working on complex converter

src/ao_two_e_ints/EZFIO.cfg

@@ -18,3 +18,8 @@ interface: ezfio,provider,ocaml
 default: False
 ezfio_name: direct
 
+[df_num]
+type: integer
+doc: Size of df basis
+interface: ezfio, provider
+

src/utils_periodic/Gen_Ezfio_from_integral_complex_3idx.sh

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

src/utils_periodic/MolPyscfToQPkpts.py

@@ -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 tools
     from pyscf.pbc.gto import ecp
+    from pyscf.data import nist
     import h5py
     import scipy
 
@@ -507,9 +508,21 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
 
     natom = cell.natm
     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('num_elec per kpt', nelec)
-  
+
     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)
@@ -523,14 +536,20 @@ def pyscf2QP2(cell,mf, kpts, kmesh=None, cas_idx=None, int_threshold = 1E-8,
     naux = mf.with_df.auxcell.nao
     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_beta_num']=nelec*Nk
     qph5['mo_basis'].attrs['mo_num']=Nk*nmo
     qph5['ao_basis'].attrs['ao_num']=Nk*nao
     qph5['nuclei'].attrs['nucl_num']=Nk*natom
     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  _  ._  

src/utils_periodic/create_ezfio_complex_3idx.py

@@ -12,28 +12,38 @@ h5filename = sys.argv[2]
 #n_kpts = int(sys.argv[7])
 #n_aux = int(sys.argv[8])
 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_beta_num = qph5['electrons'].attrs['elec_beta_num']
-
 nucl_num = qph5['nuclei'].attrs['nucl_num']
-kpt_num = qph5['nuclei'].attrs['kpt_num']
-df_num = qph5['ao_basis'].attrs['df_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_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_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_integrals_bielec_df_num(n_aux)
 
-#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 )
+#(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 )
+
+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')
+nuclear_repulsion = qph5['nuclei'].attrs['nuclear_repulsion']
 ezfio.set_nuclei_nuclear_repulsion(nuclear_repulsion)
 
 # 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_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
 
 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)
-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)
+#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)
+
+
+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)