We read MO")
ezfio.set_ao_basis_ao_num(ao_num) 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_nucl([1]*ao_num) #Maybe put a realy incorrect stuff
#Just need one #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 ao_prim_num_max = 5
d = [ [0] *ao_prim_num_max]*ao_num d = [ [0] *ao_prim_num_max]*ao_num
@ -72,8 +99,15 @@ ezfio.set_mo_basis_ao_md5(ao_md5)
ezfio.set_mo_basis_mo_num(mo_num) 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)] #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([ [0]*mo_num] * ao_num)
#ezfio.set_mo_basis_mo_coef_real(c_mo) ##ezfio.set_mo_basis_mo_coef_real(c_mo)
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())
#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_periodic(True) ezfio.set_nuclei_is_periodic(True)